- G - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
- GATHER_FILES_FOR_PICKUP - Static variable in class com.compomics.util.io.file.FolderMonitor
-
- GENE_MAPPING_FILE_SUFFIX - Static variable in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
The suffix to use for files containing gene mappings.
- GeneDetailsDialog - Class in com.compomics.util.gui.genes
-
This dialog displays the gene details associated to a protein match.
- GeneDetailsDialog(Frame, ProteinMatch, GeneMaps, ProteinDetailsProvider) - Constructor for class com.compomics.util.gui.genes.GeneDetailsDialog
-
Creates a new GeneDetailsDialog.
- GeneMapping - Class in com.compomics.util.experiment.biology.genes.ensembl
-
Class for the handling of gene mappings.
- GeneMapping() - Constructor for class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
-
Constructor.
- GeneMaps - Class in com.compomics.util.experiment.biology.genes
-
The gene maps for a given project.
- GeneMaps() - Constructor for class com.compomics.util.experiment.biology.genes.GeneMaps
-
Creates new maps.
- GeneParameters - Class in com.compomics.util.parameters.identification.advanced
-
Contains methods for downloading gene and GO mappings.
- GeneParameters() - Constructor for class com.compomics.util.parameters.identification.advanced.GeneParameters
-
Create a new GenePreferences object.
- GeneParameters(GeneParameters) - Constructor for class com.compomics.util.parameters.identification.advanced.GeneParameters
-
Creates new gene preferences based on a GenePreferences object.
- GeneParametersDialog - Class in com.compomics.util.gui.parameters.identification.advanced
-
Dialog for editing the Gene Mapping Preferences.
- GeneParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.advanced.GeneParametersDialog
-
Empty default constructor
- GeneParametersDialog(JFrame, GeneParameters, SearchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.GeneParametersDialog
-
Creates a new GenePreferencesDialog with a frame as owner.
- GeneParametersDialog(JDialog, Frame, GeneParameters, SearchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.GeneParametersDialog
-
Creates a new GenePreferencesDialog with a dialog as owner.
- generateDecoy() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns whether a decoy database shall be created and searched against.
- generateQuery() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Returns a boolean indicating whether a blast query shall be generated.
- GeneratorException - Exception in com.compomics.util.db
-
This class wraps all exception that can occur while generating code.
- GeneratorException() - Constructor for exception com.compomics.util.db.GeneratorException
-
Empty default constructor
- GeneratorException(String) - Constructor for exception com.compomics.util.db.GeneratorException
-
This constructor creates an exception with just a message.
- GeneratorException(String, Exception) - Constructor for exception com.compomics.util.db.GeneratorException
-
This constructor creates an exception with a message and a nested exception.
- GenericFastaConverter - Class in com.compomics.util.experiment.io.biology.protein.converters
-
This converter writes a FASTA file with standardized headers.
- GenericFastaConverter() - Constructor for class com.compomics.util.experiment.io.biology.protein.converters.GenericFastaConverter
-
- genericMzId - Static variable in class com.compomics.util.experiment.identification.Advocate
-
Advocate type for mzId files where no software is annotated.
- get() - Method in class com.compomics.util.sun.SwingWorker
-
Return the value created by the construct
method.
- getAaAfter(Peptide, String, int, int, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns the amino acids before the given peptide as a string.
- getAaAfter(Peptide, int, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns the amino acids before the given peptide as a string in a map
based on the peptide protein mapping.
- getAaBefore(Peptide, String, int, int, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns the amino acids before the given peptide as a string in a map
based on the peptide protein mapping.
- getAaBefore(Peptide, int, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns the amino acids before the given peptide as a string in a map
based on the peptide protein mapping.
- getAACoverage(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Indicates the validation level of every amino acid in the given protein.
- getAaIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAIdentityFeature
-
Returns the index on the sequence.
- getAaIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAPropertyFeature
-
Returns the index on the sequence.
- getAaNumber(int) - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
Returns the 1 based index of the amino acid which generated this ion.
- getAaSubstitutionMatrix() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Returns the amino acid substitution matrix to use.
- getAaTargeted() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns the map of targeted amino acids.
- getAbbreviatedFASTAHeader() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
This method returns an abbreviated version of the Header, suitable for
inclusion in FASTA formatted files.
- getAbbreviatedFASTAHeader(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
This method returns an abbreviated version of the Header, suitable for
inclusion in FASTA formatted files.
- getAbbreviatedFASTAHeaderWithAddenda() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
This method returns an abbreviated version of the Header, suitable for
inclusion in FASTA formatted files.
- getAbbreviation() - Method in class com.compomics.util.experiment.units.UnitOfMeasurement
-
Returns the abbreviated name of the unit.
- getAbsoluteError() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Get the absolute matching error in Da.
- getAbsoluteError(int, int) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Get the absolute matching error in Da after isotope removal.
- getAbsoluteFilePath() - Method in class com.compomics.software.autoupdater.MavenJarFile
-
Returns the absolute file path.
- getAccession() - Method in class com.compomics.util.experiment.biology.proteins.Protein
-
Getter for the protein accession.
- getAccession() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the accession.
- getAccession() - Method in class com.compomics.util.pride.CvTerm
-
Returns the accession.
- getAccessionOrRest() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the accession or if this is null the rest.
- getAccessions() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Returns the accessions of the proteins in this match.
- getAccessions() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getAccessions() - Method in class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
-
- getAccessions() - Method in interface com.compomics.util.experiment.io.biology.protein.SequenceProvider
-
Returns all accessions loaded in the provider.
- getAccountedNeutralLosses() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
-
Returns an arraylist of the names of the implemented neutral losses.
- getActicationType() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Returns the activation type.
- getAddenda() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
This method allows the caller to retrieve all addenda for the current
header, or 'null' if there aren't any.
- getAdvocate(int) - Static method in class com.compomics.util.experiment.identification.Advocate
-
Returns the advocate corresponding to the given index.
- getAdvocate(String) - Static method in class com.compomics.util.experiment.identification.Advocate
-
Returns the advocate with the given name.
- getAdvocate() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Get the used advocate.
- getAdvocateColorMap() - Static method in class com.compomics.util.experiment.identification.Advocate
-
Returns the advocate color map.
- getAdvocateFromFile(String) - Static method in class com.compomics.util.experiment.identification.Advocate
-
- getAdvocates() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Returns the advocates supporting hits for this spectrum.
- getAdvocates() - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
-
Returns the advocates with a specific scoring.
- getAdvocateToolTipMap() - Static method in class com.compomics.util.experiment.identification.Advocate
-
Returns the advocate tool tip map.
- getAlgorithm() - Method in interface com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter
-
Returns the identification algorithm.
- getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
- getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
- getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
- getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
- getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
- getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
- getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
- getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
-
- getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
- getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
- getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
- getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
- getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
- getAlgorithmDeltaPEP() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the difference in identification algorithm level PEP with the
next best peptide assumption with sequence difference for the given
search engine.
- getAlgorithms() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the algorithms for which specific parameters are stored.
- getAlgorithmSpecificParameters() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the algorithm specific parameters in a map: algorithm as indexed
in the Advocate class > parameters.
- getAlignmentBlocks() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
-
Returns the alignment blocks.
- getAlignNonConfidentModifications() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Indicates whether the non confidently localized modifications should be
aligned on the confident sites.
- getAllAlignments() - Method in class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerAlingmentReader
-
Get all alignments in the json string.
- getAllFeatures() - Method in class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerResultReader
-
Get all features in the XML string.
- getAllIsotopicElements(Class, Logger) - Static method in class com.compomics.util.general.IsotopicElement
-
Static method that gives all the isotopicElements from the isotopicElement.txt file
- getAllModifications(Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
-
Returns a set of the names of all modifications found on a peptide.
- getAllModifications(Tag, ModificationParameters, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
-
Returns a set of the names of all modifications found on a tag.
- getAllModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
-
Returns a list of all searched modifications.
- getAllModificationTitles() - Static method in class com.compomics.util.protein.ModificationFactory
-
This method returns all modification titles known to the Factory.
- getAllNotFixedModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
-
Returns a list of all searched modifications but the fixed ones.
- getAllocatedBytes() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
Computes the number of allocated bytes.
- getAllocatedBytes() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
-
Returns the number of bytes for the allocated arrays.
- getAllocatedBytes() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
-
Returns the number of bytes for the allocated arrays.
- getAllPeptideAssumptions(int) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Returns all peptide assumptions for the specified search engine indexed
by their score.
- getAllPeptideAssumptions() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Returns a stream of all peptide assumptions
- getAllPossibleSequences() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns all possible sequences which can be obtained from the targeted
amino acids.
- getAllProperties() - Method in interface com.compomics.util.db.interfaces.DBElement
-
This method will return a HashMap with all the properties for this DBElement.
- getAllPtmLocations() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns the sites of all localized PTMs.
- getAllReferenceAreasXAxis() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns all the x-axis references areas as a hashmap, with the labels as
the keys.
- getAllReferenceAreasYAxis() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns all the y-axis references areas as a hashmap, with the labels as
the keys.
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in interface com.compomics.util.experiment.io.identification.IdfileReader
-
Retrieves all the spectrum matches from an identification file as a list
of spectrum matches, one spectrum match per spectrum.
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in interface com.compomics.util.experiment.io.identification.IdfileReader
-
Retrieves all the spectrum matches from an identification file as a list
of spectrum matches, one spectrum match per spectrum.It is very important
to close the file reader after creation.
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
-
- getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
-
- getAllTableColumns() - Method in interface com.compomics.util.gui.VisibleTableColumnsDialogParent
-
Returns all the table columns, both visible and hidden.
- getAllTableColumns() - Method in class com.compomics.util.gui.XYPlottingDialog
-
- getAllTagAssumptions(int) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Returns all tag assumptions for the specified search engine indexed by
their score.
- getAllTagAssumptions() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Returns a stream of all tag assumptions
- getAlpha() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Get the alpha level (transparency).
- getAlphaLevel() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the alpha level.
- getAmbiguityKey() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns the ambiguity key.
- getAmbiguouslyLocalizedModifications() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
-
Returns a list of modifications presenting at least an ambiguous site.
- getAmbiguousModificationsAtRepresentativeSite(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
-
Returns the ambiguous modification assignments registered at the given
representative site in a map: secondary site > modifications.
- getAmbiguousModificationSiteNumber(IdentificationMatch) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns a summary of the number of modifications present on the sequence
ambiguously assigned to an amino acid grouped by representative site
followed by secondary ambiguous sites.
- getAmbiguousModificationSiteNumber(IdentificationMatch, ArrayList<String>) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns a summary of the number of modifications present on the sequence
ambiguously assigned to an amino acid grouped by representative site
followed by secondary ambiguous sites.
- getAmbiguousModificationSites(IdentificationMatch, String) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns a list of the modifications present on the sequence ambiguously
assigned to an amino acid grouped by representative site followed by
secondary ambiguous sites.
- getAmbiguousModificationSites(IdentificationMatch, String, ArrayList<String>) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns a list of the modifications present on the sequence ambiguously
assigned to an amino acid grouped by representative site followed by
secondary ambiguous sites.
- getAmbiguousModificationsSites(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
-
Returns the ambiguous modification sites registered for the given
modification.
- getAminoAcid(String) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the amino acid corresponding to the letter given.
- getAminoAcid(char) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the amino acid corresponding to the single letter code given.
- getAminoAcid() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAIdentityFeature
-
Returns the amino acid targeted represented as single letter code.
- getAminoAcidAfter() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
-
Getter for the amino acids potentially following the cleavage.
- getAminoAcidAt(int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
Returns the amino acid at the given index on the sequence.
- getAminoAcidBefore() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
-
Getter for the amino acids potentially preceding the cleavage.
- getAminoAcidCombinations(int) - Static method in class com.compomics.util.experiment.identification.TagFactory
-
Returns all the amino acid combinations for a given tag length.
- getAminoAcidFeature1() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
-
Returns the first amino acid feature.
- getAminoAcidFeature2() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
-
Returns the second amino acid feature.
- getAminoAcidFromGeneticCode(String) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the amino acid from the standard genetic code.
- getAminoAcidPatternFromString(String) - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Parses the amino acid pattern from the given string as created by the
toString() method.
- getAminoAcidPatternFromString(String, int) - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Parses the amino acid pattern from the given string as created by the
toString() method.
- getAminoAcidProperties() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
-
- getAminoAcidProperties() - Method in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.MultipleAAPropertyFeature
-
Returns the amino acid properties to consider.
- getAminoAcidProperty() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAPropertyFeature
-
- getAminoAcidProperty() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature
-
- getAminoAcidProperty() - Method in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.SingleAAPropertyFeature
-
Returns the amino acid property to consider.
- getAminoAcids() - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Convenience method returning an array of all implemented amino acids
represented by their singe letter code.
- getAminoAcidsAtTarget() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns the targeted amino acids at position "target".
- getAminoAcidsAtTargetSet() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns a set containing the amino acids at target.
- getAminoAcidScores() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the amino acid scores.
- getAminoAcidsList() - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Convenience method returning an arrayList of all implemented amino acids.
- getAnnotationIntensityLimit() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns the intensity percentile to consider for annotation.
- getAnnotationParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the annotation parameters used for identification.
- getAnnotationSettings() - Method in class com.compomics.util.gui.parameters.identification.advanced.AnnotationParametersDialog
-
Returns the annotation settings as set by the user.
- getApplicationFolder(CompomicsTools) - Method in class com.compomics.util.io.PropertiesManager
-
Get the application folder that contains the appropriate properties.
- getAreaColor() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Get the area color.
- getAreaUnderCurveColors() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the list of colors used for the datasets.
- getArray(int) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
-
Returns an array containing only the given index.
- getArtifactId() - Method in class com.compomics.software.autoupdater.MavenJarFile
-
Returns the artifact id.
- getAs() - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
-
Returns a histogram of the as found in the previously interpolated
scores.
- getAscii(String) - Method in class com.compomics.util.io.ftp.FTP
-
GET a file from the FTP server in Ascii mode.
- getAssayCount(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns the assay count for a given project.
- getAssayDetail(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns the assay details for a given assay.
- getAssayDetailList(String) - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
-
Convert from JSON to a list of AssaytDetails.
- getAssayDetails(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns the assay details for a given project.
- getAssayFileCount(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a count of file details for a given assay.
- getAssayFileDetails(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a list of file details for a given assay.
- getAssembly(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
-
Returns the Ensembl assembly corresponding to the given NCBI taxon.
- getAssembly(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
-
Returns the Ensembl assembly corresponding to the given NCBI taxon.
- getAsStringPattern(SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns the amino acid pattern as case insensitive pattern for String
matching.
- getAssumptionFilter() - Method in class com.compomics.util.experiment.identification.filtering.PsmFilter
-
Returns the filter used to filter at the assumption level.
- getAtom(String) - Static method in class com.compomics.util.experiment.biology.atoms.Atom
-
Returns the atom corresponding to the given short name.
- getAtom() - Method in class com.compomics.util.gui.atoms.AtomPanel
-
Returns the currently selected atom.
- getAtomChain(String) - Static method in class com.compomics.util.experiment.biology.atoms.AtomChain
-
Returns an atom chain from the input as string.
- getAtomChain() - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
-
Returns the atom chain as a list of AtomImpl.
- getAtomChainAdded() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns the atom chain added.
- getAtomChainAdded() - Method in class com.compomics.util.gui.atoms.AtomChainDialog
-
Returns the added atom chain as edited by the user.
- getAtomChainRemoved() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns the atom chain removed.
- getAtomChainRemoved() - Method in class com.compomics.util.gui.atoms.AtomChainDialog
-
Returns the removed atom chain as edited by the user.
- getAtomicComposition() - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the atomic composition.
- getAtomSymbol() - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
-
Returns the atom symbol as specified in the Atom class.
- getAuc() - Method in class com.compomics.util.math.roc.DataRoc
-
- getAuc() - Method in class com.compomics.util.math.roc.DistributionRoc
-
- getAuc() - Method in interface com.compomics.util.math.statistics.ROC
-
Returns an estimation of the area under the curve.
- getAutoUpdate() - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
-
Indicates whether the gene mappings should be automatically updated.
- getAverageMassDelta(String) - Method in interface com.compomics.util.interfaces.Modification
-
This method returns a double with the average mass difference
conferred on the sequence by this modification for the specified residue.
- getAverageMassDelta(String) - Method in class com.compomics.util.protein.ModificationImplementation
-
This method returns a double with the average mass difference
conferred on the sequence by this modification for the specified residue.
- getAverageMassDelta(String) - Method in class com.compomics.util.protein.ModificationTemplate
-
This method returns a double with the average mass difference
conferred on the sequence by this modification for the specified residue.
- getBackedUpModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
-
Returns the modifications backed-up as a map.
- getBackgroundPeakWidth() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the current width of the background peaks.
- getBackgroundSpecies() - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
-
Returns the taxon of the species selected as background species.
- getBase64String() - Method in class com.compomics.util.BinaryArrayImpl
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the basicity according to PMID 14730315.
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
-
- getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
-
- getBatchSize() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the batch size.
- getBestPeptideAssumption() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Getter for the best peptide assumption.
- getBestTagAssumption() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Getter for the best tag assumption.
- getBin(double) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Returns the bin corresponding to the given m/z.
- getBinary(String) - Method in class com.compomics.util.io.ftp.FTP
-
GET a file from the FTP server in Binary mode.
- getBinaryDataAsNumberArray(String, MzmlFileIterator.Precision, byte[]) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileIterator
-
Retrieve the binary data as an array of numeric values.
- getBinMax() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Returns the highest bin.
- getBinMin() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Returns the lowest bin.
- getBinnedCumulativeProbability(double) - Method in class com.compomics.util.experiment.mass_spectrometry.SimpleNoiseDistribution
-
Get the binned cumulative probability.
- getBinnedCumulativeProbabilityLog(double) - Method in class com.compomics.util.experiment.mass_spectrometry.SimpleNoiseDistribution
-
Get the binned logged cumulative probability.
- getBins() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
-
Returns the bins in the map.
- getBins() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Returns the bins in the map as a list.
- getBiomartEnsemblGenomeMappingFile(String) - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns the Ensembl Genome BioMart file.
- getBiomartEnsemblMappingFile(String) - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns the Ensembl BioMart file.
- getBiomartMapping() - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns the BioMart mapping.
- getBlob - Variable in class com.compomics.util.db.object.objects.BlobObject
-
Object representation of the blob.
- getBlob() - Method in class com.compomics.util.db.object.objects.BlobObject
-
Returns the byte representation of the object.
- getBlock() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Returns the block.
- getBlocks() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
Returns the blocks.
- getBlockSequence(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Get the blocked sequence.
- getBorderColor() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Returns the border color.
- getBorderWidth() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Returns the border width.
- getBs() - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
-
Returns a histogram of the bs found in the previously interpolated
scores.
- getCacheSize() - Method in class com.compomics.util.db.object.ObjectsCache
-
Returns the cache size in number of objects.
- getCategories() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
-
Returns the different categories of the features in this map.
- getCategoriesAsString() - Static method in enum com.compomics.util.experiment.biology.modifications.ModificationCategory
-
Returns all of the modification category options as a string.
- getCategory() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns the modification category.
- getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureAbsolute
-
- getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureRelative
-
- getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureAbsolute
-
- getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureRelative
-
- getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
-
- getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonAminoAcidFeature
-
- getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonAminoAcidFeature
-
- getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature
-
- getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
-
- getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideAminoAcidFeature
-
- getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
-
- getCategory() - Method in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature
-
Returns the category of the feature.
- getCharacterInfo(int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
-
Returns the character and rank at a given index.
- getCharge() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
-
Getter for the charge
- getCharge() - Method in interface com.compomics.util.interfaces.SpectrumFile
-
This method reports on the charge of the precursor ion.
- getChargeAsFormattedString(int) - Static method in class com.compomics.util.experiment.biology.ions.Charge
-
Returns the charge as a string of + or -.
- getChargePrideCvTerm() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the pride CV term for the ion match charge.
- getChartPanel() - Method in class com.compomics.util.gui.spectrum.IntensityHistogram
-
Returns the chart panel.
- getChartPanel() - Method in class com.compomics.util.gui.spectrum.MassErrorBubblePlot
-
Returns the chart panel.
- getChartPanel() - Method in class com.compomics.util.gui.spectrum.MassErrorPlot
-
Returns the chart panel.
- getChartPanel() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Returns the chart panel.
- getChoice() - Method in class com.compomics.util.gui.SampleSelection
-
Getter for the users choice.
- getChromosome(String) - Method in class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
-
Returns the chromosome for a given gene.
- getChromosome(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Returns the chromosome corresponding to a given gene name.
- getClassInCache(Class) - Method in class com.compomics.util.db.object.ObjectsCache
-
Returns the class type of the objects in cache.
- getClassObjectIDs(Class) - Method in class com.compomics.util.db.object.ObjectsDB
-
Returns an iterator of all objects of a given class.
- getClassObjectIDs(Class, String) - Method in class com.compomics.util.db.object.ObjectsDB
-
Returns an iterator of all objects of a given class.
- getClassObjects(Class) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the keys of the objects of the given class,
- getClassObjects(Class, String) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the keys of the objects of the given class,
- getClassSizeMultiplier() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns the intensity class size multiplier.
- getCleavage(int) - Method in class com.compomics.util.protein.DualEnzyme
-
This method returns the residues that are used for cleavage at the respective
locations.
- getCleavage() - Method in class com.compomics.util.protein.DualEnzyme
-
Simple getter for the cleavable residues of the Enzyme.
- getCleavage() - Method in class com.compomics.util.protein.Enzyme
-
Simple getter for the cleavagable residues of the Enzyme.
- getCleavage() - Method in class com.compomics.util.protein.RegExEnzyme
-
- getCleavageParameter() - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
-
Returns the cleavage parameters.
- getCleavageParameters(int) - Static method in enum com.compomics.util.parameters.identification.search.DigestionParameters.CleavageParameter
-
Returns the cleavage parameter of the given index.
- getClipNtermMethionine() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns if the starting methionine peptides will be included both with
and without the starting M.
- getClusterMembers(int) - Method in class com.compomics.util.math.clustering.KMeansClustering
-
Get the sample names of all the members in the given cluster.
- getClusterMembersData(int) - Method in class com.compomics.util.math.clustering.KMeansClustering
-
Returns a hashmap with the values for the members in the given cluster.
- getCmsFilePath(File, File) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
Returns the path of the cms file expected for the given mass spectrometry
file and cms folder.
- getCmsFilePaths() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getCmsFilePaths() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getCmsFilePaths() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the absolute path to the cms file indexed by ms file name without
file extension.
- getCode() - Method in interface com.compomics.util.interfaces.Modification
-
This method returns the short code for the modification, eg.
- getCode() - Method in class com.compomics.util.protein.ModificationImplementation
-
This method returns the short code for the modification, eg.
- getCode() - Method in class com.compomics.util.protein.ModificationTemplate
-
This method returns the short code for the modification, eg.
- getCodedColumnType(String) - Method in class com.compomics.util.db.DBMetaData
-
This method returns the coded column type for the specified column.
- getCodedColumnType(int) - Method in class com.compomics.util.db.DBMetaData
-
This method returns the coded columntype for the specified column index.
- getCodedColumnTypes() - Method in class com.compomics.util.db.DBMetaData
-
This method reports on all the coded column types.
- getColor(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns the color used to code the given modification.
- getColor() - Method in class com.compomics.util.experiment.identification.Advocate
-
Returns the color of the advocate.
- getColor() - Method in interface com.compomics.util.gui.interfaces.SpectrumAnnotation
-
This method returns the color for the annotation.
- getColor() - Method in class com.compomics.util.gui.protein.ModificationProfile
-
Returns the PTM color.
- getColor() - Method in class com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation
-
This method returns the color for the annotation.
- getColor(String) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
-
Returns the color used to code the given modification.
- getColor(int) - Static method in class com.compomics.util.Util
-
Returns the color object corresponding to the given rgb representation.
- getColors() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
-
Returns the modification colors as a map.
- getColummnNames() - Method in class com.compomics.util.gui.XYPlottingDialog
-
Return the column names.
- getColumn(int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getColumnClass(int) - Method in class com.compomics.util.db.DBResultSet
-
Returns Object.class
regardless of columnIndex
.
- getColumnClass(int) - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
-
- getColumnClass(int) - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
-
- getColumnClass(int) - Method in class com.compomics.util.sun.TableMap
-
- getColumnCount() - Method in class com.compomics.util.db.DBMetaData
-
This method returns the column count for this table.
- getColumnCount() - Method in class com.compomics.util.db.DBResultSet
-
This method reports on the number of columns in the resultset.
- getColumnCount() - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
-
- getColumnCount() - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
-
- getColumnCount() - Method in class com.compomics.util.sun.TableMap
-
- getColumnName(int) - Method in class com.compomics.util.db.DBMetaData
-
This method returns the name of the specified column.
- getColumnName(int) - Method in class com.compomics.util.db.DBResultSet
-
Returns a default name for the column using spreadsheet conventions:
A, B, C, ...
- getColumnName(int) - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
-
- getColumnName(int) - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
-
- getColumnName(int) - Method in class com.compomics.util.sun.TableMap
-
- getColumnNames() - Method in class com.compomics.util.db.DBMetaData
-
This method reports on all the column names.
- getColumnNames() - Method in class com.compomics.util.db.DBResultSet
-
This method reports on all the columnn ames.
- getColumns() - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getColumnSize(String) - Method in class com.compomics.util.db.DBMetaData
-
This method returns the column size for the specified column.
- getColumnSize(int) - Method in class com.compomics.util.db.DBMetaData
-
This method returns the column size for the specified column index.
- getColumnSizes() - Method in class com.compomics.util.db.DBMetaData
-
This method reports on all the column sizes.
- getCombination(int, int) - Static method in class com.compomics.util.math.BasicMathFunctions
-
Returns the number of k-combinations in a set of n elements.
- getCombination(BigInteger, BigInteger) - Static method in class com.compomics.util.math.BigFunctions
-
Returns the number of k-combinations in a set of n elements as a big
decimal.
- getCombinationDouble(int, int) - Static method in class com.compomics.util.math.BasicMathFunctions
-
Returns the number of k-combinations in a set of n elements.
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the amino acids combinations which might represent this amino
acid.
- getCombinations(String) - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
Returns a list of all combinations which can be created from a sequence
when expanding ambiguous amino acids like Xs.
- getCommandLineArgument(ArrayList<File>) - Static method in class com.compomics.software.cli.CommandLineUtils
-
Returns the list of file as argument for the command line.
- getCommandLineArgument(File) - Static method in class com.compomics.software.cli.CommandLineUtils
-
Returns the file as argument for the command line.
- getCommandLineDescription() - Static method in enum com.compomics.util.parameters.identification.search.DigestionParameters.CleavageParameter
-
Returns the different options as command line description.
- getCommandLineDescription() - Static method in enum com.compomics.util.parameters.identification.search.DigestionParameters.Specificity
-
Returns the different options as command line description.
- getCommandLineOption() - Static method in enum com.compomics.util.io.export.ExportFormat
-
Returns the command line description when the format is used as command
line argument.
- getCommandLineOptions() - Static method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
-
Returns the different implemented scores as list of command line option.
- getCommandLineOptions() - Static method in enum com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters.IntensityThresholdType
-
Returns the different intensity threshold types as command line
options description.
- getCommandLineOptions() - Static method in enum com.compomics.util.experiment.io.identification.MzIdentMLVersion
-
Returns a string describing the different options.
- getCommandLineOptions() - Static method in enum com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters.MatchingType
-
Returns the different matching types as command line options
description.
- getCommandLineOptions() - Static method in enum com.compomics.util.parameters.searchgui.OutputParameters
-
Convenience method returning all possibilities in a command line option description format.
- getCommonName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
-
Returns the common name corresponding to the given NCBI taxon.
- getCommonName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
-
Returns the common name corresponding to the given NCBI taxon.
- getComparatorForItem(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Returns the comparator set for a given filtering item.
- getComplementaryIonsFeatures(Peptide, int, int, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation.FeaturesGenerator
-
Returns the ms2pip features for the complementary ions of the given
peptide at the given charge.
- getComplementMzTolerance() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the complement m/z tolerance.
- getComplementScoreWeight() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the complement score weight.
- getComposition() - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
-
The composition of the loss.
- getComputeExactPValues() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true if the exact p-values are to be computed.
- getComputeSpScore() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true of the SP score is to be computed.
- getComputeXCorr() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns true if a Sequest-like cross correlation score will be calculated
for the top ranking hits in each spectrum’s result set.
- getConcatenatTargetDecoy() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true if the target and decoy results are to be concatenated.
- getCondition() - Method in interface com.compomics.util.experiment.filtering.Filter
-
Returns a description of the condition to match for the filter to
validate.
- getCondition() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
- getConfidence() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the confidence.
- getConfidenceLevel(int) - Static method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Convenience method returning the given confidence level as a string.
- getConfidenceMargin() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Returns the margin to the threshold to use as factor of the resolution.
- getConfidenceThreshold() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Returns the confidence below which a peptide is considered absent.
- getConfident() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Returns a boolean indicating whether the modification is confidently
localized on the sequence.
- getConfidentlyLocalizedModifications() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
-
Returns a list of modifications presenting at least a confident site.
- getConfidentModificationsAt(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
-
Returns the main potential modifications at the given amino acid index.
- getConfidentModificationSites(IdentificationMatch, String) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns a summary of all modifications present on the sequence
confidently assigned to an amino acid.
- getConfidentModificationSites(IdentificationMatch, String, ArrayList<String>) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns a summary of the modifications present on the peptide sequence
confidently assigned to an amino acid with focus on given list of
modifications.
- getConfidentModificationSitesNumber(IdentificationMatch) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the number of confidently localized variable modifications.
- getConfidentModificationSitesNumber(IdentificationMatch, ArrayList<String>) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the number of confidently localized variable modifications.
- getConfidentPtmLocations() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns the confidently and very confidently localized PTMs.
- getConfidentSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
-
Returns a list of all confident modification sites.
- getConfidentSitesForModification(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
-
Returns the confident sites for the given modification.
- getConsecutiveIonProbability() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the consecutive ion probability.
- getContactGroups() - Method in class com.compomics.util.pride.PrideObjectsFactory
-
Returns the contact groups.
- getContacts() - Method in class com.compomics.util.pride.prideobjects.ContactGroup
-
Returns the contacts.
- getContent() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Returns the content of this tag as a list.
- getContentPane() - Method in class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
-
This methods gives a JPanel holding everything from this frame
- getControlSamples() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
Returns the indexes of the samples labeled as control.
- getConvertedColumnType(String) - Method in class com.compomics.util.db.DBMetaData
-
This method returns the converted column type for the specified column.
- getConvertedColumnType(int) - Method in class com.compomics.util.db.DBMetaData
-
This method returns the converted columntype for the specified column index.
- getConvertedColumnTypes() - Method in class com.compomics.util.db.DBMetaData
-
This method reports on all the converted column types.
- getCopyRight() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
Returns the copyright.
- getCoreHeader() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
This method reports on the core information for the header, which is
comprised of the ID and the accession String:
- getCorrelation(ArrayList<Double>, ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
-
Returns the population Pearson correlation r between series1 and series2.
- getCoverableAA(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns an array of the likelihood to find identify a given amino acid in
the protein sequence.
- getCoveredAminoAcids(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
- getCreationTime() - Method in class com.compomics.util.experiment.ProjectParameters
-
- getCtermAsString(boolean, int, String[]...) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns the C-terminal annotation as string.
- getCTerminal(boolean, ModificationParameters, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Returns the C-terminal tag of this tag as a string for sequence display.
- getCTerminalGap() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Returns the C-terminal gap of the tag.
- getcTermModification() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Returns the C-term modification.
- getCtermModification(PeptideDraft, String, int) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
-
Returns the c-terminal modification for the given peptide draft.
- getCTermTruncatedProtein(int) - Method in class com.compomics.util.protein.Protein
-
This method truncates the sequence for this protein on the C-terminus
to the requested size.
- getCTermTruncatedSequence(int) - Method in class com.compomics.util.protein.AASequenceImpl
-
This method will return an AASequenceImpl that represents
a C-terminal truncation of the current sequence.
- getCumulativeProbabilityAt(double) - Method in interface com.compomics.util.math.statistics.Distribution
-
Returns the cumulative density function value at a given position.
- getCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
-
- getCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
- getCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- getCurrentAdded() - Method in class com.compomics.util.db.object.ObjectsDB
-
Getter for the current number of added objects.
- getCurrentAnnotation(String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
- getCurrentAnnotation(String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
-
- getCurrentAnnotation(String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Returns the currently matched ions with the given settings using the
intensity filter.
- getCurrentAnnotation(String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Returns the currently matched ions with the given settings.
- getCurrentEnsemblVersion(EnsemblGenomesSpecies.EnsemblGenomeDivision) - Static method in class com.compomics.util.experiment.biology.genes.ensembl.EnsemblVersion
-
Returns the current Ensembl version number.
- getCurrentlyLoadedPeptide() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the currently inspected peptide.
- getCurrentlyLoadedSpectrumFile() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Returns the file of the spectrum currently inspected.
- getCurrentlyLoadedSpectrumTitle() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Returns the title of the spectrum currently inspected.
- getCurrentPeptideKey() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Returns the current peptide key.
- getCurrentProteinKey() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Returns the current protein key.
- getCurrentVennDiagramType() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Returns the current Venn diagram type.
- getCvTerm() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
-
Returns the CV term associated with this enzyme.
- getCVTerm(String) - Method in class com.compomics.util.pride.PtmToPrideMap
-
Returns the CV term corresponding to the given PTM name.
- getCvTerms() - Method in class com.compomics.util.pride.prideobjects.Instrument
-
Returns the CV terms.
- getCvTerms() - Method in class com.compomics.util.pride.prideobjects.Protocol
-
Returns the CV terms.
- getCvTerms() - Method in class com.compomics.util.pride.prideobjects.Sample
-
Returns the CV terms.
- getDaltonDifference() - Method in class com.compomics.util.general.IsotopicElement
-
Getter for the dalton difference with the natural form of this element
- getData() - Method in class com.compomics.util.db.DBResultSet
-
This method reports on the data stored in the resultset.
- getData() - Method in class com.compomics.util.gui.renderers.ByteArrayRenderer
-
This method returns the data that is currently cached by the renderer.
- getDatabaseDirectory() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the database directory.
- getDatabaseType() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the database type as inferred from the header structure.
- getDatabaseTypeAsString(ProteinDatabase) - Static method in class com.compomics.util.experiment.io.biology.protein.Header
-
Convenience method returning the database name as a String.
- getDatabaseTypesAsString() - Static method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the implemented database types as an array of String.
- getDataEndian() - Method in class com.compomics.util.BinaryArrayImpl
-
Returns the endian value of the binary array (mzData element
.../data/endian).
- getDataFilters() - Method in class com.compomics.util.gui.XYPlottingDialog
-
Return the data filters.
- getDataFormats(Boolean, Boolean) - Static method in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
-
Returns a list of formats.
- getDataLength() - Method in class com.compomics.util.BinaryArrayImpl
-
Returns the length of the binary array (mzData element
.../data/length).
- getDataPrecision() - Method in class com.compomics.util.BinaryArrayImpl
-
Returns the precision of the binary array (mzData element
.../data/precision).
- getDataset(String) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.BiomartMapping
-
Returns the Ensembl dataset for the given assembly.
- getDaTolerance(double, double) - Static method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the absolute tolerance in Dalton corresponding to the relative
tolerance in ppm at the given reference mass.
- getDB() - Method in class com.compomics.util.db.object.ObjectsDB
-
Getter for the persistence manager.
- getDbFile() - Method in class com.compomics.util.db.object.ObjectsDB
-
Getter for the database file.
- getDbFolder() - Method in class com.compomics.util.db.object.ObjectsDB
-
Getter for the database folder.
- getDbFolder() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the last used database folder.
- getDbSummaryFolder() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the folder where FASTA files summary statistics are stored.
- getDecodedByteArray() - Method in class com.compomics.util.BinaryArrayImpl
-
Returns the contents of the binary array decoded using the
Base64 algorithm.
- getDeconvolutionIntensityRatio() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the deconvolution intensity ratio.
- getDeconvolutionMassTolerance() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the deconvolution mass tolerance.
- getDeconvolutionMassToleranceType() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the deconvolution mass tolerance type.
- getDecoyAccessions() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getDecoyAccessions() - Method in class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
-
- getDecoyAccessions() - Method in interface com.compomics.util.experiment.io.biology.protein.SequenceProvider
-
Returns the decoy accessions.
- getDecoyFlag() - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
-
Returns the decoy flag.
- getDecoyFormat() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the decoy format.
- getDecoyMode() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns the decoy mode.
- getDecoyParameters(FastaParameters) - Static method in class com.compomics.util.experiment.io.biology.protein.converters.DecoyConverter
-
Returns the FASTA parameters of the target-decoy database based on the
parameters of the target database.
- getDecoySeed() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the decoy seed.
- getDecoysInFirstBin() - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
-
Returns the minimal number of decoys to include in a bin to set the bin
size of the score histogram.
- getDecoySummary(File, FastaSummary) - Static method in class com.compomics.util.experiment.io.biology.protein.converters.DecoyConverter
-
Returns the FASTA summary of the target-decoy database based on the
summary of the target database.
- getDecoyType() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the decoy type.
- getDecreasingScore(Peptide, int, String, String, Spectrum, IdentificationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters, PeptideSpectrumAnnotator, int) - Method in class com.compomics.util.experiment.identification.psm_scoring.PsmScoresEstimator
-
Scores the match between the given peptide and spectrum using the given
score.
- getDefaultColor(String) - Static method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns a default color based on the modification name.
- getDefaultCVTerm(String) - Static method in class com.compomics.util.pride.PtmToPrideMap
-
- getDefaultDescription() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Indicates whether the description is automatically generated.
- getDefaultExportFolder() - Method in class com.compomics.util.gui.VennDiagramDialog
-
- getDefaultFeaturesMap() - Static method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMapManager
-
Returns the default features map used in the c implementation, see
https://github.com/mvaudel/ms2pip_c.
- getDefaultInstruments() - Static method in class com.compomics.util.pride.prideobjects.Instrument
-
Returns a list of predefined instruments.
- getDefaultLosses(Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the possible neutral losses expected by default for a given
peptide.
- getDefaultLosses(Tag, ModificationParameters, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
-
Returns the possible neutral losses expected by default for a given tag.
- getDefaultLosses(SpectrumIdentificationAssumption, ModificationParameters, SequenceProvider, SequenceMatchingParameters, SpectrumAnnotator) - Static method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Returns the possible neutral losses expected by default for a given
peptide.
- getDefaultModifications() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns the names of the default modifications.
- getDefaultModificationsOrdered() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns the alphabetically (case insensitive) ordered names of the
default modifications.
- getDefaultNeutralLosses() - Static method in class com.compomics.util.experiment.biology.ions.IonFactory
-
Returns the default neutral losses.
- getDefaultParameters() - Static method in class com.compomics.util.parameters.identification.search.DigestionParameters
-
Returns default digestion parameters.
- getDefaultPeptideFDR() - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
-
Returns the default peptide FDR.
- getDefaultProteinFDR() - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
-
Returns the default protein FDR.
- getDefaultProtocols() - Static method in class com.compomics.util.pride.prideobjects.Protocol
-
Returns a list of default protocols.
- getDefaultPsmFDR() - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
-
Returns the default PSM FDR.
- getDefaultReference(String, String, int) - Static method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
Returns the default reference for an identification.
- getDefaultReferences() - Static method in class com.compomics.util.pride.prideobjects.ReferenceGroup
-
Returns the default references.
- getDefaultSamples() - Static method in class com.compomics.util.pride.prideobjects.Sample
-
Returns a list of default samples.
- getDefaultScores() - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
-
Returns the default scores.
- getDefaultSequenceMatching() - Static method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Returns default preferences from amino acid matching.
- getDeisotopingMode() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the deisotoping flag value.
- getDeletedAminoAcid() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Deletion
-
- getDeltaMass(double, boolean, int, int) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the precursor mass error (in ppm or Da).
- getDeltaMassWindow() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Get the size of the window to use when searching for matches in the known
masses list when the user hovers over a second data point after clicking
a previous data point.
- getDeltaPEP() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the difference in identification algorithm level PEP with the
next best peptide assumption with sequence difference across all search
engines.
- getDeltaScore(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns the delta score at a given site.
- getDeNovoCharge() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns the charge to use for the fragment ions in the de novo
sequencing.
- getDeNovoGuiPath() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the path to the DeNovoGUI installation.
- getDescendingCumulativeProbabilityAt(double) - Method in interface com.compomics.util.math.statistics.Distribution
-
Returns the cumulative density function value at a given position when
starting from the high values.
- getDescendingCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
-
- getDescendingCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
- getDescendingCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- getDescription() - Method in interface com.compomics.software.settings.PathKey
-
Returns the description of the path.
- getDescription() - Method in enum com.compomics.software.settings.UtilitiesPathParameters.UtilitiesPathKey
-
- getDescription() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
-
Returns the description of the cleavage of this enzyme.
- getDescription() - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
-
Returns the description of this substitution matrix.
- getDescription() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Deletion
-
- getDescription() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Insertion
-
- getDescription() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Substitution
-
- getDescription() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Swap
-
- getDescription() - Method in interface com.compomics.util.experiment.biology.variants.Variant
-
Returns the description of the variant as string.
- getDescription() - Method in interface com.compomics.util.experiment.filtering.Filter
-
Returns a description for the filter.
- getDescription() - Method in interface com.compomics.util.experiment.filtering.FilterItem
-
Returns a description of the item.
- getDescription() - Method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
-
- getDescription() - Method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
-
- getDescription() - Method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
-
- getDescription() - Method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
-
- getDescription() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
- getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureAbsolute
-
- getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureRelative
-
- getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureAbsolute
-
- getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureRelative
-
- getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
-
- getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonAminoAcidFeature
-
- getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonFeature
-
- getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonAminoAcidFeature
-
- getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonFeature
-
- getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
-
- getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideAminoAcidFeature
-
- getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
-
- getDescription() - Method in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature
-
Returns the description of the feature.
- getDescription(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getDescription() - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
-
Returns the description for this database.
- getDescription() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the description.
- getDescription(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
-
Returns the description of the protein with the given accession.
- getDescription() - Method in class com.compomics.util.experiment.patient.PatientInformation
-
Returns the description of the information.
- getDescription() - Method in interface com.compomics.util.io.export.ExportFeature
-
Returns the description of the feature.
- getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsAnnotationFeature
-
- getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
-
- getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
-
- getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
-
- getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
-
- getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
-
- getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
-
- getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
-
- getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
-
- getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
-
- getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
-
- getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
-
- getDescription() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
-
- getDescription() - Method in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
-
- getDescription() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
-
- getDescription() - Method in class com.compomics.util.io.file.filefilters.DatFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.DtaFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.FastaFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.JpegFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.MgfFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.Ms2FileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.MzDataFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.MzMlFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.MzXmlFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.OmxFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.OutFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.PdfFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.PeffFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.PepXmlFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.PklFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.PklSpoFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.PkxFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.PngFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.ProtXmlFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.SequestParamsFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.SvgFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.TiffFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.filefilters.XmlFileFilter
-
The description of the filter.
- getDescription() - Method in class com.compomics.util.io.file.FilenameExtensionFilter
-
- getDescription() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the description of the parameters.
- getDescriptionProteinName() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the protein name as inferred from the description.
- getDescriptionShort() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the short description.
- getDestinationFile() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
-
Returns the file where to save the identification parameters.
- getDestinationFile() - Method in class com.compomics.util.io.ftp.FTP
-
This method reports on the destinationfile currently used in transfer.
- getDetector() - Method in class com.compomics.util.pride.prideobjects.Instrument
-
Returns the instrument detector.
- getDeterminant() - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getDifference() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
-
Returns the difference.
- getDifference() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Returns the difference.
- getDifferenceToMonoisotopic(int) - Method in class com.compomics.util.experiment.biology.atoms.Atom
-
Returns the mass difference between the given isotope and the
monoisotopic mass.
- getDigestionParameters() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the digestion preferences.
- getDigestionType() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the enzyme digestion type.
- getDiscardLowQualitySpectra() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Returns a boolean indicating whether low quality spectra shall be
discarded.
- getDisplayedTips() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the list of displayed tips.
- getDisplayName() - Method in class com.compomics.util.experiment.units.UnitOfMeasurement
-
Returns the name to display, e.g.
- getDisplayProgress() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- getDisplayProgress() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- getDisplayProgress() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- getDisplayProgress() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- getDisplayProgress() - Method in interface com.compomics.util.waiting.WaitingHandler
-
Returns if the waiting handler is to show the progress for the current
process or not.
- getDissociationType() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the dissociation type.
- getDivision(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
-
Returns the division corresponding to the given NCBI taxon.
- getDoi() - Method in class com.compomics.util.pride.prideobjects.Reference
-
Returns the Digital Object Identifier (DOI) of the reference.
- getDoPrecursorDeconvolution() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns true if precursor deconvolution is to be carried out.
- getDoubleArray() - Method in class com.compomics.util.BinaryArrayImpl
-
Checks if all the necessary information is provided and then converts the
decoded binary array into an array of double values (that for example
could be used to draw a spectra).
- getDoubleChargeWindow() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the window size for doubly charged ions.
- getDoubleListFromString(String, String) - Static method in class com.compomics.software.cli.CommandLineUtils
-
Parses a list of doubles from a command line option.
- getDScoreThreshold() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Returns the D-score threshold.
- getDSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns a set of sites where a D-score is available
- getDuplicatedSpectrumTitles() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns a map of the duplicated spectrum titles, can be null.
- getDuration() - Method in class com.compomics.util.waiting.Duration
-
Returns the duration in milliseconds.
- getDynamicRange() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns the dynamic range for spectrum filtering.
- getElement() - Method in class com.compomics.util.general.IsotopicElement
-
Getter for the MolecularElement
- getElement() - Method in exception com.compomics.util.general.UnknownElementMassException
-
Simple getter for the element variable.
- getElementCount(MolecularElement) - Method in class com.compomics.util.protein.MolecularFormula
-
Getter for the count of a specific element
- getEMail() - Method in class com.compomics.util.pride.prideobjects.Contact
-
Returns the contact e-mail.
- getEnd() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Get the end value.
- getEnd() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the end.
- getEndBlock() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Returns the block end.
- getEndLocation() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
This method reports on the end index of the header.
- getEndPosition() - Method in class com.compomics.util.pdbfinder.das.readers.StartEndPosition
-
Returns the end position.
- getEndProtein() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Returns the protein end.
- getEnsemblAccession(String) - Method in class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
-
Returns the Ensembl accession for a given gene.
- getEnsemblAssembly(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns the Ensembl assembly to use for the given taxon.
- getEnsemblDataset(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns the Ensembl dataset to use for the given taxon.
- getEnsembleSpecies() - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns a map of the species in Ensembl.
- getEnsemblGenomeDivisionFromName(String) - Static method in enum com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies.EnsemblGenomeDivision
-
Returns the EnsemblGenomeDivision corresponding to the given Ensembl name.
- getEnsemblGenomesSpecies() - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns the Ensembl genome species mapping.
- getEnsemblGenomesSpeciesFile(String) - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns the Ensembl genome species file.
- getEnsemblId(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Returns the Ensembl ID corresponding to the given gene name.
- getEnsemblSchemaName(EnsemblGenomesSpecies.EnsemblGenomeDivision) - Static method in class com.compomics.util.experiment.biology.genes.ensembl.EnsemblVersion
-
Returns the name of the Ensembl schema for BioMart queries.
- getEnsemblSpecies() - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns the Ensembl species mapping.
- getEnsemblSpeciesFile(String) - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns the Ensembl species file.
- getEnsemblSpeciesVersions(File) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
Gets the information contained into the Ensembl species file.
- getEnsemblVersion(Integer) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
Returns the Ensembl version for a given species.
- getEnsemblVersionFromFile(File, String) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
Gets the Ensembl version of a given species from a file.
- getEnsemblVersionsFile() - Static method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
Returns the Ensembl version file.
- getEnsemblVersionsMap() - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Returns the Ensembl version map.
- getEntitiesForPoint(int, int) - Method in class com.compomics.util.gui.VennDiagramPanel
-
Returns a list of the entities at the given x, y view location.
- getEntitiesForPoint(int, int) - Method in class com.compomics.util.gui.XYPlottingDialog
-
Returns a list of the entities at the given x, y view location.
- getEnzyme(String) - Method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
-
Returns the enzyme corresponding to the given name.
- getEnzyme() - Method in class com.compomics.util.gui.parameters.identification.pride.EnzymeParametersDialog
-
Returns the selected enzyme.
- getEnzyme(String) - Method in class com.compomics.util.io.MascotEnzymeReader
-
This method will return a copy of an Enzyme instance
for the given name, or 'null' if the enzyme was not found in the current list.
- getEnzymeNames() - Method in class com.compomics.util.io.MascotEnzymeReader
-
This method reports on all the known names for enzymes in this reader.
- getEnzymes() - Method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
-
Get the imported enzymes.
- getEnzymes() - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
-
Returns the enzymes used for digestion in a list.
- getEnzymeToAdd() - Method in class com.compomics.cli.enzymes.EnzymesCLIInputBean
-
Returns the enzyme to add.
- getEnzymeToRemove() - Method in class com.compomics.cli.enzymes.EnzymesCLIInputBean
-
Returns the name of the enzyme to remove.
- getEnzymeType() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the enzyme type.
- getError(boolean, int, int) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the error.
- getError(boolean) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the error.
- getErrorKeys() - Static method in class com.compomics.software.settings.UtilitiesPathParameters
-
Returns a list containing the keys of the paths where the tool is not
able to write.
- getErrorMargin() - Method in interface com.compomics.util.gui.interfaces.SpectrumAnnotation
-
This method returns the allowed error margin (both sides)
for the M/Z of the annotation (eg., 0.1 means an allowed
interval of [M/Z-0.1, M/Z+0.1].
- getErrorMargin() - Method in class com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation
-
This method returns the allowed error margin (both sides)
for the M/Z of the annotation (eg., 0.1 means an allowed
interval of [M/Z-0.1, M/Z+0.1].
- getErrors() - Method in class com.compomics.util.pride.validation.PrideXmlValidator
-
Returns the XML validation error object.
- getErrorsAsList() - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
-
Returns the errors as a list.
- getErrorsAsString() - Method in class com.compomics.util.pride.validation.PrideXmlValidator
-
Returns the errors formatted as s single string.
- getErrorsFormattedAsHTML() - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
-
Returns the errors formatted as HTML.
- getErrorsFormattedAsPlainText() - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
-
Returns the errors formatted as plain text.
- getEValueMap(ArrayList<Double>) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
-
Returns the e-value corresponding to a list of scores in a map.
- getEValueMap(ArrayList<Double>, boolean) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
-
Returns the e-value corresponding to a list of scores in a map.
- getEvenRowColor() - Method in class com.compomics.util.AlternateRowColoursJTable
-
This method returns the Color used for the even numbered rows, or 'null' if the
default JTable background color is maintained for these rows.
- getExceptions() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Returns the exceptions to the rule.
- getExceptionType(Exception) - Static method in class com.compomics.util.exceptions.ExceptionHandler
-
Returns the exception type.
- getExpectedIons(SpecificAnnotationParameters, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the expected ions in a map indexed by the possible charges.
- getExpectedIons(SpecificAnnotationParameters, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, HashMap<Integer, HashMap<Integer, ArrayList<Ion>>>) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the expected ions in a map indexed by the possible charges.
- getExpectedIons(SpecificAnnotationParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Returns the expected ions in a map indexed by the possible charges.
- getExpectedModifications(double, ModificationParameters, Peptide, double, SequenceProvider, SequenceMatchingParameters, SearchParameters) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
-
Returns the expected modifications for a given modification mass indexed
by site.
- getExpectedVariableModifications(SearchParameters) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns the expected variable modifications given the search parameters.
- getExperiment_type() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
Returns the experiment type.
- getExperimentType() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
-
Returns the experiment type.
- getExportFeatures(String, boolean) - Method in interface com.compomics.util.io.export.ExportFactory
-
Returns the export features implemented for the given section.
- getExportFeatures(boolean) - Method in interface com.compomics.util.io.export.ExportFeature
-
Returns a list of all implemented export features.
- getExportFeatures(String) - Method in class com.compomics.util.io.export.ExportScheme
-
Returns the export features to be included in the given section.
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsAnnotationFeature
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
-
- getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
-
- getExportFormat() - Method in class com.compomics.util.io.export.ExportWriter
-
Returns the export of the format.
- getExportScheme(String) - Method in interface com.compomics.util.io.export.ExportFactory
-
Returns the export scheme indexed by the given name.
- getExportWriter(ExportFormat, File, String, int, boolean) - Static method in class com.compomics.util.io.export.ExportWriter
-
Returns an export writer for the desired format.
- getExtension() - Method in enum com.compomics.util.enumeration.ImageType
-
Returns the extension.
- getExtension() - Method in interface com.compomics.util.experiment.io.identification.IdfileReader
-
Returns the extension of the file for which this IdfileReader can be
used.
- getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
-
- getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader
-
- getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
- getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader
-
- getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader
-
- getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
-
- getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader
-
- getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
-
- getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
-
- getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader
-
- getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
-
- getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
-
- getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
-
- getExtension(File) - Static method in class com.compomics.util.io.file.filefilters.FileFilterUtils
-
Get the extension of a file.
- getExtension(File) - Static method in class com.compomics.util.io.IoUtil
-
Returns the extensions of a file.
- getExtension(String) - Static method in class com.compomics.util.io.IoUtil
-
Returns the extensions of a file name.
- getFactorialsCache() - Static method in class com.compomics.util.math.BasicMathFunctions
-
Returns factorial 0 to 20 in an array.
- getFastaParameters() - Method in class com.compomics.cli.fasta.FastaParametersInputBean
-
Returns the FASTA parameters as parsed from the command line.
- getFastaParameters() - Method in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
-
Returns the FASTA parameters.
- getFastaParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the FASTA processing parameters.
- getFastaSettings() - Method in class com.compomics.util.gui.protein.FastaParametersDialog
-
Returns the FASTA settings as set by the user.
- getFastIndexFolderName() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the name of the FASTA index folder.
- getFeature() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature
-
Returns the peptide feature;
- getFeatureFamily() - Method in interface com.compomics.util.io.export.ExportFeature
-
Returns the family type of this export feature.
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsAnnotationFeature
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
-
- getFeatureFamily() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
-
- getFeatureId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the feature ID.
- getFeatureLabel() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the feature label.
- getFeatures(String) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
-
Returns the features in the map for the given category.
- getFeed(String, String, ArrayList<String>) - Static method in class com.compomics.util.messages.FeedBack
-
Creates a feed object.
- getFeed(String, String) - Static method in class com.compomics.util.messages.FeedBack
-
Creates a general feed with no key word.
- getFile() - Method in class com.compomics.util.gui.file_handling.FileAndFileFilter
-
Returns the file.
- getFileDetailList(String) - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
-
Convert from JSON to a list of FileDetails.
- getFileFilter() - Method in class com.compomics.util.gui.file_handling.FileAndFileFilter
-
Returns the file filter.
- getFileIn() - Method in class com.compomics.cli.enzymes.EnzymesCLIInputBean
-
Returns the file provided as input.
- getFileIn() - Method in class com.compomics.cli.modifications.ModificationsCLIInputBean
-
Returns the file provided as input.
- getFileName() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns the name of the indexed file.
- getFilename() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
-
Getter for the filename
- getFilename() - Method in interface com.compomics.util.interfaces.SpectrumFile
-
This method reports on the filename for the file.
- getFileName(String) - Static method in class com.compomics.util.io.IoUtil
-
An OS independent getName alternative.
- getFileName(File) - Static method in class com.compomics.util.io.IoUtil
-
An OS independent getName alternative.
- getFileName() - Method in class com.compomics.util.io.PklFile
-
- getFileName() - Method in interface com.compomics.util.pride.PrideObject
-
Returns the name to use when serializing the object.
- getFileName() - Method in class com.compomics.util.pride.prideobjects.Contact
-
- getFileName() - Method in class com.compomics.util.pride.prideobjects.ContactGroup
-
- getFileName() - Method in class com.compomics.util.pride.prideobjects.Instrument
-
- getFileName() - Method in class com.compomics.util.pride.prideobjects.Protocol
-
- getFileName() - Method in class com.compomics.util.pride.prideobjects.Reference
-
- getFileName() - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
-
- getFileName() - Method in class com.compomics.util.pride.prideobjects.Sample
-
- getFilenameExtensionLowerCase(String) - Static method in class com.compomics.util.io.IoUtil
-
Returns the given file name with lower-case extension.
- getFileOut() - Method in class com.compomics.cli.enzymes.EnzymesCLIInputBean
-
Returns the file provided as output.
- getFileOut() - Method in class com.compomics.cli.modifications.ModificationsCLIInputBean
-
Returns the file provided as output.
- getFilePaths() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getFilePaths() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getFilePaths() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the absolute path to the original mass spec file containing the
spectra in a map indexed by file name without file extension.
- getFileReader(File) - Method in class com.compomics.util.experiment.io.identification.IdfileReaderFactory
-
This method returns the proper identification file reader depending on
the format of the provided file.
- getFileReader(File) - Static method in interface com.compomics.util.io.flat.SimpleFileReader
-
Returns a file reader, text or gz, according to the extension of the file.
- getFiles(String, ArrayList<String>) - Static method in class com.compomics.software.cli.CommandLineUtils
-
Returns a list of files as imported from the command line option.
- getFileSize(URL) - Static method in class com.compomics.util.io.IoUtil
-
Returns the size of the file located at the given URL.
- getFilter(Integer) - Static method in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardFilter
-
Returns the filter designed by the given number.
- getFilter(String) - Static method in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardFilter
-
Returns the filter designed by the given name.
- getFilter() - Method in class com.compomics.util.gui.filtering.FilterDialog
-
Returns the filter as set by the user.
- getFilter() - Method in class com.compomics.util.gui.parameters.identification.advanced.MatchesImportParametersDialog
-
Returns the id filter as set by the user.
- getFilteredInput(ArrayList<Double>, ArrayList<Double>, double) - Static method in class com.compomics.util.math.statistics.linear_regression.filters.ProbabilityFilter
-
Returns a list containing first the filtered xs and then the filtered ys.
- getFilteredInputFixedBins(ArrayList<Double>, ArrayList<Double>, int) - Static method in class com.compomics.util.math.statistics.linear_regression.filters.BinningFilter
-
Returns a list containing first the filtered xs and then the filtered ys.
- getFilteredInputFixedBinsSize(ArrayList<Double>, ArrayList<Double>, int) - Static method in class com.compomics.util.math.statistics.linear_regression.filters.BinningFilter
-
Returns a list containing first the filtered xs and then the filtered ys.
- getFilterItem(String) - Method in class com.compomics.util.experiment.identification.filtering.AssumptionFilter
-
- getFilterItem(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Returns the filter item corresponding to the given name.
- getFilterItem(String) - Method in class com.compomics.util.experiment.identification.filtering.PeptideFilter
-
- getFilterItem(String) - Method in class com.compomics.util.experiment.identification.filtering.ProteinFilter
-
- getFilterItem(String) - Method in class com.compomics.util.experiment.identification.filtering.PsmFilter
-
- getFilters() - Method in class com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters
-
Returns the index of the filters selected.
- getFiltersMap() - Method in class com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters
-
Returns the filters map, filter index - value.
- getFixedAaModifications() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Returns the modifications at specific amino acids.
- getFixedModificationAtAa(char) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
-
Returns the fixed modification that can be found at the given amino acid.
- getFixedModifications(boolean, boolean, ModificationParameters, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
Returns the fixed modifications for this sequence based on the given
modification parameters.
- getFixedModifications(ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the fixed modifications for this peptide based on the given
modification parameters.
- getFixedModifications() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Returns the fixed modifications for the peptide.
- getFixedModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
-
Returns the searched fixed modifications names.
- getFixedModificationsAsString(Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns the peptide modifications as a string.
- getFixedVariants() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
returns the fixed variants
- getFlags() - Method in class com.compomics.util.general.CommandLineParser
-
This method will report on all flags that have been found, or return an
empty String[] if none were present.
- getFlanking() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Return whether the flanking amino acids of a mapped peptide are to be
reported.
- getFontSize() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Get the font size.
- getFontSizeLegend() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Get the font size for the legend.
- getForeignAccession() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the foreign accession.
- getForeignDescription() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the foreign description.
- getForeignID() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the foreign ID.
- getFormat() - Method in class com.compomics.util.gui.ExportFormatSelectionDialog
-
Returns the selected format.
- getFormatFromCommandLineOption(String) - Static method in enum com.compomics.util.io.export.ExportFormat
-
Returns the export format designed by the given command line option.
- getForwardIons() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the forward ions searched as list of integers as indexed in the
FragmentIon class.
- getForwardIonsFeatures(Peptide, int, int, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation.FeaturesGenerator
-
Returns the ms2pip features for the forward ions of the given peptide at
the given charge.
- getForwardStart(String) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
-
Returns the amino acid where a neutral loss should start being accounted
for when predicting b ions (counting from N-terminus, first aa is 1).
- getFoundCharges() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the found charges.
- getFoundModifications() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the variable modifications found in the currently loaded dataset.
- getFoundModifications() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the names of the variable modifications found in the dataset.
- getFractionConfidence(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the fraction confidence.
- getFractionMolecularWeightRanges() - Method in class com.compomics.util.parameters.identification.advanced.FractionParameters
-
Returns the user provided molecular weight ranges for the fractions.
- getFractionOfPeaksForChargeEstimation() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the fraction of peaks to be retained for charge >1 estimation.
- getFractionParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the fraction parameters.
- getFractionPEP(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the fraction pep.
- getFractionPEP() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the fraction pep map.
- getFractionPsmMatches() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the list of fraction PSM matches.
- getFractions() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the fractions.
- getFractions() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Return the fractions where this match was found.
- getFractionScore(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the fraction score.
- getFractionScore() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Return the fractions where this match was found.
- getFractionSettings() - Method in class com.compomics.util.gui.parameters.identification.advanced.FractionParametersDialog
-
Returns the fraction settings as set by the user.
- getFractionValidatedPeptides(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Get the number of validated peptides in the given fraction.
- getFractionValidatedSpectra(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Get the number of validated spectra in the given fraction.
- getFragmentAccuracyType() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the fragment accuracy type.
- getFragmentationMethod() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns the fragmentation method used.
- getFragmentationMethod() - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
-
Returns the fragmentation method.
- getFragmentationModel() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Returns the name of the fragmentation model.
- getFragmentationRule() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns the fragmentation rule.
- getFragmentationTerminus() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the fragmentation terminus.
- getFragmentationType() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Return the fragmentation ID.
- getFragmentBinOffset() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the fragment ion bin offset.
- getFragmentIonAccuracy() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns the fragment ion accuracy.
- getFragmentIonAccuracy() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Returns the fragment ion accuracy.
- getFragmentIonAccuracy() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the MS2 ion m/z tolerance.
- getFragmentIonAccuracyInDa(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns the fragment ion accuracy in Da.
- getFragmentIonAccuracyInDa(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Returns the fragment ion accuracy in Da.
- getFragmentIonAccuracyInDaltons() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the absolute fragment ion tolerance in Dalton.
- getFragmentIonAccuracyInDaltons(double) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the absolute fragment ion tolerance in Dalton.
- getFragmentIons(Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.ions.IonFactory
-
This method returns all the theoretic ions expected from a peptide.
- getFragmentIons(Peptide, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.ions.IonFactory
-
This method returns the theoretic ions expected from a peptide.
- getFragmentIons(Tag, ModificationParameters, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.ions.IonFactory
-
This method returns the theoretic ions expected from a tag.
- getFragmentIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns the type of peptide fragment ions annotated.
- getFragmentIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Returns the type of peptide fragment ions annotated.
- getFullFilePath(String) - Static method in class com.compomics.util.junit.TestCaseLM
-
This method finds a file from the current classpath and attempts to reconstruct its
full filename.
- getFullHeaderWithAddenda() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
This method reports on the full header, with the addenda (if present).
- getFullName() - Method in enum com.compomics.util.experiment.io.biology.protein.ProteinDatabase
-
Returns the full name of the database, null if not set.
- getFullName() - Method in class com.compomics.util.experiment.units.UnitOfMeasurement
-
Returns the full name of the unit.
- getFunction() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature
-
Returns the function used to compare the amino acid properties.
- getGeneMappingFile(String) - Static method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
Returns the gene mapping file.
- getGeneMappingFolder() - Static method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
Returns the path to the folder containing the gene mapping files.
- getGeneMaps(GeneParameters, FastaSummary, SequenceProvider, ProteinDetailsProvider, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
Returns the gene maps for the given proteins.
- getGeneName(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getGeneName() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the gene name.
- getGeneName(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
-
Returns the gene name for the given protein.
- getGeneNameToAccession() - Method in class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
-
Returns the gene name to protein accession map.
- getGeneNameToChromosome() - Method in class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
-
Returns the gene name to chromosome map.
- getGeneNameToChromosomeMap() - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Returns the gene name to chromosome map.
- getGeneNameToEnsemblIdMap() - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Returns the gene name to Ensembl ID map.
- getGeneParameters() - Method in class com.compomics.util.gui.parameters.identification.advanced.BackgroundSpeciesDialog
-
Returns the gene preferences.
- getGeneParameters() - Method in class com.compomics.util.gui.parameters.identification.advanced.GeneParametersDialog
-
Returns the gene preferences.
- getGeneParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the gene parameters.
- getGeneratedKeys() - Method in interface com.compomics.util.db.interfaces.Persistable
-
This method will return the automatically generated key for the insert if
one was triggered, or 'null' otherwise.
- getGenericIon(Ion.IonType, int, NeutralLoss[]) - Static method in class com.compomics.util.experiment.biology.ions.Ion
-
Convenience method returning a generic ion based on the given ion type.
- getGenericIon(Ion.IonType, int) - Static method in class com.compomics.util.experiment.biology.ions.Ion
-
Convenience method returning a generic ion based on the given ion type
without neutral losses.
- getGoAccession(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Returns the GO Term accession corresponding to the given name.
- getGoAccessionLink(String) - Method in class com.compomics.util.gui.genes.GeneDetailsDialog
-
Returns the GO accession number as a web link to the given GO term at
QuickGO.
- getGoAccessions(String) - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
-
Returns the GO accessions linked to a given protein accession.
- getGoAccessionToProteinMap() - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Returns the GO to protein accession map.
- getGoDomainsFile() - Static method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
Returns the GO domains file.
- getGoMappingFile(String) - Static method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
Returns the GO mapping file.
- getGoNamesForProtein(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Returns the go terms names for a protein accession.
- getGoNamesMap() - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Returns the GO accession to names map.
- getGoNamesMap() - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
-
Returns the GO accession to name map.
- getGoTermsForProtein(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Returns the go terms accessions for a protein accession.
- getGoToProteinMap() - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
-
Returns the GO to protein accession map.
- getGPtmCategories() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the modification categories to include in the G-PTM search.
- getGravy() - Method in class com.compomics.util.protein.AASequenceImpl
-
This method gets the GRAVY score (Kyte & Doolittle) from
the cache, or, if it isn't cached, reconstructs it.
- getGroupId() - Method in class com.compomics.software.autoupdater.MavenJarFile
-
Returns the group id.
- getGroupNames() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Returns a standard map of the group names.
- getGuiOptions() - Static method in enum com.compomics.util.parameters.peptide_shaker.ProjectType
-
Returns the different options as they should be displayed on the GUI.
- getHeader() - Static method in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
-
IdentificationParametersCLI header message when printing the usage.
- getHeader() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.AccessionMetaData
-
Returns the parsed header.
- getHeader(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getHeader(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
-
- getHeader(String) - Method in interface com.compomics.util.experiment.io.biology.protein.SequenceProvider
-
Returns the FASTA header of the protein as found in the FASTA file.
- getHeader() - Method in class com.compomics.util.nucleotide.NucleotideSequence
-
This method reports on the nucleotide header.
- getHeader() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
-
Returns the header.
- getHeader() - Method in class com.compomics.util.protein.Protein
-
This method reports on the header for the current
protein.
- getHeaderAsString() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.AccessionMetaData
-
Returns the header string representation.
- getHeaderHeight() - Method in class com.compomics.util.io.export.styles.DefaultStyle
-
- getHeaderHeight() - Method in interface com.compomics.util.io.export.WorkbookStyle
-
Returns the height of a header row.
- getHeaderStyle() - Method in class com.compomics.util.io.export.styles.DefaultStyle
-
- getHeaderStyle(int) - Method in class com.compomics.util.io.export.styles.DefaultStyle
-
- getHeaderStyle() - Method in interface com.compomics.util.io.export.WorkbookStyle
-
Returns the standard cell style of a header.
- getHeaderStyle(int) - Method in interface com.compomics.util.io.export.WorkbookStyle
-
Returns the standard cell style of a header at the given hierarchical
depth.
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the helicity according to PMID 14730315.
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
-
- getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
-
- getHidden() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns whether a match is hidden or not.
- getHighestIntensity() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
-
Method that find the intensity of the most intense peak
- getHighestIntensity() - Method in interface com.compomics.util.interfaces.SpectrumFile
-
This method returns the intensity of the highest intensity peak in
this spectrum.
- getHighestVersionNumber() - Method in class com.compomics.software.autoupdater.MetaDataXMLParser
-
Returns the highest version number.
- getHighIntensityCutOff() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the high intensity cut-off as percentage of the most intense ion
peak.
- getHistogram(int, Integer, int, int) - Method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
-
Get histogram.
- getHitListLength() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the length of the hit list for OMSSA.
- getHitListLength() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Returns the length of the hit list.
- getHomeFolder() - Static method in class com.compomics.util.io.file.FileSystemAccessor
-
Returns the user home folder.
- getHtmlTooltip() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns information about the modification as an HTML tooltip.
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the hydrophobicity according to PMID 14730315.
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
-
- getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
-
- getIconMap(Class) - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
-
Returns the default map of icons for the validation levels.
- getId() - Method in interface com.compomics.software.settings.PathKey
-
Returns the id of the path.
- getId() - Method in enum com.compomics.software.settings.UtilitiesPathParameters.UtilitiesPathKey
-
- getId(String, boolean) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
-
Returns the NCBI taxon corresponding to the given species name.
- getId() - Method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
-
Returns the id number of the score.
- getID() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the ID.
- getId() - Method in class com.compomics.util.experiment.patient.Patient
-
Returns the patient id,
- getId() - Method in class com.compomics.util.experiment.personalization.ExperimentObject
-
Returns the id of the object.
- getIdentificationAlgorithmParameter(int) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the algorithm specific parameters, null if not found.
- getIdentificationCharge() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the charge used for identification.
- getIdentificationFeaturesCache() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the identification features cache.
- getIdentificationFile() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the identification file.
- getIdentificationKeys() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the identification keys.
- getIdentificationParameters() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
-
Returns the identification parameters.
- getIdentificationParameters(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
-
Returns the identification parameters corresponding to the given name.
- getIdentificationParameters() - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
-
Returns the identification parameters as set by the user.
- getIdentificationParameters() - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersOverviewDialog
-
Returns the selected identification parameters.
- getIdentificationParameters(File) - Static method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Loads the identification parameters from a file.
- getIdentificationParameters(File) - Static method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Loads the identification parameters from a file.
- getIdentificationParametersFile(String) - Static method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
-
Returns the identification parameters corresponding to the given name.
- getIdentifier() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Returns the reference identifier.
- getIdentityMatrix(int) - Static method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getIdMatchValidationPreferences() - Method in class com.compomics.util.gui.parameters.identification.advanced.ValidationParametersDialog
-
Returns the validation settings as set by the user.
- getIdValidationParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the identification matches validation parameters.
- getImmoniumIon(int) - Static method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
Returns the immonium ion corresponding to the given subtype.
- getImmoniumIon(char) - Static method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
Returns the immonium ion produced by the given amino acid.
- getImplementedAtoms(boolean) - Static method in class com.compomics.util.experiment.biology.atoms.Atom
-
Returns an array of implemented atoms indicated by their short name.
- getImplementedIons() - Static method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Returns a set of possible subtypes.
- getImplementedIonTypes() - Static method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the implemented ion types.
- getImplementedIsotopes() - Method in class com.compomics.util.experiment.biology.atoms.Atom
-
returns an unsorted list of isotopes for which a mass is available
relative to the monoisotopic peak (+1 for carbon 13).
- getImplementedSections() - Method in interface com.compomics.util.io.export.ExportFactory
-
Returns the implemented sections.
- getIndentString() - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
-
Returns the indent string to use, e.g.
- getIndex(char) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns an index for the amino acid excluding combinations.
- getIndex() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Returns the index of a reporter ion.
- getIndex() - Method in class com.compomics.util.experiment.identification.Advocate
-
Returns the index of the advocate.
- getIndex() - Method in class com.compomics.util.experiment.identification.IdentificationMethod
-
returns the index of the identification method
- getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureAbsolute
-
- getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureRelative
-
- getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureAbsolute
-
- getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureRelative
-
- getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
-
- getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonAminoAcidFeature
-
- getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonFeature
-
- getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonAminoAcidFeature
-
- getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonFeature
-
- getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
-
- getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideAminoAcidFeature
-
- getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
-
- getIndex() - Method in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature
-
Returns an integer unique to this class.
- getIndex() - Method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
-
Returns the index on the protein.
- getIndex() - Method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
-
Returns the index associated to this possibility.
- getIndex(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns the index corresponding to the desired spectrum.
- getIndexedVariableModifications() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
Returns the variable modifications indexed by site.
- getIndexedVariableModifications() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the variable modifications indexed by site.
- getIndexes(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns the indexes where the amino acid pattern was found in the input.
- getIndexes(AminoAcidPattern, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns the indexes where the amino acid pattern was found in the input.
- getIndexes(String, String) - Static method in class com.compomics.util.Util
-
Returns at which indexes a small string can be found in a big string.
- getIndexOnProtein() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Returns the peptide index on the protein.
- getInferred() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Returns a boolean indicating whether the modification is inferred from
another peptide.
- getInitiatorMethionineBehavior() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the initiator methionine behavior.
- getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.AndromedaParametersDialog
-
Returns the user selection as Andromeda parameters object.
- getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.CometParametersDialog
-
Returns the user selection as Comet parameters object.
- getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.DirecTagParametersDialog
-
Returns the DirecTag parameters as set by the user.
- getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MetaMorpheusParametersDialog
-
Returns the user selection as MetaMorpheus parameters object.
- getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsAmandaParametersDialog
-
Returns the user selection as MS Amanda parameters object.
- getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsgfParametersDialog
-
Returns the user selection as MS-GF+ parameters object.
- getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MyriMatchParametersDialog
-
Returns the user selection as MyriMatch parameters object.
- getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.NovorParametersDialog
-
Returns the Novor parameters as set by the user.
- getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.OmssaParametersDialog
-
Returns the user selection as OMSSA parameters object.
- getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.PepNovoParametersDialog
-
Returns the PepNovo+ parameters as set by the user.
- getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.TideParametersDialog
-
Returns the user selection as Tide parameters object.
- getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
-
Returns the user selection as X!tandem parameters object.
- getInputFile() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
-
Returns the input parameters file.
- getInputFile() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
Returns the spectrum file name as found in the parameters section.
- getInsertedAminoAcid() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Insertion
-
- getInstance() - Static method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
-
Static method to get an instance of the factory.
- getInstance() - Static method in class com.compomics.util.experiment.biology.ions.IonFactory
-
Static method which returns the instance of the factory.
- getInstance() - Static method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Static method to get the instance of the factory.
- getInstance() - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Static method returning the instance of the factory.
- getInstance() - Static method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
-
Static method to get the instance of the factory.
- getInstance() - Static method in class com.compomics.util.experiment.io.identification.IdfileReaderFactory
-
A static method to retrieve the instance of the factory.
- getInstance() - Static method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
-
Constructor for the factory.
- getInstance() - Static method in class com.compomics.util.io.PropertiesManager
-
Get the singleton instance to access properties of Computational Omics tools.
- getInstance() - Static method in class com.compomics.util.pride.PrideObjectsFactory
-
Method returning the instance of the factory.
- getInstitution() - Method in class com.compomics.util.pride.prideobjects.Contact
-
Returns the instituition.
- getInstrumentID() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Return the instrument ID.
- getInstrumentID() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Return the instrument ID.
- getInstruments() - Method in class com.compomics.util.pride.PrideObjectsFactory
-
Returns the instruments.
- getIntegerListFromString(String, String) - Static method in class com.compomics.software.cli.CommandLineUtils
-
Parses a list of integers from a command line option.
- getIntegerParameter(String) - Method in class com.compomics.util.experiment.ProjectParameters
-
- getIntensities(int, Integer, int) - Method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
-
Get intensity.
- getIntensity(Ion) - Static method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.SequestFragmentationModel
-
Returns the intensity expected for the given ion.
- getIntensity() - Static method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.UniformFragmentation
-
Returns a default intensity of 1.0.
- getIntensity() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
-
Getter for the precursor intensity (here always zero)
- getIntensity() - Method in interface com.compomics.util.interfaces.SpectrumFile
-
This method reports on the intensity of the precursor ion.
- getIntensityAtP(double) - Method in class com.compomics.util.experiment.mass_spectrometry.SimpleNoiseDistribution
-
Returns the intensity at a given upper tail cumulative probability.
- getIntensityCutOffIncrement() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the intensity cut-off increment.
- getIntensityLimit(Spectrum, AnnotationParameters.IntensityThresholdType, double) - Static method in class com.compomics.util.experiment.mass_spectrometry.spectra.SpectrumUtil
-
Returns the limit in intensity according to the given threshold.
- getIntensityPrideCvTerm() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the pride CV term for the ion match intensity.
- getIntensityScoreWeight() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the intensity score weight.
- getIntensityThresholdType() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns the intensity threshold type.
- getIntensityValues() - Method in class com.compomics.util.io.PklFile
-
- getIntentisy(Ion) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.FragmentItensityPredictor
-
Returns the intensity expected for the given peak.
- getIntermediateScore(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the desired intermediate score.
- getIntermediateScores() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the intermediate scores map.
- getInterpolation(ArrayList<Double>, Double, Double) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
-
Returns the interpolation of a list of hyperscores using a linear
interpolation of the form result = a * log(score) + b.
- getInterpolation(double, double, double) - Static method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
-
Returns the interpolated value for a given score in log.
- getInterpolationValues(int[], boolean) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
-
Returns the interpolation values for the given scores in the form {a, b}.
- getInterpolationValues(HashMap<Integer, Integer>, boolean) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
-
Returns the interpolation values for the given score histogram in the
form {a, b}.
- getIonAtRow(int) - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
-
Returns the ion type at the given row.
- getIonMassErrorPrideCvTerm(int, int) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the pride CV term for the ion match error.
- getIonMatches(SpectrumIndex, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotator
-
Returns the ions matched in the given spectrum at the given charge.
- getIonMatches(SpectrumIndex, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotatorNL
-
Returns the ions matched in the given spectrum at the given charge.
- getIonMatches(SpectrumIndex) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ImmoniumIonAnnotator
-
Returns the ions matched in the given spectrum.
- getIonMatches(SpectrumIndex, int, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.PrecursorAnnotator
-
Returns the ions matched in the given spectrum at the given charge.
- getIonMatches(SpectrumIndex) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ReporterIonAnnotator
-
Returns the ions matched in the given spectrum.
- getIonMatches(SpectrumIndex, int, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator
-
Returns the ion matches for the given spectrum.
- getIons() - Static method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Getter for the list of ion symbols used.
- getIonType(String) - Static method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
Returns the ion index corresponding to the given symbol in the drop down
menu.
- getIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns the type of ions annotated.
- getIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Returns the map of ions to annotate.
- getIsotope() - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
-
Returns the isotope, 0 for monoisotope.
- getIsotope() - Method in class com.compomics.util.gui.atoms.AtomPanel
-
Returns the currently selected isotope.
- getIsotopeCorrection() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the isotope correction setting.
- getIsotopeMass(int) - Method in class com.compomics.util.experiment.biology.atoms.Atom
-
Returns the mass corresponding to the given isotope number.
- getIsotopeMzTolerance() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the deisotoping m/z tolerance.
- getIsotopeNumber(Integer) - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
-
Returns the isotope number corresponding to the given rounded mass.
- getIsotopeNumber(int, int) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the distance in number of neutrons between the experimental mass
and theoretic mass, image of the isotope number: 1 typically indicates
C13 isotope.
- getIsotopeNumber(double, int, int) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the precursor isotope number according to the number of protons.
- getIsotopicDistribution() - Method in class com.compomics.util.protein.AASequenceImpl
-
This method gives the IsotopicDistribution for the sequence
- getItem(String) - Static method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
-
Returns the item designated by the given name.
- getItem(String) - Static method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
-
Returns the item designated by the given name.
- getItem(String) - Static method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
-
Returns the item designated by the given name.
- getItem(String) - Static method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
-
Returns the item designated by the given name.
- getItemsNames() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Returns the name of the items used to filter.
- getIterativeReplaceEvalue() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the e-value threshold to use to replace a hit for the iterative
search.
- getIterativeSequenceEvalue() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the e-value threshold to use to consider a sequence for the
iterative search.
- getIterativeSpectrumEvalue() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the e-value threshold to use consider a spectrum for the
iterative search.
- getiXAxisMax() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the maximum value of the x-axis.
- getiXAxisMin() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the minimum value of the x-axis.
- getiYAxisMax() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the maximum value of the y-axis.
- getiYAxisMin() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the minimum value of the y-axis.
- getJarFilePath() - Method in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
-
Returns the path to the jar file.
- getJarFilePath() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersCLI
-
Returns the path to the jar file.
- getJarFilePath() - Method in class com.compomics.cli.paths.PathSettingsCLI
-
Returns the path to the jar file.
- getJarFilePath(String, String) - Static method in class com.compomics.software.CompomicsWrapper
-
Returns the path to the jar file.
- getJarPath() - Method in class com.compomics.software.autoupdater.MavenJarFile
-
Returns the path to the jar file.
- getJavaHome() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the Java Home folder.
- getJavaHomeAndOptions(String) - Method in class com.compomics.software.CompomicsWrapper
-
Returns an array list containing the Java home plus any parameters to the
JVM.
- getJOptionEditorPane(String) - Static method in class com.compomics.util.gui.JOptionEditorPane
-
Returns a JEditorPane with HTML support to be used in a JOptionsPane.
- getJsonStringFromFile(File) - Method in class com.compomics.util.io.json.JsonMarshaller
-
Convert JSON string from file.
- getKeepTerminalAminoAcids() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the option for keeping the terminal amino acids when generating
the decoys.
- getKey() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the reference key of a peptide.
- getKey(String, ModificationMatch[]) - Static method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the reference key of a peptide.
- getKey() - Method in class com.compomics.util.experiment.identification.IdentificationMatch
-
Returns the key of a match.
- getKey() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
- getKey() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
- getKey(String, String) - Static method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Returns a key to use for the spectrum match based on the file where the
spectrum was found and its title.
- getKey() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
- getKeyFromId(String) - Static method in enum com.compomics.software.settings.UtilitiesPathParameters.UtilitiesPathKey
-
Returns the key from its id.
- getKeysInBackend() - Method in class com.compomics.util.db.object.ObjectsDB
-
Returns the keys in backend set.
- getKeyToPathMap() - Method in class com.compomics.software.settings.gui.PathParametersDialog
-
Returns the path settings in a map: key | path.
- getKeyWords() - Method in class com.compomics.util.messages.FeedBack
-
Returns the key words for this report.
- getKnownMassDeltas() - Static method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Get all the known mass deltas (if any).
- getLabel() - Method in interface com.compomics.util.gui.interfaces.SpectrumAnnotation
-
This method returns the label for the annotation.
- getLabel() - Method in class com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation
-
This method returns the label for the annotation.
- getLabel() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Returns the label.
- getLabelColor() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Returns the label color.
- getLabelWidth() - Static method in class com.compomics.util.gui.TableProperties
-
Returns the label width for the sparklines.
- getLastHeader() - Method in class com.compomics.util.experiment.io.biology.protein.iterators.FastaIterator
-
Returns the header corresponding to the last protein.
- getLastModified() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns when the file was last modified.
- getLastSelectedFolder() - Method in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
-
Returns the last selected folder.
- getLastSelectedFolder() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Returns the last selected folder.
- getLastSelectedFolder(String) - Method in class com.compomics.util.io.file.LastSelectedFolder
-
Returns the last selected folder according to the given use case.
- getLastSelectedFolder() - Method in class com.compomics.util.io.file.LastSelectedFolder
-
Returns the last selected folder according to the given use case.
- getLastSelectedFolder() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the last selected folder.
- getLatestVersionNumberFromRemoteRepo(URL) - Static method in class com.compomics.software.autoupdater.WebDAO
-
Fetches the latest Maven deployed version from a Maven built repository.
- getLatinName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
-
Returns the Latin name corresponding to the given NCBI taxon.
- getLatinName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns the Latin name of the species corresponding to the given taxon
according to the UniProt mapping.
- getLeadingAccession() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Returns the leading accession for this match.
- getLegendDatasetAFourWay() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Returns the legend location of dataset A in a four way Venn diagram.
- getLegendDatasetAThreeWay() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Returns the legend location of Dataset A in a three way Venn diagram.
- getLegendDatasetBFourWay() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Returns the legend location of dataset B in a four way Venn diagram.
- getLegendDatasetBThreeWay() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Returns the legend location of dataset B in a three way Venn diagram.
- getLegendDatasetCFourWay() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Returns the legend location of dataset C in a four way Venn diagram.
- getLegendDatasetCThreeWay() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Returns the legend location of dataset C in a three way Venn diagram.
- getLegendDatasetDFourWay() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Returns the legend location of dataset D in a four way Venn diagram.
- getLength() - Method in class com.compomics.util.experiment.biology.proteins.Protein
-
Returns the number of amino acids in the sequence.
- getLength() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
-
- getLength() - Method in interface com.compomics.util.interfaces.Sequence
-
This method reports on the length of the current sequence.
- getLength() - Method in class com.compomics.util.nucleotide.NucleotideSequence
-
This method reports on the length of the sequence for the current nucleotide sequence.
- getLength() - Method in class com.compomics.util.nucleotide.NucleotideSequenceImpl
-
This method reports on the length of the current sequence.
- getLength() - Method in class com.compomics.util.protein.AASequenceImpl
-
This method reports on the length of the current sequence.
- getLength() - Method in class com.compomics.util.protein.Protein
-
This method reports on the length of the sequence for the current protein.
- getLengthDiff() - Method in class com.compomics.util.experiment.identification.matches.PeptideVariantMatches
-
Returns the length difference induced by the variants.
- getLengthInAminoAcid() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Returns the amino acid length of the tag when mass gaps are considered
like one amino acid
- getLetter() - Method in class com.compomics.util.experiment.biology.atoms.Atom
-
Returns the symbol for the atom.
- getLicense() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
Returns the license information of this file.
- getLimitX() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Returns the maximal share of X's a match can contain, range [0.0-1.0].
- getLine(int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getLinearRegression(ArrayList<Double>, ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.linear_regression.regressions.MedianRegression
-
Returns a robust linear regression based on the median of statistics.
- getLinearRegression(ArrayList<Double>, ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.linear_regression.regressions.SimpleLinearRegression
-
Returns a simple linear regression.
- getLines() - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getLink() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the link.
- getLinkHref() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the linkHref.
- getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class com.compomics.util.gui.renderers.AlignedListCellRenderer
-
- getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer
-
- getLn10(MathContext) - Static method in class com.compomics.util.math.BigMathUtils
-
Returns the value of ln(10) according to the mathContext.
- getLocalizationConfidence(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns the confidence of the PTM localization.
- getLocalPrideFolder() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the local PRIDE folder.
- getLocation() - Method in interface com.compomics.util.interfaces.Modification
-
This method returns the location of the modification in the sequence.
- getLocation() - Method in class com.compomics.util.protein.ModificationImplementation
-
This method returns the location of the modification in the sequence.
- getLocationToDownloadOnDisk(String) - Method in class com.compomics.software.autoupdater.FileDAO
-
Try to find an at least somewhat sane location to download files to.
- getLocationToDownloadOnDisk(String) - Method in class com.compomics.software.autoupdater.GUIFileDAO
-
Try to find an at least somewhat sane location to download files to.
- getLocationToDownloadOnDisk(String) - Method in class com.compomics.software.autoupdater.HeadlessFileDAO
-
Try to find an at least somewhat sane location to download files to.
- getLogFolder() - Method in class com.compomics.cli.paths.PathSettingsCLIInputBean
-
Returns the folder where to save the log files.
- getLogIntensityAtP(double) - Method in class com.compomics.util.experiment.mass_spectrometry.SimpleNoiseDistribution
-
Returns the log10 intensity at a given upper tail cumulative probability.
- getLongestAminoAcidSequence() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Returns the longest amino acid sequence contained in this tag.
- getLossesMass(NeutralLoss[]) - Static method in class com.compomics.util.experiment.biology.ions.IonFactory
-
Convenience summing the masses of various neutral losses.
- getLowerClearMzRange() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the lower mass value for the clear mz range.
- getLowerPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Returns the lower precursor mass.
- getLowIntensityCutOff() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the low intensity cut-off as percentage of the most intense ion
peak.
- getMagicNumber() - Static method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileUtils
-
Returns the magic number of currently supported CMS files.
- getMainTitle() - Method in class com.compomics.util.io.export.ExportScheme
-
Returns the main title of the report.
- getMainTitleRowHeight() - Method in class com.compomics.util.io.export.styles.DefaultStyle
-
- getMainTitleRowHeight() - Method in interface com.compomics.util.io.export.WorkbookStyle
-
Returns the row height for the main title.
- getMainTitleStyle() - Method in class com.compomics.util.io.export.styles.DefaultStyle
-
- getMainTitleStyle() - Method in interface com.compomics.util.io.export.WorkbookStyle
-
Returns the cell style for the main title.
- getManualValidation() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Returns the manually validated items.
- getManualValidation() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Indicates whether the match validation was manually inspected.
- getMap() - Method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
-
Get the map.
- getMass() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
- getMass() - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
-
Returns the mass of the atomic chain as sum of the individual atoms.
- getMass() - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
-
Returns the mass of the atom.
- getMass() - Method in class com.compomics.util.experiment.biology.atoms.ElementaryElement
-
Returns the mass of the element.
- getMass(int) - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
-
Get the glycan mass.
- getMass() - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
-
Returns the mass of the neutral loss, from the atomic composition if
available, from the mass field otherwise.
- getMass() - Method in class com.compomics.util.experiment.biology.ions.NeutralLossCombination
-
Returns the mass of this combination.
- getMass() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Getter for the mass difference induced by this modification.
- getMass() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the mass, does not attempt to estimate it.
- getMass(ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the mass, estimates it if not done before.
- getMass() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.MassGap
-
- getMass() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Returns the mass of the tag.
- getMass(boolean, boolean) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Returns the theoretic mass of the tag, eventually without terminal gaps.
- getMass() - Method in interface com.compomics.util.experiment.identification.amino_acid_tags.TagComponent
-
Returns the mass of the tag component.
- getMass(String, IdfileReader, SearchParameters, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationMassMapper
-
Returns the mass indicated by the identification algorithm for the given
modification.
- getMass() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Returns the mass.
- getMass(int) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
-
Returns the mass associated with the given bin, the middle of the bin.
- getMass(int) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Returns the mass associated with the given bin, the middle of the bin.
- getMass(int) - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
-
Returns the mass of the compound with the given charge.
- getMass(int) - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
-
Returns the mass of the precursor with the given charge.
- getMass() - Method in interface com.compomics.util.interfaces.Sequence
-
This method will return the mass for the sequence.
- getMass() - Method in class com.compomics.util.nucleotide.NucleotideSequence
-
This method returns the nucleotide sequence weight in Da.
- getMass() - Method in class com.compomics.util.nucleotide.NucleotideSequenceImpl
-
This method will return the mass for the sequence.
- getMass() - Method in class com.compomics.util.protein.AASequenceImpl
-
This method calculates the mass for the current sequence.
- getMass() - Method in class com.compomics.util.protein.Protein
-
This method returns the protein weight in Da.
- getMassAnalyzer() - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
-
Returns the mass analyzer.
- getMassAndromeda(String, ModificationProvider, SearchParameters) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationMassMapper
-
Returns the mass indicated by the Andromeda for the given modification.
- getMassByMass(String) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationMassMapper
-
Returns the mass indicated by the identification algorithm for the given
modification.
- getMassByName(String, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationMassMapper
-
Returns the mass indicated by the identification algorithm for the given
modification.
- getMassDelta(String, int) - Method in class com.compomics.util.protein.ModificationImplementation
-
This method returns the mass delta for the specified residue, measured either
monoisotopically or averaged.
- getMassDelta(String, int) - Method in class com.compomics.util.protein.ModificationTemplate
-
This method returns the mass delta for the specified residue, measured either
monoisotopically or averaged.
- getMassDiffAcceptorType() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the mass difference acceptor type.
- getMassErrorDistribution(String) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the precursor mass error distribution of validated peptides in a
spectrum file.
- getMassGap() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
Returns the mass gap comprised in this ion.
- getMassOmssa(String, ModificationProvider, SearchParameters) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationMassMapper
-
Returns the mass indicated by the OMSSA for the given modification.
- getMassShift() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Returns the m/z shift applied to the fragment ions.
- getMassShiftCTerm() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Returns the C-terminal m/z shift applied to all reverse ions.
- getMassShiftNTerm() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Returns the N-terminal m/z shift applied to all forward ions.
- getMatchingAminoAcid(char, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns a matching amino acid using the given preferences.
- getMatchingKey() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the key accounting for sequence matching preferences
- getMatchingKey(SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns a unique key for the peptide when considering the given matching
preferences.
- getMatchingPeaks(double) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Returns the peaks matching the given m/z.
- getMatchingSequence(String, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the matching sequence of a given sequence.
- getMatchingSpectra(double) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
-
Returns a list containing the precursors matching the given m/z.
- getMatchingType(int) - Static method in enum com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters.MatchingType
-
Returns the matching type corresponding to the given index.
- getMatchKey(Ion, int) - Static method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the key for the ion match uniquely representing a peak
annotation.
- getMatchKey(Ion, int, IonMatchKeysCache) - Static method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the key for the ion match uniquely representing a peak
annotation.
- getMatchKey(int, int, int, String, int) - Static method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the key based on the different attributes of a match.
- getMatchKey(Ion, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.IonMatchKeysCache
-
Returns the key for the ion match uniquely representing a peak
annotation.
- getMatchValidationLevel() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the validation level of the match.
- getMatchValidationLevel(String) - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
-
Returns the match validation level associated to a given name.
- getMatchValidationLevel(int) - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
-
Returns the match validation level associated to a given index.
- getMatchValidationLevel() - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
-
Returns the lowest validation level considered as an integer as indexed
in the MatchValidationLevel enum.
- getMavenJarFileFromFolderWithArtifactId(File, String) - Method in class com.compomics.software.autoupdater.FileDAO
-
Fetches a Maven built jar file from a folder for the given artifact id
(e.g peptideshaker or ms-lims).
- getMaxCharge() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the maximal charge among found charges.
- getMaxCharge() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns the maximal charge found in the mgf file.
- getMaxChargeSearched() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the maximal charge searched.
- getMaxCombinations() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns the maximal number of combinations.
- getMaxDynamicMods() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the maximum number of dynamic mods.
- getMaxDynamicMods() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns the maximum number of variable modifications.
- getMaxEValue() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the maximal e-value searched for.
- getMaxEValue() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns the maximal e-value searched for.
- getMaxExp(MathContext) - Static method in class com.compomics.util.math.BigFunctions
-
Returns the estimated maximal value exp can be calculated on according to
the mathContext.
- getMaxFragmentCharge() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the maximum fragment ion charge.
- getMaxFragmentCharge() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the maximal fragment charge.
- getMaxFragmentPerSeries() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the maximal number of fragments to retain per series.
- getMaxFragmentSize() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the max fragmentation size.
- getMaxHeterozygousVariants() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the max heterozygous variants.
- getMaxHitsPerSpectrumPerCharge() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the maximal number of hits searched per spectrum and per charge.
- getMaximum() - Method in interface com.compomics.util.interfaces.Monitorable
-
This method reports on the total amount steps the task can take before
completion.
- getMaximum() - Method in class com.compomics.util.io.file.MonitorableFileInputStream
-
This method reports on the maximum scale for the monitor.
- getMaximum() - Method in class com.compomics.util.io.file.MonitorableInputStream
-
This method reports on the total amount of bytes that can be read
from the monitored InputStream.
- getMaximumExpectationValueRefinement() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns the maximum expectation value to use for refinement.
- getMaximumValue() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
-
Returns the current maximum value for the progressbar.
- getMaxIndex() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns the maximal index where amino acids are found.
- getMaxIntensity() - Method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
-
Returns the max intensity.
- getMaxIntensity() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns the maximum precursor intensity in this file.
- getMaxIntensity() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
-
Returns the max intensity value.
- getMaxIsotopes() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Returns the maximal number of isotopes allowed (inclusive).
- getMaxIsotopicCorrection() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the maximal isotopic correction.
- getMaxIterations() - Method in class com.compomics.util.math.clustering.KMeansClustering
-
Returns the maximum number of iterations.
- getMaxLoadedProteins() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns the maximum number of proteins loaded into memory.
- getMaxLoadedSpectra() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns the maximum number of spectra loaded into memory.
- getMaxMass() - Method in class com.compomics.util.gui.events.RescalingEvent
-
Returns the maximum mass.
- getMaxMissedCleavages() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Returns the maximum number of missed cleavages.
- getMaxModificationIsoforms() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the max modification isoforms.
- getMaxModifications() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns the maximum number of modifications per peptide.
- getMaxModificationSites() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns the maximum number of modifications sites per modification per
peptide.
- getMaxModsForPeptide() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the max mods for peptide.
- getMaxMW() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the molecular weight of the fattest protein in the dataset.
- getMaxMz() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns the maximum m/z in this file.
- getMaxMz() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
-
Returns the maximal m/z encountered among the precursors.
- getMaxMz() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
-
Returns the max mz value.
- getMaxMzDeviation() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Returns the maximal m/z deviation allowed.
- getMaxMzLadders() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the maximal m/z ladder length.
- getMaxNeutralLosses() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns the maximum number of water and ammonia losses per peptide.
- getMaxNeutralLossesPerModification() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns the maximum number identical modification specific losses per
peptide.
- getMaxNPeptides() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the maximal number of peptides among the proteins of the dataset.
- getMaxNPsms() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the the maximal number of PSMs among the proteins of the dataset.
- getMaxNSpectra() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the maximum number of spectra accounted by a single peptide Match
all found in a protein match.
- getMaxNumberOfModifications() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns the maximal number of modifications.
- getMaxPadding() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the max padding (distance between the axes and the border of the
panel).
- getMaxPeakCount() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns the maximum peak count in this file.
- getMaxPeakCount() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the maximum peak count.
- getMaxPeakCount() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns the max peak count.
- getMaxPepLength() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Returns the maximal peptide length allowed.
- getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the maximal peptide length allowed.
- getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the maximum peptide length.
- getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns the maximum peptide length.
- getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Returns the maximal peptide length allowed.
- getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns the maximal peptide length allowed.
- getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the maximal peptide length allowed.
- getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the maximal peptide length allowed.
- getMaxPeptideLengthNoEnzyme() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns the maximal peptide length to use when searching with no enzyme.
- getMaxPeptideMass() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns the maximal peptide mass.
- getMaxPeptidePrecursorErrorDa() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Return the max peptide precursor mass error in Dalton.
- getMaxPeptidePrecursorErrorPpm() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the max peptide precursor mass error in ppm.
- getMaxPrecInt(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getMaxPrecInt() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getMaxPrecInt(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getMaxPrecInt() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getMaxPrecInt(String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the maximum precursor intensity in a given file.
- getMaxPrecInt() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the maximum precursor intensity among all files.
- getMaxPrecMz(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getMaxPrecMz() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getMaxPrecMz(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getMaxPrecMz() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getMaxPrecMz(String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the maximum precursor m/z in a given file.
- getMaxPrecMz() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the maximum precursor m/z among all files.
- getMaxPrecRT(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getMaxPrecRT() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getMaxPrecRT(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getMaxPrecRT() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getMaxPrecRT(String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the maximum precursor RT in a given file.
- getMaxPrecRT() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the maximum precursor RT among all files.
- getMaxPrecursorAdjustment() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the maximum precursor adjustment.
- getMaxPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the maximum precursor mass.
- getMaxPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns the maxPrecursorMass precursor mass.
- getMaxPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the maxPrecursorMass precursor mass.
- getMaxPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- getMaxPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- getMaxPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- getMaxPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- getMaxPrimaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
-
Returns the max primary progress counter.
- getMaxProteinAccessionLength() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the max protein accession length.
- getMaxProteinAveragePrecursorIntensity() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the maximum protein average precursor intensity.
- getMaxProteinSummedPrecursorIntensity() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the maximum summed protein precursor intensity.
- getMaxPtmsPerTagPeptide() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Returns the maximum number of PTMs to consider when mapping tags to
protein sequences.
- getMaxRank() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns the maximum rank.
- getMaxRT() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns the maximal RT in this file.
- getMaxSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- getMaxSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- getMaxSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- getMaxSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- getMaxSecondaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
-
Returns the max secondary progress counter.
- getMaxSpectrumChargeRange() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the maximum charge added when the charge is missing for a given
spectrum.
- getMaxSpectrumCount() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Returns the maximal amount of PSMs for the peptides in the current
peptide list.
- getMaxSpectrumCounting() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the maximal spectrum counting value of the proteins of the
dataset.
- getMaxSpectrumMz() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the max spectrum m/z to search for.
- getMaxTagCount() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the maximum number of tags per spectrum to be generated.
- getMaxTagPrecursorErrorDa() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Return the max tag precursor mass error in Dalton.
- getMaxTagPrecursorErrorPpm() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the max tag precursor mass error in ppm.
- getMaxValidatedPeptidesPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the maximum validated peptides at the fraction level.
- getMaxValidatedSpectraPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the maximum validated spectra at the fraction level.
- getMaxValueForProbability(double) - Method in interface com.compomics.util.math.statistics.Distribution
-
The value after which the density function will be smaller than p.
- getMaxValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
-
- getMaxValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
- getMaxValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- getMaxVariableModifications() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns the maximum number of variable modifications per peptide.
- getMaxVariableModificationsPerPeptide() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the maximum number of variable modifications allowed on a single
peptide.
- getMaxVariableModificationsPerTypePerPeptide() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the maximum number of variable modifications of each modification
type allowed on a single peptide.
- getMaxVariableMods() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the maximum number of variable modifications per peptide.
- getMaxXAxisValue() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This method reports on the largest x-axis value in the point collection
across all datasets.
- getMaxXsInSequence() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
-
Returns the maximal number of Xs to account for in a sequence.
- getMDScore(ArrayList<SpectrumIdentificationAssumption>, Peptide, ArrayList<String>, SequenceMatchingParameters, Integer) - Static method in class com.compomics.util.experiment.identification.modification.scores.MDScore
-
Returns the MD score for the given peptide in a spectrum match.
- getMean() - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
Returns the mean of the distribution.
- getMedianValue(HashMap<Double, Integer>) - Static method in class com.compomics.util.math.HistogramUtils
-
Returns the median of a histogram.
- getMedianValue(HashMap<Double, Integer>, int) - Static method in class com.compomics.util.math.HistogramUtils
-
Returns the median of a histogram.
- getMeek() - Method in class com.compomics.util.protein.AASequenceImpl
-
This method will return an estimated 'net' HPLC retention
time for the sequence based on the table by Meek.
It does NOT take a t0 value, specific to a setup, into account.
- getMemoryParameter() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the upper memory limit in MB.
- getMemoryShare() - Method in class com.compomics.util.db.object.ObjectsCache
-
Returns the share of heap size which can be used before emptying the
cache.
- getMendianA() - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
-
Returns the rounded median of the as found in the previously interpolated
scores.
- getMendianB() - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
-
Returns the rounded median of the bs found in the previously interpolated
scores.
- getMessage() - Method in exception com.compomics.util.db.GeneratorException
-
This method returns a String with the description for this exception.
- getMessage() - Method in class com.compomics.util.messages.FeedBack
-
Returns the message.
- getMessages() - Method in class com.compomics.util.io.StreamGobbler
-
Returns the messages.
- getMethod() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the method.
- getMethodId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the method ID.
- getMethods() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
-
Returns the methods implemented in the factory.
- getMethodsNames() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
-
Returns the name of the methods present in the factory.
- getMethodsNamesAsArray() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
-
Returns the methods names as array.
- getMethodUsed() - Method in class com.compomics.util.experiment.quantification.Quantification
-
getter for the method used
- getMetrics() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the metrics.
- getMetricsPrefix() - Method in class com.compomics.util.experiment.units.UnitOfMeasurement
-
Returns the metrics prefix.
- getMgfFileName(String) - Static method in class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
-
Returns the name of the mgf file corresponding to the given Andromeda
file name.
- getMgfFileName(String) - Static method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
-
Returns the spectrum file name.This method assumes that the PepNovo
output file is the mgf file name + ".out"
- getMgfFileName(String) - Static method in class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
-
Returns the spectrum file name.This method assumes that the pNovo output
file is the mgf file name + ".pnovo.txt"
- getMgfFileName(String) - Static method in class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
-
Returns the spectrum file name.
- getMgfIndex(File) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.IndexedMgfReader
-
Returns the index of all spectra in the given mgf file.
- getMgfIndex(File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.IndexedMgfReader
-
Returns the index of all spectra in the given MGF file.
- getMgfMaxSize() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the max mgf file size before splitting.
- getMgfNSpectra() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Get the max number of spectra in an mgf file.
- getMH() - Method in class com.compomics.util.experiment.refinement_parameters.PepnovoAssumptionDetails
-
Returns the PepNovo mH.
- getMinAllowedIntensityRatioToBasePeak() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the minimum allowed intensity ratio to base peak.
- getMinAminoAcidScore() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Returns the minimum amino acid score.
- getMinAnnotatedPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the minimal number of annotated peaks a peptide should have.
- getMinChargeSearched() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the minimal charge searched.
- getMinCtermMass() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
-
Returns the minimal mass to consider for a c-terminus.
- getMinFragmentMz() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns the minimal fragment m/z.
- getMinimalChargeForMultipleChargedFragments() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the minimal precursor charge to account for multiply charged
fragments in OMSSA.
- getMinimalLocalizationConfidence() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns the minimal confidence among the PTM sites of this scoring.
- getMinimumValue() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
-
Returns the current minimum value for the progressbar.
- getMinIndex() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns the minimal index where amino acids are found.
- getMinIsotopes() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Returns the minimal number of isotopes allowed (inclusive).
- getMinIsotopicCorrection() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the minimal isotopic correction.
- getMinMass(char[]) - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
Returns the minimal mass that an amino acid sequence can have taking into
account ambiguous amino acids.
- getMinMass() - Method in class com.compomics.util.gui.events.RescalingEvent
-
Returns the minimum mass.
- getMinMissedCleavages() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Returns the minimum number of missed cleavages.
- getMinMz() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
-
Returns the minimal m/z encountered among the precursors.
- getMinMz() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
-
Returns the min mz value.
- getMinPeakIntensity() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the minimum peak intensity.
- getMinPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the minimum number of peaks.
- getMinPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the minimal number of peaks a spectrum should contain.
- getMinPeaksPerSpectrum() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns the minimal number of peaks per spectrum.
- getMinPepLength() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Returns the maximal peptide length allowed.
- getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Sets the minimal peptide length allowed.
- getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the minimum peptide length.
- getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns the minimum peptide length.
- getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Sets the minimal peptide length allowed.
- getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Sets the minimal peptide length allowed.
- getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the minimal peptide length allowed.
- getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Sets the minimal peptide length allowed.
- getMinPeptideLengthNoEnzyme() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns the minimal peptide length to use when searching with no enzyme.
- getMinPrecMz(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getMinPrecMz() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getMinPrecMz(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getMinPrecMz() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getMinPrecMz(String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the minimum precursor m/z in a given file.
- getMinPrecMz() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the minimum precursor m/z among all files.
- getMinPrecPerSpectrum() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the minimal number of precursors per spectrum.
- getMinPrecursorAdjustment() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the minimum precursor adjustment.
- getMinPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the minimum precursor mass.
- getMinPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns the minimum precursor mass.
- getMinPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the minimum precursor mass.
- getMinPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns the minimal precursor mass.
- getMinRT() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns the minimum RT in this file.
- getMinSpectrumChargeRange() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the minimum charge added when the charge is missing for a given
spectrum.
- getMinSpectrumMz() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Return the min spectrum m/z to search for.
- getMinSpectrumPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the min number of peaks in a spectrum.
- getMinTagLength() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Returns the minimum tag length.
- getMinTerminiCleavages() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns the minimum number of termini cleavages.
- getMinus1() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Returns the isotopic correction factor at -1 Da.
- getMinus2() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Returns the isotopic correction factor at -2 Da.
- getMinValueForProbability(double) - Method in interface com.compomics.util.math.statistics.Distribution
-
The value before which the density function will be smaller than p.
- getMinValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
-
- getMinValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
- getMinValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- getMinVariantDepth() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the min variant depth.
- getMinXAxisValue() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This method reports on the smallest x-axis value in the point collection
across all datasets.
- getMiscleavages() - Method in class com.compomics.util.protein.Enzyme
-
Simple getter for the number of allowed missed cleavages for the Enzyme.
- getMissedCleavages() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Returns the number of missed cleavages.
- getModel() - Method in class com.compomics.util.sun.TableMap
-
- getModification(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
- getModification(String) - Method in interface com.compomics.util.experiment.biology.modifications.ModificationProvider
-
Returns the modification with the given name name.
- getModification() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Getter for the theoretic PTM name.
- getModification(String) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
-
Returns the back-ed up modification with the given name.
- getModification(String, int) - Static method in class com.compomics.util.protein.ModificationFactory
-
This method will return a Modification instance from a title.
- getModification(String, String, int) - Static method in class com.compomics.util.protein.ModificationFactory
-
This method takes a code and a residue (the residue for the N-terminus is NTERMINUS and for the
C-terminus CTERMINUS!) and converts this into a Modification instance if possible.
- getModificationLocalizationParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the modification localization scoring parameters.
- getModificationMass(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
-
Returns the mass corresponding to a given modification.
- getModificationName(double, Peptide, int) - Method in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
-
Returns the name of the modification corresponding to he given
modification mass at the given site on the given peptide.
- getModificationName(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns the name of the modification indexed by the given index.
- getModificationName(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the name of the modification indexed by the given index.
- getModificationParameters() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the modification settings.
- getModificationPattern(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
-
Returns the modification pattern that is targeted by the given
modification.
- getModificationPlotData(Peptide, Modification, int, String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
-
Returns the modification plot series in the JFreechart format for one
PSM.
- getModificationProfile() - Method in class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
-
Returns the modification profile corresponding to the input by the user.
- getModifications() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns the names of all imported Modifications.
- getModifications(ModificationCategory...) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns the names of all modifications in the given categories.
- getModifications() - Method in class com.compomics.util.protein.AASequenceImpl
-
Simple getter for the modifications.
- getModificationsAtRepresentativeSite(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
-
Returns the modifications which have a representative ambiguous site at
the given site.
- getModificationScoring(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
-
Returns the modification scoring for the desired modification (null if
none found).
- getModificationsForPsiAccession(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns an array list of the utilities modification names mapping to the
given PSI-MOD accession number.
- getModificationTableContent(PeptideAssumption, Modification, int, String, String, Spectrum, AnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
-
Get the table content.
- getModificationToAdd() - Method in class com.compomics.cli.modifications.ModificationsCLIInputBean
-
Returns the modification to add.
- getModificationToRemove() - Method in class com.compomics.cli.modifications.ModificationsCLIInputBean
-
Returns the name of the modification to remove.
- getModificationType() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns the modification type.
- getModifiedAaIndex(int, int) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns the index of a modification on the amino acid sequence.
- getModifiedSequence(IdentificationMatch, String) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the match sequence annotated with modifications.
- getModifiedSequence() - Method in class com.compomics.util.protein.AASequenceImpl
-
This method will return the sequence with annotated modifications.
- getModPeptidesAreDifferent() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns true if modified peptides are considered different.
- getMolecularFormula() - Method in class com.compomics.util.protein.AASequenceImpl
-
This method calculates the molecular formula based on the sequence
- getMonoisotopicAtomChain() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the monoisotopic atom chain representing this amino acid.
- getMonoisotopicMass() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the mass of the amino acid.
- getMonoisotopicMass() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
-
- getMonoisotopicMass() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
-
- getMonoisotopicMass() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
-
- getMonoisotopicMass() - Method in class com.compomics.util.experiment.biology.atoms.Atom
-
Returns the monoisotopic mass.
- getMonoisotopicMassDelta(String) - Method in interface com.compomics.util.interfaces.Modification
-
This method returns a double with the monoisotopic mass difference
conferred on the sequence by this modification for the specified residue.
- getMonoisotopicMassDelta(String) - Method in class com.compomics.util.protein.ModificationImplementation
-
This method returns a double with the monoisotopic mass difference
conferred on the sequence by this modification for the specified residue.
- getMonoisotopicMassDelta(String) - Method in class com.compomics.util.protein.ModificationTemplate
-
This method returns a double with the monoisotopic mass difference
conferred on the sequence by this modification for the specified residue.
- getMonoisotopicPrecursor() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true if the precursor mass is monoisotopic, false if average.
- getMsConvertParameters() - Method in class com.compomics.util.gui.parameters.proteowizard.MsConvertParametersDialog
-
Returns the parameters as created by the user.
- getMsFileIterator(File, WaitingHandler) - Static method in interface com.compomics.util.experiment.io.mass_spectrometry.MsFileIterator
-
Returns the file reader for the given mass spectrometry file based on its
extension.
- getMsFormat() - Method in class com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters
-
Returns the format to convert to.
- getMyriMatchFormat() - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
-
Get the MyriMatch enzyme format.
- getMZ() - Method in interface com.compomics.util.gui.interfaces.SpectrumAnnotation
-
This method returns the M/Z of the feature to annotate.
- getMZ() - Method in class com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation
-
This method returns the M/Z of the feature to annotate.
- getMz(int) - Method in class com.compomics.util.protein.AASequenceImpl
-
This method calculates the mass over charge ratio for a given charge
for the current sequence.
- getMzBinOffset() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the m/z bin offset.
- getMzBinWidth() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the m/z bin width.
- getMzErrorType(int) - Static method in enum com.compomics.util.experiment.identification.matches.IonMatch.MzErrorType
-
Returns the error type corresponding to the given index.
- getMzFidelityScoreWeight() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the mzFidelity score weight.
- getMzIdentMLVersion(int) - Static method in enum com.compomics.util.experiment.io.identification.MzIdentMLVersion
-
Returns the mzIdentML format corresponding to the given index.
- getMzidOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true if the mzid output is to be created.
- getMZPrideCvTerm() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the pride CV term for the ion match m/z.
- getMzValues() - Method in class com.compomics.util.io.PklFile
-
- getnAaDeletions() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Returns the number of amino acid deletions allowed.
- getnAaInsertions() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Returns the number of amino acid insertions allowed.
- getnAaSubstitutions() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Returns the number of amino acid substitutions allowed.
- getnAaSwap() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Returns the number of amino acid swaps allowed.
- getName() - Method in class com.compomics.util.db.object.ObjectsDB
-
Returns the database name.
- getName() - Method in enum com.compomics.util.enumeration.CompomicsTools
-
Getter for the name of the tool or library.
- getName() - Method in class com.compomics.util.experiment.biology.atoms.Atom
-
Returns the name of the atom.
- getName() - Method in class com.compomics.util.experiment.biology.atoms.ElementaryElement
-
Returns the name of the element.
- getName() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
-
Get the enzyme name.
- getName() - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
-
- getName() - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
-
- getName() - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
- getName() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
- getName() - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
-
- getName() - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
-
- getName() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
This method returns the name of the reporter ion.
- getName() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
- getName() - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the name of the ion.
- getName() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Getter for the modification name.
- getName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
-
Returns the name corresponding to the given NCBI taxon.
- getName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns the name of the species corresponding to the given taxon
according to the UniProt mapping.
- getName() - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
-
Returns the name of this substitution matrix.
- getName() - Method in interface com.compomics.util.experiment.filtering.Filter
-
Returns the name of the filter.
- getName() - Method in interface com.compomics.util.experiment.filtering.FilterItem
-
Returns the name of the item.
- getName() - Method in class com.compomics.util.experiment.identification.Advocate
-
Returns the name of the advocate.
- getName() - Method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
-
- getName() - Method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
-
- getName() - Method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
-
- getName() - Method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
-
- getName() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
- getName() - Method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
-
Returns the name of the score.
- getName() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns the name of the inspected protein.
- getName() - Method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
-
Returns the name of this possibility.
- getName() - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
-
Returns the name of the database.
- getName() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Returns the name of the reagent.
- getName() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
-
Returns the name of the method.
- getName() - Method in class com.compomics.util.io.export.ExportScheme
-
Returns the name of the scheme.
- getName() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the name of the parameters.
- getName() - Method in class com.compomics.util.pride.CvTerm
-
Returns the name.
- getName() - Method in class com.compomics.util.pride.prideobjects.Contact
-
Returns the contact name.
- getName() - Method in class com.compomics.util.pride.prideobjects.ContactGroup
-
Returns the contact group name.
- getName() - Method in class com.compomics.util.pride.prideobjects.Instrument
-
Returns the instrument name.
- getName() - Method in class com.compomics.util.pride.prideobjects.Protocol
-
Returns the protocol name.
- getName() - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
-
Returns the references group name.
- getName() - Method in class com.compomics.util.pride.prideobjects.Sample
-
Returns the name of the sample.
- getNameForGoTerm(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Returns the name of a GO term.
- getNameWithGapAndNumber() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
Returns the name with number and mass gap.
- getNameWithNumber() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
Returns the name with number.
- getNameWithNumber() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
Returns the name with number.
- getnAnnotatedMostIntensePeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the minimal number of annotated most intense peaks.
- getNCleavageSites(String, ArrayList<Enzyme>) - Static method in class com.compomics.util.experiment.identification.utils.ProteinUtils
-
Returns the number of cleavage sites.
- getnClusters() - Method in class com.compomics.util.math.clustering.settings.KMeansClusteringSettings
-
Returns the number of clusters to use.
- getNColumns() - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getNConfidentPeptides(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the number of confident peptides for a given protein match.
- getNConfidentProteins() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the number of confident proteins.
- getnConfidentProteins() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the number of confident proteins.
- getNConfidentSpectra(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the number of confident spectra for a given protein match.
- getNConfidentSpectraForPeptide(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the number of confident spectra for a given peptide match.
- getNEnzymaticTermini(Peptide, String) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the maximal number of termini for the given peptide on the given
protein.
- getNEnzymaticTermini(int, int, String, Enzyme) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns the number of enzymatic termini for the given peptide coordinates
and enzyme on this protein.
- getNestedException() - Method in exception com.compomics.util.db.GeneratorException
-
This method returns the nested exception for this exception, or
'null' if none is present.
- getNeutralLoss(String) - Static method in class com.compomics.util.experiment.biology.ions.NeutralLoss
-
Returns the neutral loss associated to the given name in the static map
of the class.
- getNeutralLossCombination() - Method in class com.compomics.util.experiment.biology.ions.NeutralLossCombination
-
Returns the neutral losses in this combination.
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the possible neutral losses of this ion type.
- getNeutralLosses(ModificationParameters) - Static method in class com.compomics.util.experiment.biology.ions.IonFactory
-
Returns a list containing the default neutral losses and the losses found
in the given modifications.
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns the neutral losses possibly encountered with this modification.
- getNeutralLosses() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns the considered neutral losses.
- getNeutralLossesAsString() - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the neutral loss (if any), the empty string if no loss.
- getNeutralLossesAsString(NeutralLoss[]) - Static method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the neutral loss (if any), the empty string if no loss.
- getNeutralLossesCombinations(HashSet<String>) - Method in class com.compomics.util.experiment.biology.ions.IonFactory
-
Returns the possible neutral losses combinations as array of arrays of
neutral losses.
- getNeutralLossesMap() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Returns the map of neutral losses to annotate.
- getNeutronMassMultiple(int) - Static method in class com.compomics.util.experiment.biology.atoms.ElementaryElement
-
Returns the mass of the neutron multiplied by i.
- getNeutronThreshold() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the mass after which exact neutron mass should be considered in
the calculation.
- getNew() - Method in class com.compomics.util.experiment.identification.filtering.AssumptionFilter
-
- getNew() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Returns a new empty filter.
- getNew() - Method in class com.compomics.util.experiment.identification.filtering.PeptideFilter
-
- getNew() - Method in class com.compomics.util.experiment.identification.filtering.ProteinFilter
-
- getNew() - Method in class com.compomics.util.experiment.identification.filtering.PsmFilter
-
- getNextFeature() - Method in class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerResultReader
-
Get the next feature in the XML string.
- getNextHeader(WaitingHandler) - Method in class com.compomics.util.experiment.io.biology.protein.iterators.HeaderIterator
-
Returns the next header.Null if none.
- getNextPeptide() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.NoDigestionCombinationIterator
-
- getNextPeptide() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.NoDigestionIterator
-
- getNextPeptide() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeCombinationIterator
-
- getNextPeptide() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeIterator
-
- getNextPeptide() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.UnspecificCombinationIterator
-
- getNextPeptide() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.UnspecificIterator
-
- getNextPeptide() - Method in interface com.compomics.util.experiment.identification.protein_sequences.digestion.SequenceIterator
-
Returns the next peptide that can be generated from the iterator.
- getNextProtein() - Method in class com.compomics.util.experiment.io.biology.protein.iterators.FastaIterator
-
- getNextProtein() - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinIterator
-
Returns the next protein.
- getNextSequence() - Method in class com.compomics.util.experiment.identification.protein_sequences.AmbiguousSequenceIterator
-
Returns the next sequence, null if none.
- getnFeatures() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
-
Returns the number of features in the map.
- getNLines() - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getNmissedCleavages(String) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
-
Returns the number of missed cleavages in an amino acid sequence.
- getNMissedCleavages(Enzyme) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the number of missed cleavages using the specified enzyme.
- getNMissedCleavages(DigestionParameters) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the number of missed cleavages using the digestion preferences.
- getnMissedCleavages(String) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
-
Returns the number of allowed missed cleavages for the given enzyme.
- getNoModPeptide(HashSet<String>) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns a version of the peptide which does not contain the given list of
modifications.
- getNonDiagonalScore() - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
Returns a score based on the non-diagonal values.
- getNonEnzymatic(long, DigestionParameters) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns a list of non-enzymatic peptides for a given protein match.
- getNoOneHitWonders() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns true if one hit wonders are excluded.
- getNoProlineRuleSeries() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the id numbers of ion series to apply no product ions at proline
rule at.
- getNormalDistribution(ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
Returns the normal distribution corresponding to a given list of double
calibrated on mean and standard deviation.
- getNormalIcon() - Method in class com.compomics.util.gui.VennDiagramDialog
-
- getNormalIcon() - Method in class com.compomics.util.gui.XYPlottingDialog
-
- getNormalizationFactors() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
Returns the normalization factors.
- getNormalize() - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
-
Indicates whether the spectrum counting index should be normalized.
- getNormalizedSpectrumCounting(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the spectrum counting metric of the protein match of interest
using the preference settings normalized to the injected protein amount
using the spectrum counting preferences of the identification features
generator.
- getNormalizedSpectrumCounting(long, SpectrumCountingParameters, Metrics) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the spectrum counting metric of the protein match of interest
using the preference settings normalized to the injected protein amount
using the given spectrum counting preferences.
- getNormalizedSpectrumCounting(long, UnitOfMeasurement, SpectrumCountingMethod) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the spectrum counting metric of the protein match of interest
using the preference settings normalized to the injected protein amount.
- getNormalizedSpectrumCounting(long, Metrics, UnitOfMeasurement, Double, SpectrumCountingMethod) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the spectrum counting metric of the protein match of interest
using the preference settings normalized to the injected protein amount.
- getNormalizePeaksAcrossAllWindows() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the normalize peaks across all windows.
- getNote() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the note.
- getNotSelectedRowHtmlTagFontColor() - Static method in class com.compomics.util.gui.TableProperties
-
Returns the color to use for the HTML tags for the rows that are not
selected, in HTML color code.
- getNoVariantPreferences() - Static method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Returns the preferences corresponding to no variants allowed.
- getNovorPtmMap() - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
-
Returns the Novor to utilities PTM map.
- getNPeaks() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
-
Returns the number of peaks.
- getnPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns the number of most intense peaks to consider.
- getNPeaksAboveThreshold(Spectrum, int, int, double) - Static method in class com.compomics.util.experiment.mass_spectrometry.spectra.SpectrumUtil
-
Returns the number of peaks between the start index (inclusive) and the end index (exclusive) above the intensity threshold (inclusive).
- getnPeaksInDoubleChargeWindow() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the number of peaks in doubly charged windows.
- getnPeaksInSingleChargeWindow() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the number of peaks in singly charged windows.
- getnProcessingNode() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
Returns the number of processing nodes used.
- getNProperties() - Static method in enum com.compomics.util.experiment.biology.aminoacids.AminoAcid.Property
-
Returns the number of implemented properties.
- getNProteins() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Returns the number of proteins for this match.
- getNSpectra(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Estimates the number of spectra for the given protein match.
- getNSpectra() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns the number of imported spectra.
- getNTargetedAA(int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns the number of targeted amino acids at the given index.
- getNtermAsString(boolean, String[]...) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns the N-terminal annotation as string.
- getNTerminal(boolean, ModificationParameters, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Returns the N-terminal tag of this tag as a string for sequence display.
- getNTerminalGap() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Returns the N-terminal gap of the tag.
- getnTermModification() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Returns the N-term modification.
- getNtermModification(boolean, char, String) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
-
Returns the N-term modification for the given amino acid.
- getNTermTruncatedProtein(int) - Method in class com.compomics.util.protein.Protein
-
This method truncates the sequence for this protein on the N-terminus
to the requested size.
- getNTermTruncatedSequence(int) - Method in class com.compomics.util.protein.AASequenceImpl
-
This method will return an AASequenceImpl that represents
an N-terminal truncation of the current sequence.
- getnThreads() - Method in class com.compomics.util.parameters.tools.ProcessingParameters
-
Returns the number or threads to use.
- getNumber(Class) - Method in class com.compomics.util.db.object.ObjectsDB
-
Returns the number of instances of a given class stored in the db.
- getNumber() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
Returns the number of the fragment in the sequence.
- getNumber() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
Returns the number of the fragment in the tag.
- getNumber(Class) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the number of objects of a given class
- getNumberOfBatches() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Set the number of batches per node to strive for when using the MPI-based
parallelization features.
- getNumberOfCandidates() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns the number of candidates.
- getNumberOfClusters() - Method in class com.compomics.util.math.clustering.KMeansClustering
-
Returns the number of clusters.
- getNumberOfDataPointsInPlot() - Method in class com.compomics.util.gui.spectrum.MassErrorBubblePlot
-
Returns the current number of data points in the mass error plot.
- getNumberOfDataPointsInPlot() - Method in class com.compomics.util.gui.spectrum.MassErrorPlot
-
Returns the current number of data points in the mass error plot.
- getNumberOfModificationsPerPeptide() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Returns the maximum number of modifications per peptide.
- getNumberOfPeaksToKeepPerWindow() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Return the number of peaks to keep per window.
- getNumberOfPeptides() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Returns the number of peptides to report per spectrum.
- getNumberOfSpectrumMatches() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the maximum number of spectrum matches.
- getNumberOfSpectrumMatches() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Returns the maximum number of spectrum matches.
- getNumberOfSpectrumMatches() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns the maximum number of spectrum matches.
- getNumberOfSpectrumMatches() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the number of PSMs to report per spectrum.
- getNumberOfTasks() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Returns the number of tasks, null if not set.
- getNumberOfWindows() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the number of windows.
- getNumberTolerableTermini() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Returns the number of tolerable termini.
- getNumChargeStates() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the number of charge states.
- getNumericParameter(String) - Method in class com.compomics.util.experiment.ProjectParameters
-
- getNumIntensityClasses() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the number of intensity classes.
- getNumIntensityClasses() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns the number of intensity classes.
- getNUnique() - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the number of amino acids excluding combinations.
- getNUniquePeptides(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the number of unique peptides for this protein match.
- getNUniqueValidatedPeptides(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the number of unique validated peptides for this protein match.
- getNValidatedPeptides(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the number of validated peptides for a given protein match.
- getNValidatedProteinGroups(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Indicates whether a peptide is found in a single protein match.
- getNValidatedProteinGroups(long, WaitingHandler) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Indicates whether a peptide is found in a single protein match.
- getNValidatedProteins() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the number of validated proteins.
- getnValidatedProteins() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the number of validated proteins.
- getnValidatedPsms() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Returns the number of validated PSMs for the currently selected peptide.
- getNValidatedPsms() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the number of validated PSMs for the last selected peptide /!\
This value is only available after getSortedPsmKeys has been called.
- getNValidatedSpectra(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the number of validated spectra for a given protein match.
- getNValidatedSpectraForPeptide(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the number of validated spectra for a given peptide match.
- getNVariableModifications(double) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the number of variable modifications found with the given mass.
- getNVariableModifications() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the number of modifications carried by this peptide.
- getnVariants() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Returns the total number of variants allowed.
- getnX() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Returns the number of Xs already considered in this draft.
- getObject(long) - Method in class com.compomics.util.db.object.ObjectsCache
-
Returns the objects if present in the cache.
- getObject(IdentificationFeaturesCache.ObjectType, long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Returns an object if present in the cache.
- getObject() - Method in class com.compomics.util.general.BoxedObject
-
Returns the boxed object.
- getObjectsCache() - Method in class com.compomics.util.db.object.ObjectsDB
-
Returns the cache used by this database.
- getObjectsDB() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the objects database used in this class.
- getObservableAminoAcids(String, ArrayList<Enzyme>, double) - Static method in class com.compomics.util.experiment.identification.utils.ProteinUtils
-
Returns the observable amino acids in the sequence when using the given
enzymes with the given maximal peptide length.
- getObservableCoverage(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the best protein coverage possible according to the given
cleavage settings.
- getObservableLength(String, ArrayList<Enzyme>, double) - Static method in class com.compomics.util.experiment.identification.utils.ProteinUtils
-
Returns the number of observable amino acids in the sequence.
- getObservedFractionalMassesAll() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the observed molecular masses in kDa for each fraction.
- getOccurrence(Atom, Integer) - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
-
Returns the occurrence of a given atom in the chain.
- getOccurrence() - Method in class com.compomics.util.general.IsotopicElement
-
Getter for the occurrence of this element
- getOccurrence() - Method in class com.compomics.util.gui.atoms.AtomPanel
-
Returns the occurrence of the selected atom.
- getOccurrence(String, char) - Static method in class com.compomics.util.Util
-
Returns the occurrence of a character in a string.
- getOlsAccessionLink(String) - Method in class com.compomics.util.gui.enzymes.EnzymesDialog
-
Returns a web link to the given PSI-MS CV term at
https://www.ebi.ac.uk/ols/ontologies/ms.
- getOlsAccessionLink(String) - Method in class com.compomics.util.gui.modification.ModificationsDialog
-
Returns a web link to the given PSI-MOD CV term at
https://www.ebi.ac.uk/ols/ontologies/mod.
- getOMSSAIndexes(File) - Static method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Imports the OMSSA indexes from an XML file.
- getOmssaOutputTypes() - Static method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the output types available.
- getOneOverCombinationDouble(int, int) - Static method in class com.compomics.util.math.BasicMathFunctions
-
Returns the invert of the number of k-combinations in a set of n
elements.
- getOntology() - Method in class com.compomics.util.pride.CvTerm
-
Returns the ontology.
- getOperatingSystem() - Static method in class com.compomics.util.io.file.FileSystemAccessor
-
Get the operating system.
- getOptionIDs() - Static method in enum com.compomics.cli.paths.PathSettingsCLIParams
-
Returns the list of supported command line options.
- getOptionParameter(String) - Method in class com.compomics.util.general.CommandLineParser
-
This method will report the option parameter for an option that can take
a parameter itself.
- getOptions() - Method in class com.compomics.util.general.CommandLineParser
-
This method will report on all options that have been found, or return an
empty String[] if none were present.
- getOptionsAsString() - Static method in enum com.compomics.cli.enzymes.EnzymesCLIParams
-
Returns the options as a string.
- getOptionsAsString() - Static method in enum com.compomics.cli.fasta.FastaParametersCLIParams
-
Returns the options as a string.
- getOptionsAsString() - Method in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
-
Returns the options left to the user as a string.
- getOptionsAsString() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersCLI
-
- getOptionsAsString() - Static method in enum com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
-
Returns the options as a string.
- getOptionsAsString() - Static method in enum com.compomics.cli.modifications.ModificationsCLIParams
-
Returns the options as a string.
- getOptionsAsString() - Static method in enum com.compomics.cli.paths.PathSettingsCLIParams
-
Returns the options as a string.
- getOrderedDSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns an ordered list of sites where the D-score was used.
- getOrderedFileNamesWithoutExtensions() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getOrderedFileNamesWithoutExtensions() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getOrderedFileNamesWithoutExtensions() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the spectrum file names without file extensions.
- getOrderedProbabilisticSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns an ordered list of sites where the probabilistic score was used.
- getOrderedPtmLocations() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns sites of all localized PTMs ordered increasingly.
- getOrganismIdentifier(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getOrganismIdentifier() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the organism identifier.
- getOrganismIdentifier(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
-
Returns the organism identifier for the given protein.
- getOrientation() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the orientation.
- getOriginalAminoAcid() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Substitution
-
- getOriginalAminoAcids(Character) - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
-
Returns the possible original amino acids for the given substituted amino
acid as a list of their single letter code.
- getOriginalAminoAcids() - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
-
Returns the amino acids where a substitution has been registered.
- getOutputFolder() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the last used output folder.
- getOutputFolderName() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the name of the output folder.
- getOutputFormat() - Method in class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserParameters
-
Returns the format to convert to.
- getOutputFormat() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns the output format.
- getOutputFormat() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns the output format.
- getOutputOptions() - Static method in enum com.compomics.util.parameters.searchgui.OutputParameters
-
Returns an array of the indexes of the different output options.
- getOutputParameters(int) - Static method in enum com.compomics.util.parameters.searchgui.OutputParameters
-
Returns the output option of the given index.
- getOutputParametersNames() - Static method in enum com.compomics.util.parameters.searchgui.OutputParameters
-
Returns an array of the names of the different options.
- getOutputResults() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns the output results filter.
- getOutputSuffix() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the output tags suffix.
- getP(char) - Method in class com.compomics.util.experiment.identification.protein_sequences.AaOccurrence
-
Returns the log10 of the share of the given amino acid in the database.
- getP(char[], int, int, double) - Method in class com.compomics.util.experiment.identification.protein_sequences.AaOccurrence
-
Returns the sum of the log10 of the share of the given amino acids in the
database.
- getPackageName() - Method in enum com.compomics.util.enumeration.CompomicsTools
-
Return the package name of the tool.
- getPanelIndex() - Method in class com.compomics.util.gui.atoms.AtomPanel
-
Returns the panel index.
- getParameterKey() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
-
- getParameterKey() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
- getParameterKey() - Method in interface com.compomics.util.experiment.personalization.UrParameter
-
This method returns the key of the parameter.
- getParameterKey() - Method in class com.compomics.util.experiment.refinement_parameters.PepnovoAssumptionDetails
-
- getParameters() - Method in class com.compomics.util.general.CommandLineParser
-
This method will report on all parameters that have been found, or return
an empty String[] if none were present.
- getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.AndromedaParametersDialog
-
- getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.CometParametersDialog
-
- getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.DirecTagParametersDialog
-
- getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MetaMorpheusParametersDialog
-
- getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsAmandaParametersDialog
-
- getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsgfParametersDialog
-
- getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MyriMatchParametersDialog
-
- getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.NovorParametersDialog
-
- getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.OmssaParametersDialog
-
- getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.PepNovoParametersDialog
-
- getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.PNovoParametersDialog
-
- getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.TideParametersDialog
-
- getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
-
- getParameters() - Method in interface com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog
-
Returns the parameters as set by the user.
- getParametersList() - Method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
-
Returns an ordered list of the names of the implemented parameters.
- getParametersOptionsAsString() - Static method in enum com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
-
Returns the options as a string.
- getParentFolder() - Static method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
-
Returns the parent folder.
- getParentFolder() - Static method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFolder
-
Returns the parent folder where to write cms files.
- getParentMonoisotopicMassIsotopeError() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns true if the parent ion mass tolerance is expanded by opening up
multiple tolerance windows centered on the first and second 13C isotope
peaks for a peptide.
- getPath(String) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
-
Returns the path at the given line.
- getPath() - Method in class com.compomics.util.db.object.ObjectsDB
-
Returns the path to the database.
- getPathID(String) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
-
Returns the path id line.
- getPathOfClass(String) - Static method in class com.compomics.util.io.file.FileSystemAccessor
-
Returns the absolute path of the underlying file system of the given
class.
- getPathParameter(UtilitiesPathParameters.UtilitiesPathKey) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
-
Returns the path according to the given key and path.
- getPatientInformation(PatientInformation) - Method in class com.compomics.util.experiment.patient.Patient
-
Returns patient information,
- getPattern() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns the amino acid pattern targeted by this modification.
- getPattern() - Method in class com.compomics.util.gui.AminoAcidPatternDialog
-
Returns the pattern as edited by the user.
- getPdbAccession() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
-
Returns the PDB accession.
- getPdbAccession() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
-
Returns the PDB accession.
- getPdbaccession() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
Returns the PDB accessions.
- getPdbEnd() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
-
Returns the PDB end.
- getPdbGroup() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
-
Returns the PDB groups.
- getPdbs() - Method in class com.compomics.util.pdbfinder.FindPdbForUniprotAccessions
-
Returns a vector of the PDB files mapped to the given protein accession
number.
- getPdbStart() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
-
Returns the PDB start.
- getPeakAnnotation() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the annotation to use for the ion match as a String.
- getPeakAnnotation(Ion, int) - Static method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the annotation to use for a given ion and charge as a String.
- getPeakAnnotation(boolean, Ion, int) - Static method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the annotation to use for a given ion and charge as a String.
- getPeakAnnotation(boolean) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the annotation to use for the given ion match as a String.
- getPeakListAsString() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
-
Returns the peak list as an array list formatted as text, e.g.
- getPeaks(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
Returns the peaks of the spectrum with the given title.
- getPeaks(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getPeaks(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getPeaks(String, String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the spectrum peaks.
- getPeaks() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
-
Getter for the peaks
- getPeaks() - Method in interface com.compomics.util.interfaces.SpectrumFile
-
This method reports on the peaks in the spectrum, with the
Doubles for the masses as keys in the HashMap, and the intensities
for each peak as Double value for that mass key.
- getPeaksAboveIntensityThreshold(Spectrum, AnnotationParameters.IntensityThresholdType, double) - Static method in class com.compomics.util.experiment.mass_spectrometry.spectra.SpectrumUtil
-
Returns the peaks above intensity threshold as an array of double (mz,
intensity).
- getPeaksInBin(int) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Returns the indexes of the peaks at the given bin indexed by m/z.
- getPeaksMap() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Returns the peaks map.
- getPeakWaterMarkColor() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Get the peak water mark color.
- getPeakWidth() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the current width of the peaks.
- getPepNovoPtmMap() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Returns the PepNovo to utilities PTM map.
- getPeptide() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
Getter for the peptide.
- getPeptide(double, double) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Returns a peptide from the peptide draft.
- getPeptide(double, double, BoxedObject<Boolean>) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Returns a peptide from the peptide draft.
- getPeptide() - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
-
Get the theoretic peptide.
- getPeptideAssumptionFilter() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the filter used when importing PSMs.
- getPeptideAssumptionsMap() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Returns the peptide assumptions map: advocate id > score > list of
assumptions.
- getPeptideCount() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Returns the number of peptides found.
- getPeptideDetailList(String) - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
-
Convert from JSON to a list of ProteinDetails.
- getPeptideEnd(String, int) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the 0 based end index of the peptide on the protein sequence.
- getPeptideEvidenceKey(String, int, long) - Static method in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
-
Returns the peptide evidence key as string for the given peptide
attributes.
- getPeptideFilters() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Returns the list of peptide quality filters.
- getPeptideFromProtein(char[], int, double, double) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
-
Returns a peptide from the given sequence.
- getPeptideFromProtein(char[], String, int, Double, Double) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
-
Returns a peptide from the given sequence on the given protein.
- getPeptideFromProtein(char[], String, int, double, double, BoxedObject<Boolean>) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
-
Returns a peptide from the given sequence on the given protein.
- getPeptideHideFilters() - Method in class com.compomics.util.gui.filtering.FilterParameters
-
Returns the peptide hide filters.
- getPeptideIdentification() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a list of the keys of all encountered peptides.
- getPeptideLengthDistribution() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the distribution of validated peptide lengths.
- getPeptideList() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Returns the current peptide list.
- getPeptideMatch(long) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the peptide match with the given key.
- getPeptideMatchesIterator(long[], WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a peptide matches iterator for a given key list.
- getPeptideMatchesIterator(WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a peptide matches iterator for all PeptideMatches.
- getPeptideMatchesKeys() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Getter for the peptide keys.
- getPeptideNormalisationFactor(String) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
-
Returns the peptide normalization factor for the given sample, 1.0 if not
set.
- getPeptideProteinIndexesMap(ArrayList<PeptideProteinMapping>) - Static method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
-
Returns a map made from the given mappings containing the indexes of the
peptides in the protein sequences indexed by peptide sequence and protein
accession.
- getPeptideProteinMap(ArrayList<PeptideProteinMapping>) - Static method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
-
Returns a map made from the given mappings containing protein accessions
for every peptide sequence.
- getPeptides(ArrayList<PeptideProteinMapping>, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
-
Aggregates the given mapping into a list of peptides.
- getPeptideSelected() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the color for a selected peptide.
- getPeptideSequence() - Method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
-
Returns the peptide sequence.
- getPeptideSequences() - Method in class com.compomics.util.gui.spectrum.IsotopicDistributionPanel
-
Get the set of peptide sequences.
- getPeptideShakerPath() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the path to the PeptideShaker installation.
- getPeptideStarFilters() - Method in class com.compomics.util.gui.filtering.FilterParameters
-
Returns the peptide star filters.
- getPeptideVariantMatches() - Method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
-
Returns eventual variants found.
- getPeptideVariantsParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the peptide variant parameters.
- getPeptideVariantsPreferences() - Method in class com.compomics.util.gui.parameters.identification.advanced.PeptideVariantsParametersDialog
-
Returns the peptide variants settings as set by the user.
- getPepXmlOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true if the pepxml output is to be created.
- getPercentLength() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Returns the length of the reference area in percent.
- getPercentualScreenDimension(JFrame, double) - Static method in class com.compomics.util.gui.MonitorDimension
-
This method returns a Dimension with a percentual width and height in relation to the JFrame.
- getPercentualScreenDimension(JPanel, double) - Static method in class com.compomics.util.gui.MonitorDimension
-
This method returns a Dimension with a percentual width and height in realtion to the JPanel.
- getPercMax() - Method in class com.compomics.util.general.IsotopicDistribution
-
Getter for result of the isotopic distributions calculation.
- getPercTot() - Method in class com.compomics.util.general.IsotopicDistribution
-
Getter for result of the isotopic distributions calculation.
- getPhase() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the phase.
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the pI.
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
-
- getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
-
- getPinOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true if the Percolator output is to be created.
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the pK1.
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
-
- getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the pK2.
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
-
- getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the pKa.
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
-
- getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
-
- getPlus1() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Returns the isotopic correction factor at +1 Da.
- getPlus2() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Returns the isotopic correction factor at +2 Da.
- getPmid() - Method in class com.compomics.util.experiment.identification.Advocate
-
Returns the PubMed id of the reference of the advocate of interest.
- getPmid() - Method in enum com.compomics.util.experiment.io.biology.protein.ProteinDatabase
-
Returns the PubMed id of the database, null if not set.
- getPmid() - Method in class com.compomics.util.pride.prideobjects.Reference
-
Returns the PubMed ID of the reference.
- getPNovoParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.PNovoParametersDialog
-
Returns the pNovo parameters as set by the user.
- getPNovoPtmMap() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Returns the pNovo to utilities PTM map.
- getPNovoPtmResiduesMap() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Returns the pNovo to original amino acids residue map.
- getPosition() - Method in class com.compomics.util.protein.Enzyme
-
Simple getter for the cleavage position of the Enzyme.
- getPossibilities() - Method in interface com.compomics.util.experiment.filtering.FilterItem
-
In case the filter has predefined values, return the possible values, null otherwise.
- getPossibilities() - Method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
-
- getPossibilities() - Method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
-
- getPossibilities() - Method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
-
- getPossibilities() - Method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
-
- getPossibleChargesAsString() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
-
Returns the possible charges as a string.
- getPossibleConfidenceLevels() - Static method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Convenience method returning all confidence levels as string.
- getPossibleFilterItems() - Method in class com.compomics.util.experiment.identification.filtering.AssumptionFilter
-
- getPossibleFilterItems() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Returns the filter items accepted by this filter.
- getPossibleFilterItems() - Method in class com.compomics.util.experiment.identification.filtering.PeptideFilter
-
- getPossibleFilterItems() - Method in class com.compomics.util.experiment.identification.filtering.ProteinFilter
-
- getPossibleFilterItems() - Method in class com.compomics.util.experiment.identification.filtering.PsmFilter
-
- getPossibleFilterItemsNames() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Returns the filter items accepted by this filter.
- getPossibleModificationNames(Peptide, ModificationMatch, IdfileReader, SearchParameters, SequenceMatchingParameters, SequenceProvider, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
-
Returns the possible modification names.
- getPossibleModificationNamesAndromeda(Peptide, ModificationMatch, SearchParameters, SequenceMatchingParameters, SequenceProvider, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
-
Returns the possible Andromeda modification names.
- getPossibleModificationNamesByMass(Peptide, ModificationMatch, SearchParameters, SequenceMatchingParameters, SequenceProvider, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
-
Returns the possible modifications names by mass.
- getPossibleModificationNamesByName(Peptide, ModificationMatch, SearchParameters, SequenceMatchingParameters, SequenceProvider, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
-
Returns the possible modifications by name.
- getPossibleModificationNamesOmssa(Peptide, ModificationMatch, SearchParameters, SequenceMatchingParameters, SequenceProvider, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
-
Returns the possible OMSSA modification names.
- getPossibleModificationSites(Peptide, Modification, SequenceProvider, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
-
Returns an array of the possible modification sites for the given
modification on the given peptide.
- getPossibleModificationSites(AminoAcidSequence, boolean, boolean, Modification, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
-
Returns an array of the possible modification sites for the given
modification on the given peptide.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
-
Returns the possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.Glycan
-
Returns the possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
Returns the possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
Returns the possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
-
Returns the possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
-
Returns the possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Returns the possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
Returns the possible subtypes.
- getPossibleSubtypes(Ion.IonType) - Static method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns an array of possible subtypes.
- getPossibleSubtypesAsSet(Ion.IonType) - Static method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns a hashset of possible subtypes.
- getPossibleTags(boolean, int, int, int) - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
-
Computes the possible tag assumptions which can be obtained from this one
by accounting for other charges and isotopes.
- getPossibleValues() - Method in interface com.compomics.util.experiment.filtering.FilterItem
-
Returns the possible items of this kind.
- getPossibleValues() - Method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
-
- getPossibleValues() - Method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
-
- getPossibleValues() - Method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
-
- getPossibleValues() - Method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
-
- getPotentialModificationSites(Modification, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Returns the potential modification sites as an ordered list of string.
- getPotentialModificationSitesNoCombination(Modification, String, int) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the potential modification sites as an ordered list of sites.
- getPpm() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Returns whether the precursor mass tolerance is in ppm.
- getPpmError(double, double) - Static method in class com.compomics.util.Util
-
Returns the ppm value of the given mass error relative to its theoretical
m/z value.
- getPpmTolerance(double, double) - Static method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the relative tolerance in ppm corresponding to the absolute
tolerance in Dalton at the given reference mass.
- getPrecurorCharge() - Method in class com.compomics.util.io.PklFile
-
- getPrecursor(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
Returns the precursor of the spectrum with the given title.
- getPrecursor(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getPrecursor(BufferedRandomAccessFile, long, String) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.IndexedMgfReader
-
Returns the next precursor starting from the given index.
- getPrecursor(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getPrecursor() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
-
Returns the precursor.
- getPrecursor(String, String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the precursor.
- getPrecursorAccuracy() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the precursor tolerance.
- getPrecursorAccuracyType() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the precursor accuracy type.
- getPrecursorAdjustmentStep() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the precursor adjustment step.
- getPrecursorCharge() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Returns the charge of the precursor.
- getPrecursorIntensity() - Method in class com.compomics.util.io.PklFile
-
- getPrecursorIntensityAveragePerFraction(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Get the average precursor intensity in the given fraction.
- getPrecursorIntensityAveragePerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the fraction precursor intensity average map.
- getPrecursorIntensityPerFraction(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Get the precursor intensity in the given fraction.
- getPrecursorIntensityPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the precursor intensity per fraction map.
- getPrecursorIntensitySummedPerFraction(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Get the summed precursor intensity in the given fraction.
- getPrecursorIntensitySummedPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the fraction summed intensity map.
- getPrecursorMatch(double, double) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the ion match.
- getPrecursorMz(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
Returns the m/z of the precursor of the spectrum with the given title.
- getPrecursorMz(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getPrecursorMz(int) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns the precursor mz for the spectrum at the given index.
- getPrecursorMz(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getPrecursorMz(String, String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the measured precursor m/z.
- getPrecursorMZ() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
-
Getter for the precursor MZ
- getPrecursorMZ() - Method in interface com.compomics.util.interfaces.SpectrumFile
-
This method reports on the precursor M/Z
- getPrecursorMz() - Method in class com.compomics.util.io.PklFile
-
- getPrecursorRt(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
Returns the RT of the precursor of the spectrum with the given title.
- getPrecursorRt(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getPrecursorRt(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getPrecursorRt(String, String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the precursor RT window.
- getPrecursorsInBin(int) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
-
Returns the precursors at the given bin indexed by mass.
- getPrecursorToleance() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Returns the precursor tolerance.
- getPreferredAccessionColumnWidth(JTable, int, int) - Method in class com.compomics.util.gui.genes.GeneDetailsDialog
-
Gets the preferred width of the column specified by colIndex.
- getPreferredColumnWidth(JTable, int, int) - Method in class com.compomics.util.examples.UtilitiesDemo
-
Gets the preferred width of the column specified by vColIndex.
- getPreferredWidthOfCell(JTable, int, int) - Static method in class com.compomics.util.gui.GuiUtilities
-
Returns the preferred width of a given cell in a table.
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the CV term adapted to the fragment ion.
- getPrideFolder() - Static method in class com.compomics.util.pride.PrideObjectsFactory
-
Returns the folder where pride annotation information should be saved.
- getPrimaryKeyColumns() - Method in class com.compomics.util.db.DBMetaData
-
This method reports on the primary key columns for the table.
- getPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- getPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- getPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- getPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- getPrimaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
-
Returns the primary progress counter.
- getPrintExpectScore() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns true if the export score is to be printed.
- getPrintPeptides() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true of a list of the peptides should be printed to the output
folder.
- getPrintProgressIndicatorSize() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the progress indicator size.
- getProbabilisticScore(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns the probabilistic score at a given site.
- getProbabilisticScoreThreshold() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Returns the probabilistic score threshold (inclusive).
- getProbabilisticSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns a set of sites where a probabilistic score is available
- getProbability() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the match probability.
- getProbabilityAt(double) - Method in interface com.compomics.util.math.statistics.Distribution
-
Returns the density function value at a given position.
- getProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
-
- getProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
- getProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- getProcessedProteinKeys(WaitingHandler, FilterParameters) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the sorted list of protein keys.
- getProcessingParameters() - Method in class com.compomics.util.gui.parameters.tools.ProcessingParametersDialog
-
Returns the processing parameters as set by the user.
- getProcessingType() - Method in class com.compomics.util.parameters.tools.ProcessingParameters
-
Returns the processing type.
- getProfile() - Method in class com.compomics.util.gui.protein.ModificationProfile
-
Returns the profile.
- getProgress() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
-
This method reports on the current progress of the progressdialog.
- getProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
Returns the progress bar for updates from external processes.
- getProgressInPercent() - Method in class com.compomics.util.experiment.io.biology.protein.iterators.FastaIterator
-
Returns the progress reading the file in percent.
- getProgressInPercent() - Method in class com.compomics.util.io.flat.readers.SimpleGzReader
-
- getProgressInPercent() - Method in class com.compomics.util.io.flat.readers.SimpleTextReader
-
- getProgressInPercent() - Method in interface com.compomics.util.io.flat.SimpleFileReader
-
Returns the progress reading the file in percent.
- getProjectCount(String, PrideFilter...) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a project count for the given criteria and filters.
- getProjectDetail(String) - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
-
Convert from JSON to a list of ProjectDetails.
- getProjectDetail(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns the project details for a given accession.
- getProjectFileCount(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a count of file details for a given project.
- getProjectFileDetails(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a list of file details for a given project.
- getProjectSummaryList(String) - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
-
Convert from JSON to a list of ProjectDetails.
- getProjectSummaryList(String, PrideFilter...) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a ProjectSummaryList for the given query and filters.
- getProjectType(String) - Static method in enum com.compomics.util.parameters.peptide_shaker.ProjectType
-
Returns the project type corresponding to the given GUI option.
- getProjectUniqueName() - Method in class com.compomics.util.experiment.ProjectParameters
-
- getProjectUniqueName(String) - Method in class com.compomics.util.experiment.ProjectParameters
-
- getProperties(CompomicsTools, String) - Method in class com.compomics.util.io.PropertiesManager
-
Get a Properties instance for the parameter properties filename.
- getPropertiesFile(String) - Static method in class com.compomics.util.junit.TestCaseLM
-
This method will read a Properties file from the current ClassLoader
and return a Properties instance with the Properties from the file.
- getProperty(AminoAcid.Property) - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns a property of the amino acid.
- getProperty(int) - Method in enum com.compomics.util.experiment.biology.aminoacids.AminoAcid.Property
-
Returns the property at index.
- getProperty() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
-
Returns the feature property.
- getProperty() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
-
Returns the feature property;
- getPrositeFormat() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns the pattern in the PROSITE format.
- getProteinAccession() - Method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
-
Returns the accession of the protein.
- getProteinAccessions(String) - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
-
Returns the protein accessions linked to a given GO term.
- getProteinConfidenceMwPlots() - Method in class com.compomics.util.parameters.identification.advanced.FractionParameters
-
Returns the protein confidence for inclusion in MW plots.
- getProteinDatabase(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getProteinDatabase(String) - Method in enum com.compomics.util.experiment.io.biology.protein.ProteinDatabase
-
Returns the protein database with the given full name, null if not found.
- getProteinDatabase(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
-
Returns the the protein database for the given protein.
- getProteinDetailList(String) - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
-
Convert from JSON to a list of ProteinDetails.
- getProteinEvidencAsString(Integer) - Static method in class com.compomics.util.experiment.io.biology.protein.Header
-
Return the UniProt protein evidence type as text.
- getProteinEvidence(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getProteinEvidence() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the protein evidence level as indexed in UniProt.
- getProteinEvidence(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
-
Returns an integer representing the protein evidence level as indexed by
UniProt.
- getProteinFilters() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Returns the list of protein quality filters.
- getProteinHideFilters() - Method in class com.compomics.util.gui.filtering.FilterParameters
-
Returns the protein hide filters.
- getProteinIdentification() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a list of the keys of all encountered proteins.
- getProteinIdentificationByAssay(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a list of protein details for a given assay.
- getProteinIdentificationByProject(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a list of protein details for a given project.
- getProteinIdentificationCountByAssay(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a count of protein details for a given assay.
- getProteinIdentificationCountByProject(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a count of protein details for a given project.
- getProteinIdentificationsByProjectAndProtein(String, String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a list of protein details for a given project and a given protein
accession.
- getProteinIdentificationsCountByProjectAndProtein(String, String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a count of protein details for a given project and a given
protein accession.
- getProteinInferenceClassAsString() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the protein inference class as a string for the given
integer-based class
- getProteinInferenceClassAsString(int) - Static method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the protein inference class as a string for the given
integer-based class.
- getProteinInferenceGroupClass() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the protein inference class of the protein match.
- getProteinInferenceParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the protein inference parameters.
- getProteinInferencePreferences() - Method in class com.compomics.util.gui.parameters.identification.advanced.ProteinInferenceParametersDialog
-
Returns the protein inference preferences.
- getProteinKey() - Method in class com.compomics.util.experiment.biology.proteins.Protein
-
Returns the key for protein indexing.
- getProteinKeys(WaitingHandler, FilterParameters) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the ordered protein keys to display when no filtering is applied.
- getProteinKeys() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the list of ordered protein keys.
- getProteinList() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Returns the protein list.
- getProteinListAfterHiding() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Returns the protein list after all hiding filters have been used.
- getProteinMap() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a map of all the protein matches which can be ascribed to a
protein indexed by its accession.
- getProteinMapping() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the protein mapping as a map of 0-based indexes for every
protein accession.
- getProteinMapping(String, SequenceMatchingParameters) - Method in interface com.compomics.util.experiment.identification.protein_inference.FastaMapper
-
Returns the protein mapping in the FASTA file loaded in the sequence
factory for the given peptide sequence in a map: peptide sequence found
in the FASTA file | protein accession | list of indexes of the peptide
sequence on the protein sequence.
- getProteinMapping(Tag, SequenceMatchingParameters) - Method in interface com.compomics.util.experiment.identification.protein_inference.FastaMapper
-
Returns the protein mappings for the given peptide sequence.
- getProteinMapping(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getProteinMapping(Tag, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getProteinMappingWithoutVariants(String, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
Exact mapping peptides against the proteome.
- getProteinMappingWithoutVariants(Tag, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
Mapping tags against proteome without variants.
- getProteinMappingWithVariants(Tag, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
Mapping tags against proteome with variants.
- getProteinMappingWithVariantsFixed(String, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
Variant tolerant mapping peptides against the proteome.
- getProteinMappingWithVariantsGeneric(String, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
Variant tolerant mapping peptides against the proteome.
- getProteinMappingWithVariantsSpecific(String, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
Variant tolerant mapping peptides against the proteome
- getProteinMatch(long) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the protein match with the given key.
- getProteinMatches(long) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the keys of the protein matches where a peptide can be found.
- getProteinMatchesIterator(long[], WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a protein matches iterator for a given key list.
- getProteinMatchesIterator(WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a protein matches iterator for all PeptideMatches.
- getProteinMatchKey(Peptide) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Convenience method which returns the protein key from a peptide.
- getProteinNormalisationFactor(String) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
-
Returns the protein normalization factor for the given sample, 1.0 if not
set.
- getProteinPtmComplexity() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns the proteinPtmComplexity.
- getProteinsForGoTerm(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Returns the protein accessions for a GO accession.
- getProteinStarFilters() - Method in class com.compomics.util.gui.filtering.FilterParameters
-
Returns the protein star filters.
- getProteinToGoMap() - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Returns the protein to GO terms accession map.
- getProteinToGoMap() - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
-
Returns the protein to GO accession map.
- getProteoWizardPath() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the path to ProteoWizard.
- getProtocol() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Returns the protocol ID.
- getProtocols() - Method in class com.compomics.util.pride.PrideObjectsFactory
-
Returns the protocols.
- getProtonMassMultiple(int) - Static method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
-
Returns the mass of the proton multiplied by i.
- getPsiModCvTerm() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns the PSI-MOD CV term associated with this modification.
- getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
-
- getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
-
- getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
- getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
- getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
-
- getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
-
- getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
- getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
- getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the CV term adapted to the fragment ion.
- getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
-
Returns the CV term for the neutral loss.
- getPSMCountByAssay(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a count of PSM details for a given assay.
- getPSMCountByAssayAndSequence(String, String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a count of PSM details for a given assay and a given peptide
sequence.
- getPSMCountByProject(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a count of PSM details for a given project.
- getPSMCountByProjectAndSequence(String, String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a count of PSM details for a given project and a given peptide
sequence.
- getPsmFilters() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Returns the list of PSM quality filters.
- getPsmHideFilters() - Method in class com.compomics.util.gui.filtering.FilterParameters
-
Returns the psm hide filters.
- getPsmList() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Returns the PSM list.
- getPsmNormalisationFactor(String) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
-
Returns the PSM normalization factor for the given sample, 1.0 if not
set.
- getPSMsByAssay(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a list of PSM details for a given assay.
- getPSMsByAssayAndSequence(String, String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a list of PSM details for a given assay and a given peptide
sequence.
- getPSMsByProject(String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a list of PSM details for a given project.
- getPSMsByProjectAndSequence(String, String) - Static method in class com.compomics.util.pride.PrideWebService
-
Returns a list of PSM details for a given project and a given peptide
sequence.
- getPsmScoringParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the scoring parameters used when scoring PSMs.
- getPsmScoringPreferences() - Method in class com.compomics.util.gui.parameters.identification.advanced.PsmScoringParametersDialog
-
Returns the PSM scoring preferences as set by the user.
- getPsmStarFilters() - Method in class com.compomics.util.gui.filtering.FilterParameters
-
Returns the psm star filters.
- getPTM(PepnovoParameters, String) - Static method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
-
Get a PTM.
- getPtmIndex(String) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns the index of a given modification, null if not found.
- getPtmIndex(String) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the index of a given modification
- getPtmIndexes() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns the PTM indexes as a map.
- getPtmIndexes() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the PTM indexes as a map.
- getPtmLocationAtAA() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns the map of the localization.
- getPtmLocations(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns the PTM locations at a given confidence level (see static
fields).
- getPtmName() - Method in class com.compomics.util.gui.protein.ModificationProfile
-
Returns the PTM name.
- getPtmResidue(Character) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Returns the original amino acids residue corresponding to the given pNovo
PTM character.
- getPtmScoringPreferences() - Method in class com.compomics.util.gui.parameters.identification.advanced.ModificationLocalizationParametersDialog
-
Returns the PTM scoring preferences as set by the user.
- getPtmToPrideMap() - Method in class com.compomics.util.pride.PrideObjectsFactory
-
Returns the utilities PTM to pride map.
- getQcCriteria() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the list of QC checks made for this match.
- getQcFilters() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the qc filters map.
- getQuantile(int, Integer, int, double) - Method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
-
Get the quantile.
- getQueryTemplate(boolean) - Method in enum com.compomics.util.pride.prideobjects.webservice.PrideQuery
-
Returns the actual query template.
- getQuoteType() - Static method in class com.compomics.software.cli.CommandLineUtils
-
Returns the quote type to use.
- getRandomIndexes(int, int, int) - Static method in class com.compomics.util.math.BasicMathFunctions
-
Returns a list of n random indexes between min and max included.
- getRandomInteger(int, int) - Static method in class com.compomics.util.math.BasicMathFunctions
-
Returns an integer randomly chosen between min and max included.
- getRandomThreshold(int, int) - Method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
-
Returns the threshold (inclusive) to use to consider an assignment
random.
- getRank(int, boolean) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
-
Returns the rank.
- getRank(int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
-
Returns the number of occurrences of a given character until position
index.
- getRank() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Get the identification rank.
- getRankOne(int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
-
Returns the rank of ones.
- getRankRecursive(int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
-
Returns the number of occurrences of a given character until position
index.
- getRankScore() - Method in class com.compomics.util.experiment.refinement_parameters.PepnovoAssumptionDetails
-
Returns the PepNovo rank score.
- getRankZero(int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
-
Returns the rank of zeros.
- getRawBins() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Returns the bins in the map as collection of keys from the map.
- getRawHeader() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the entire header.
- getRawScore() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the raw score as provided by the identification algorithm.
- getReader(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
Returns the cms file reader for the given ms file.
- getReader() - Method in class com.compomics.util.io.flat.readers.SimpleGzReader
-
- getReader() - Method in class com.compomics.util.io.flat.readers.SimpleTextReader
-
- getReader() - Method in interface com.compomics.util.io.flat.SimpleFileReader
-
Returns the underlying reader.
- getReadTweets() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the list of read tweets.
- getReagent(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
-
Returns the reagent of the given name, null if not found.
- getReagentNames() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
-
Returns the reagents available in this method.
- getReagentsSortedByMass() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
-
Returns the list of reagents sorted by ascending mass.
- getRecalibratedMz(TreeMap<Double, Double>, double[]) - Static method in class com.compomics.util.experiment.mass_spectrometry.spectra.RecalibrationUtils
-
Returns a recalibrated peak list.
- getRecalibratedPrecursor(Precursor, double, double) - Static method in class com.compomics.util.experiment.mass_spectrometry.spectra.RecalibrationUtils
-
Returns a recalibrated precursor.
- getRef() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Returns the value used as reference for the correction factors.
- getReference() - Method in class com.compomics.util.pride.prideobjects.Reference
-
Returns the reference as a string.
- getReferenceGroups() - Method in class com.compomics.util.pride.PrideObjectsFactory
-
Returns the reference groups.
- getReferenceMass() - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
-
Returns the reference total mass to use for normalization.
- getReferences() - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
-
Returns the references.
- getRefinementFixedModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
-
Return the refinement fixed modifications used for the second pass
search.
- getRefinementVariableModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
-
Return the refinement variable modifications used for the second pass
search.
- getRefMass() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the reference mass used to convert ppm to Da.
- getRefMass() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the reference mass for the conversion of the fragment ion
tolerance from ppm to Dalton.
- getRelatedIons(char) - Static method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
-
Returns the list of related ions for the given amino acid.
- getRelatedIons(AminoAcid) - Static method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
-
Returns the list of related ions for the given amino acid.
- getRelatedIons() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Indicates whether related ions should be annotated by default.
- getRelationship() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
-
Returns the relationship between the features.
- getRelativeError() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Get the relative m/z matching error in ppm.
- getRelativeError(int, int) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Get the relative m/z matching error in ppm after isotope removal.
- getRelimsPath() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the path to the Relims installation.
- getRemoveMethionine() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns true if n-term methionine is to be removed.
- getRemovePrecursor() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns if the precursor is to be removed.
- getRemovePrecursor() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true of the precursor peak is to be removed.
- getRemovePrecursorTolerance() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the precursor removal tolerance.
- getRemovePrecursorTolerance() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the tolerance with which to remove the precursor peak.
- getRemoveTempFolders() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true if the output and index folders are to be removed when the
search has completed.
- getReport(boolean) - Method in interface com.compomics.util.experiment.filtering.Filter
-
Returns a filter report depending on whether the condition was met.
- getReport(boolean) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
- getReport(File) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Returns the report.
- getReporterIndex(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
This method returns the reporter ion name associated to the given sample.
- getReporterIon(int) - Static method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Returns the reporter ion indexed by the given index.
- getReporterIon(String) - Static method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Returns the reporter ion corresponding to the given name.
- getReporterIon() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Returns the reporter ion to look for in the spectrum.
- getReporterIon(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
-
Returns the reporter ion of the given name, null if not found.
- getReporterIonNames() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
-
Returns a list containing the names of the reporter ions.
- getReporterIons(ModificationParameters) - Static method in class com.compomics.util.experiment.biology.ions.IonFactory
-
Returns the reporter ions to annotate with the given PTM settings.
- getReporterIons() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns the reporter ions possibly encountered with this modification.
- getReporterIons() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Indicates whether reporter ions should be annotated by default.
- getReporterMethod() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
Returns the reporter method used.
- getReporterMethod(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
-
Returns the reporter methods corresponding to the given name.
- getReporterPath() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the path to the Reporter installation.
- getRepresentativeSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
-
Returns a list of all representative sites of ambiguously localized
modifications.
- getRequireVariableMods() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns true if at least one variable modification is required per
peptide.
- getResidues() - Method in interface com.compomics.util.interfaces.Modification
-
This method reports on all the residues that can be modified by this Modification.
- getResidues() - Method in class com.compomics.util.protein.ModificationImplementation
-
This method reports on all the residues that can be modified by this Modification.
- getResidues() - Method in class com.compomics.util.protein.ModificationTemplate
-
This method reports on all the residues that can be modified by this Modification.
- getResolution() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
-
Returns the resolution.
- getResolution() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
Returns the resolution.
- getResponseString() - Method in class com.compomics.util.io.ftp.FTP
-
Returns all server response strings.
- getResponseStringNoReset() - Method in class com.compomics.util.io.ftp.FTP
-
This method allows the caller to read the response strings from
the server, without resetting the internal buffer (and thus not clearing the
messages read by this messages).
- getRest() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the rest of the header.
- getRestrict() - Method in class com.compomics.util.protein.Enzyme
-
Simple getter for the restricting residues of the Enzyme.
- getRestrictionAfter() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
-
Getter for the amino acids restricting when following the cleavage.
- getRestrictionBefore() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
-
Getter for the amino acids restricting when preceding the cleavage.
- getReverseComplementary() - Method in class com.compomics.util.nucleotide.NucleotideSequenceImpl
-
This method returns the reverse complementary strand for the
sequence.
- getRewindIons() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns the rewind ions searched as list of integers as indexed in the
FragmentIon class.
- getRewindStart(String) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
-
Returns the amino acid where a neutral loss should start being accounted
for when predicting b ions (counting from N-terminus, first aa is 1).
- getRobustCorrelation(ArrayList<Double>, ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
-
Returns the population Pearson correlation r between series1 and series2.
- getRobustLinearRegression(ArrayList<Double>, ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.linear_regression.LinearRegression
-
Returns a robust linear regression based on the median.
- getRobustNonSymmetricalNormalDistribution(ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
Returns the non-symmetrical distribution of the input list of double
calibrated on the median, 15.9% and 84.1% percentiles.
- getRobustNonSymmetricalNormalDistributionFromSortedArray(double[]) - Static method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
Returns the non-symmetrical distribution of the input array of double
calibrated on the median, 15.9% and 84.1% percentiles.
- getRobustNonSymmetricalNormalDistributionFromSortedList(ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
Returns the non-symmetrical distribution of the input list of double
calibrated on the median, 15.9% and 84.1% percentiles.
- getRobustNormalDistribution(ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
Returns the normal distribution corresponding to a given list of double
calibrated on median and 34.1% percentile to median distance
- getRoundedMass(int) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Getter for the rounded mass difference induced by this modification.
- getRoundedMass() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Getter for the rounded mass difference induced by this modification.
- getRowCount() - Method in class com.compomics.util.db.DBResultSet
-
This method reports on the number of rows in the resultset.
- getRowCount() - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
-
- getRowCount() - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
-
- getRowCount() - Method in class com.compomics.util.sun.TableMap
-
- getRowNumber(int) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
-
Returns the row number of the given view index.
- getRtInMinutes() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
-
Returns the retention time in minutes.
- getSameMassNotFixedModifications(double, SearchParameters) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns a list containing all not fixed modifications with the same
mass.
- getSample(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
This method returns the sample associated to the given ion.
- getSampleIndex(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
Returns the sample index for the given sample.
- getSampleIndexes() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
Returns a set containing the indexes of every sample.
- getSamples() - Method in class com.compomics.util.pride.PrideObjectsFactory
-
Returns the samples.
- getScalingFactor() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Returns the scaling factor.
- getScientificName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
-
Returns the scientific name corresponding to the given NCBI taxon.
- getScore(int) - Static method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
-
Returns the PTM score indexed by the given id.
- getScore(String) - Static method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
-
Returns the PTM score of the given name.
- getScore() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the score.
- getScore(Peptide, String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, PeptideSpectrumAnnotator, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
-
Returns the hyperscore.
- getScore(Peptide, int, Spectrum, ArrayList<IonMatch>) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
-
Returns the hyperscore.
- getScore(Peptide, int, Precursor, boolean, int, int) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.PrecursorAccuracy
-
Scores the match between the given peptide and spectrum using the
precursor m/z accuracy.
- getScore(Peptide, String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, PeptideSpectrumAnnotator, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.SnrScore
-
Returns the score.
- getScore(Peptide, Spectrum, ArrayList<IonMatch>) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.SnrScore
-
Returns the score.
- getScore(Peptide, Spectrum, HashMap<Double, ArrayList<IonMatch>>) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.SnrScore
-
Returns the score.
- getScore(int) - Static method in enum com.compomics.util.experiment.identification.psm_scoring.PsmScore
-
Returns the PSM score of the given index.
- getScore(String) - Static method in enum com.compomics.util.experiment.identification.psm_scoring.PsmScore
-
Returns the PSM score of the given name.
- getScore(Peptide, int, String, String, Spectrum, IdentificationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters, PeptideSpectrumAnnotator, int) - Method in class com.compomics.util.experiment.identification.psm_scoring.PsmScoresEstimator
-
Scores the match between the given peptide and spectrum using the given
score.
- getScore(Peptide, int, String, String, Spectrum, IdentificationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters, PeptideSpectrumAnnotator, PsmScore) - Method in class com.compomics.util.experiment.identification.psm_scoring.PsmScoresEstimator
-
Scores the match between the given peptide and spectrum using the given
score.
- getScore() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the score assigned by the advocate.
- getScore() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
This method will attribute a score to the current header, based on the
following scoring list: SwissProt : 4 IPI, SwissProt
reference : 3 IPI, TrEMBL or REFSEQ_NP reference : 2
IPI, without SwissProt, TrEMBL or REFSEQ_NP reference : 1
NCBI, SwissProt reference : 2 NCBI, other reference : 1
Unknown header format : 0
- getScore() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the score.
- getScoreCutoff() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the score cut-off.
- getScoredModifications() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
-
Returns a list of scored modifications.
- getScoredSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns a set of sites where a score is available.
- getScoreForAlgorithm(int) - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
-
Returns the scores set for a given algorithm.
- getSearchGuiOutputParameters() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the selected SearchGUI output option.
- getSearchGuiPath() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the path to the SearchGUI installation.
- getSearchParameters() - Method in class com.compomics.util.experiment.io.identification.MzIdentMLIdfileSearchParametersConverter
-
Updated the search parameters object and returns the search parameters as
a string.
- getSearchParameters() - Method in class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog
-
Returns a SearchParameters instance based on the user input in the GUI.
- getSearchParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the parameters used for the spectrum matching.
- getSearchTarget() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns true if target sequences are to be searched.
- getSearchType() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the search type.
- getSecondaryProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Returns the secondary progress bar for updates from external processes.
- getSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- getSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- getSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- getSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- getSecondaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
-
Returns the secondary progress counter.
- getSecondaryPtmLocations() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Returns the not found, randomly or doubtfully localized PTMs.
- getSections() - Method in class com.compomics.util.io.export.ExportScheme
-
returns the list of sections to be included in the scheme.
- getSelect(int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
-
Returns the position of the i-th one
- getSelectedCharges() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Returns the charges selected for annotation.
- getSelectedDate() - Method in class com.compomics.util.gui.utils.DateChooser
-
This method returns a Calendar set at the selected date,
or 'null' if no date was selected.
- getSelectedFastaFile() - Method in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
-
Returns the selected FASTA file.
- getSelectedFile() - Method in class com.compomics.util.gui.file_handling.FileSelectionDialog
-
Returns the file selected by the user.
- getSelectedFiles() - Method in class com.compomics.util.gui.file_handling.FileDisplayDialog
-
Returns the list of selected files.
- getSelectedItem() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser
-
Returns the item selected by the user.
- getSelectedItems() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser
-
Returns the items selected by the user in a list.
- getSelectedMethod() - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
-
Returns the current spectrum counting method.
- getSelectedOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the selected output type, omx, csv or pepXML.
- getSelectedOutputFormat() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the selected output format.
- getSelectedPositions() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Returns the selected positions.
- getSelectedProbabilisticScore() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Returns the selected probabilistic score.
- getSelectedRowHtmlTagFontColor() - Static method in class com.compomics.util.gui.TableProperties
-
Returns the color to use for the HTML tags for the selected rows, in HTML
color code.
- getSelectedSpecies() - Method in class com.compomics.util.gui.genes.SpeciesDialog
-
Deprecated.
Returns the species selected in the species drop down menu.
- getSelection() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Returns true if there is a selection.
- getSeparationLines() - Method in class com.compomics.util.io.export.ExportScheme
-
Returns the number of lines to be used to separate the sections.
- getSeparator() - Method in class com.compomics.util.io.export.ExportScheme
-
Returns the column separator.
- getSequence() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
Returns the sequence as String.
- getSequence() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns for the sequence.
- getSequence() - Method in class com.compomics.util.experiment.biology.proteins.Protein
-
Getter for the protein sequence.
- getSequence(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getSequence() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Returns the sequence.
- getSequence(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
-
- getSequence(String) - Method in interface com.compomics.util.experiment.io.biology.protein.SequenceProvider
-
Returns the protein sequence for the given accession.
- getSequence() - Method in interface com.compomics.util.interfaces.Sequence
-
This method will retrieve the sequence.
- getSequence() - Method in class com.compomics.util.nucleotide.NucleotideSequence
-
This method reports on the nucleotide sequence.
- getSequence() - Method in class com.compomics.util.nucleotide.NucleotideSequenceImpl
-
This method will retrieve the sequence.
- getSequence() - Method in class com.compomics.util.protein.AASequenceImpl
-
Simple getter for the sequence.
- getSequence() - Method in class com.compomics.util.protein.Protein
-
This method reports on the sequence for the current
protein.
- getSequenceCoverage(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the sequence coverage of the protein of interest.
- getSequenceIterator(String, DigestionParameters, double, double) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.IteratorFactory
-
Returns a sequence iterator for the given protein sequence and digestion
preferences.
- getSequenceMatchingParameters() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Returns the sequence matching preferences to use when mapping
modifications on amino acid sequences.
- getSequenceMatchingParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns the sequence matching parameters.
- getSequenceMatchingPreferences() - Method in class com.compomics.util.gui.parameters.identification.advanced.SequenceMatchingParametersDialog
-
Returns the sequence matching settings as set by the user.
- getSequenceMatchingType() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Returns the sequence matching type.
- getSequenceProbabilities(Peptide, ArrayList<Modification>, ModificationParameters, Spectrum, SequenceProvider, AnnotationParameters, SpecificAnnotationParameters, boolean, SequenceMatchingParameters, SequenceMatchingParameters, PeptideSpectrumAnnotator) - Static method in class com.compomics.util.experiment.identification.modification.scores.PhosphoRS
-
Returns the PhosphoRS sequence probabilities for the modification
possible locations.
- getSerializationFolder() - Static method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
-
Returns the folder where to save the factory.
- getSerializationFolder() - Static method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns the folder where the factory is saved.
- getShortDescription() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Returns a short description of the parameters.
- getShortDescription() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns a short description of the parameters.
- getShortDescription() - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
-
Returns a short description of the parameters.
- getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.FractionParameters
-
Returns a short description of the parameters.
- getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
-
Returns a short description of the parameters.
- getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
-
Returns a short description of the parameters.
- getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Returns a short description of the parameters.
- getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Returns a short description of the parameters.
- getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Returns a short description of the parameters.
- getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
-
Returns a short description of the parameters.
- getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Returns a short description of the parameters.
- getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Returns a short description of the parameters.
- getShortDescription() - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
-
Returns a short description of the parameters.
- getShortDescription() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns a short description of the parameters.
- getShortName() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Getter for the short modification name.
- getSimpleDescription(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getSimpleDescription(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
-
Returns the simple description of the protein with the given accession.
- getSimpleLinearRegression(ArrayList<Double>, ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.linear_regression.LinearRegression
-
Returns a simple linear regression.
- getSimpleLinearRegressionOutlierRemoval(ArrayList<Double>, ArrayList<Double>, Double) - Static method in class com.compomics.util.math.statistics.linear_regression.LinearRegression
-
Returns a simple linear regression performed after outlier removal.
- getSimpleProteinDescription() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns a simplified protein description for a UniProt header.
- getSimplifyGroups() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Returns a boolean indicating whether the protein groups should be
simplified.
- getSimplifyGroupsConfidence() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Returns a boolean indicating whether the protein groups should be
simplified based on the peptide confidence.
- getSimplifyGroupsEnzymaticity() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Returns a boolean indicating whether the protein groups should be
simplified based on the peptide enzymaticity.
- getSimplifyGroupsEvidence() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Returns a boolean indicating whether the protein groups should be
simplified based on the Uniprot evidence level.
- getSimplifyGroupsVariants() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Returns a boolean indicating whether the protein groups should be
simplified based on the peptide variant matching.
- getSingleAAModification(Modification) - Static method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns a clone of the given Modification targeting a single amino acid
instead of a pattern.
- getSingleAAModification(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns a clone of the given Modification targeting a single amino acid
instead of a pattern.
- getSingleChargeWindow() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Returns the window size for singly charged ions.
- getSingleLetterCodeAsChar() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the single letter code as character.
- getSite() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Getter for the modification site.
- getSite(int, int) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
-
Returns the 1-based index on the peptide.
- getSkylinePath() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns the skyline path.
- getSmallestCumulativeProbabilityAt(double) - Method in interface com.compomics.util.math.statistics.Distribution
-
Returns the cumulative density function value at a given position, starting from the low values if before the median, from the high otherwise.
- getSmallestCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
-
- getSmallestCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
- getSmallestCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- getSoftwareVersions() - Method in interface com.compomics.util.experiment.io.identification.IdfileReader
-
Returns the names and versions of the software used to generate the
identification file in a map, e.g., Mascot > (2.2 and 2.3) and
X!Tandem > Sledgehammer (2013.09.01.1).
- getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
-
- getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader
-
- getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
- getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader
-
- getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader
-
- getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
-
- getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader
-
- getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
-
- getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
-
- getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader
-
- getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
-
- getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
-
- getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
-
- getSortedEnzymeNames() - Method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
-
Get the sorted list of enzyme names.
- getSortedFeaturesList() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
-
Returns a sorted list of features categories.
- getSortedImplementedIons() - Static method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Returns an ordered list of possible subtypes.
- getSortedPeptideKeys(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns a sorted list of peptide keys from the protein of interest.
- getSortedPsmKeys(long, boolean, boolean) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the ordered list of spectrum keys for a given peptide.
- getSortedTermNames() - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
-
Returns a sorted list of all GO Terms names linked to proteins in the
proteinToGoMap.
- getSortPsmsOnRt() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns true if the PSMs are sorted on retention time, false sorts on PSM
score.
- getSource() - Method in class com.compomics.util.gui.events.RescalingEvent
-
Returns the JPanel source.
- getSource() - Method in class com.compomics.util.pride.prideobjects.Instrument
-
Returns the instrument source.
- getSourceFile() - Method in class com.compomics.util.io.ftp.FTP
-
This method reports on the sourcefile currently used in transfer.
- getSpAccession() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
-
Returns the SP accession.
- getSpAccession() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
-
Returns the SP accession.
- getSparklineColor() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Getter for the sparkline color.
- getSparklineColorDoubtful() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the color for a doubtful sparkline bar chart plots.
- getSparklineColorFalsePositives() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the color for false positives in sparkline bar chart plots.
- getSparklineColorNonValidated() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Getter for the non-validated sparkline color.
- getSparklineColorNotFound() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the color for a not found sparkline bar chart plots.
- getSparklineColorPossible() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the color for a possible sparkline bar chart plots.
- getSpeciesDescription(TreeMap<String, Integer>) - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns a listing of the species occurrence map provided.
- getSpecificAnnotationParameters(String, String, SpectrumIdentificationAssumption, ModificationParameters, SequenceProvider, SequenceMatchingParameters, SpectrumAnnotator) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns the annotation preferences specific to a spectrum and an
identification assumption.
- getSpecificity(String) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
-
Returns the expected specificity of the given enzyme.
- getSpecificity(int) - Static method in enum com.compomics.util.parameters.identification.search.DigestionParameters.Specificity
-
Returns the specificity of the given index.
- getSpecificityAt(double) - Method in class com.compomics.util.math.roc.DataRoc
-
- getSpecificityAt(double) - Method in class com.compomics.util.math.roc.DistributionRoc
-
- getSpecificityAt(double) - Method in interface com.compomics.util.math.statistics.ROC
-
Returns the 1-specificity at a given sensitivity.
- getSpectrum() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileIterator
-
- getSpectrum(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
Returns the spectrum with the given title.
- getSpectrum(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getSpectrum(BufferedRandomAccessFile, long, String) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.IndexedMgfReader
-
Returns the next spectrum starting from the given index.
- getSpectrum() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileIterator
-
- getSpectrum(BufferedRandomAccessFile, long) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns the next spectrum starting from the given index.
- getSpectrum(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getSpectrum() - Method in interface com.compomics.util.experiment.io.mass_spectrometry.MsFileIterator
-
Returns the spectrum corresponding to the title returned by the last call
to the next() method.
- getSpectrum() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileIterator
-
- getSpectrum(String, String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the spectrum with the given title in the given file.
- getSpectrumAnnotatedMirroredPeakColor() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the color to use for the annotated mirrored peaks.
- getSpectrumAnnotatedPeakColor() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the color to use for the annotated peaks.
- getSpectrumAnnotatedPeakWidth() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the width of the annotated peaks.
- getSpectrumAnnotation(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
- getSpectrumAnnotation(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the spectrum annotations of a spectrum in a list of IonMatches.
- getSpectrumAnnotation(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, HashMap<Integer, HashMap<Integer, ArrayList<Ion>>>, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the spectrum annotations of a spectrum in an array of IonMatches.
- getSpectrumAnnotation(AnnotationParameters, ModificationParameters, SequenceMatchingParameters, SpecificAnnotationParameters, String, String, Spectrum, Tag) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
-
Returns the spectrum annotations of a spectrum in a list of IonMatches
using an intensity filter.
- getSpectrumAnnotation(AnnotationParameters, ModificationParameters, SequenceMatchingParameters, SpecificAnnotationParameters, String, String, Spectrum, Tag, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
-
Returns the spectrum annotations of a spectrum in a list of IonMatches.
- getSpectrumAnnotation(IonMatch[]) - Static method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Translates the list of ion matches into a vector of annotations which can
be read by the SpectrumPanel.
- getSpectrumAnnotationStream(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
- getSpectrumAnnotationStream(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the spectrum annotations of a spectrum in a list of IonMatches.
- getSpectrumAnnotationStream(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, HashMap<Integer, HashMap<Integer, ArrayList<Ion>>>, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the spectrum annotations of a spectrum in a stream of IonMatches.
- getSpectrumBackgroundPeakColor() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the color to use for the background peaks.
- getSpectrumBackgroundPeakWidth() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the width of the background peaks.
- getSpectrumCharges() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the spectrum charges to search for.
- getSpectrumCount() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
Returns the number of spectra matched.
- getSpectrumCounting(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the spectrum counting metric of the protein match of interest
using the preference settings.
- getSpectrumCounting(long, SpectrumCountingMethod) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the spectrum counting metric of the protein match of interest for
the given method.
- getSpectrumFile() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Returns the name of the file where this spectrum was found.
- getSpectrumFileId() - Method in class com.compomics.util.io.PklFile
-
- getSpectrumFolder() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the last used spectrum folder.
- getSpectrumIdentification() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a map of the spectrum matches keys indexed by spectrum file name.
- getSpectrumIdentificationKeys() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the keys of all the spectrum matches in the db.
- getSpectrumIdentificationSize() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the number of spectrum identifications.
- getSpectrumIndex(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns the spectrum index corresponding to the desired spectrum, i.e.,
returns 0 for the first spectrum in the file, 1 for the second, etc.
- getSpectrumMatch(long) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the spectrum match with the given key.
- getSpectrumMatchesIterator(long[], WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a spectrum matches iterator for a given key list.
- getSpectrumMatchesIterator(WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a spectrum matches iterator for all SpectrumMatches.
- getSpectrumMatchesIterator(WaitingHandler, String) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a psm iterator for all SpectrumMatches.
- getSpectrumMatchesKeys() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
Returns the keys of all spectra matched.
- getSpectrumTitle() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Returns the title of the spectrum.
- getSpectrumTitle(int) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns the spectrum title corresponding to the given spectrum number.
- getSpectrumTitles(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
-
- getSpectrumTitles() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns an ordered list of all spectrum titles.
- getSpectrumTitles(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
-
- getSpectrumTitles(String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
-
Returns the spectrum titles for the given mass spectrometry file name.
- getSpEnd() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
-
Returns the SP end.
- getSpStart() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
-
Returns the SP start.
- getSqtOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true if the sqt output is to be created.
- getStandardGeneticCode() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the standard genetic triplets associated to this amino acid.
- getStandardGeneticCode() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
-
- getStandardGeneticCodeForCombination() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the genetic code as combination of the sub amino acid genetic
codes.
- getStandardHeight() - Method in class com.compomics.util.io.export.styles.DefaultStyle
-
- getStandardHeight() - Method in interface com.compomics.util.io.export.WorkbookStyle
-
Returns the height of a standard line.
- getStandardSearchPattern() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Computes a pattern which can be searched by standard search engines,
i.e., a pattern targeting a single amino acid and not a complex pattern.
- getStandardStyle() - Method in class com.compomics.util.io.export.styles.DefaultStyle
-
- getStandardStyle(int) - Method in class com.compomics.util.io.export.styles.DefaultStyle
-
- getStandardStyle() - Method in interface com.compomics.util.io.export.WorkbookStyle
-
Returns the standard cell style.
- getStandardStyle(int) - Method in interface com.compomics.util.io.export.WorkbookStyle
-
Returns the standard cell style for the given hierarchical depth.
- getStandardUnit(String) - Static method in enum com.compomics.util.experiment.units.StandardUnit
-
Returns the standard unit having the given full name.
- getStarred() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns whether a match is starred or not.
- getStart() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Get the start value.
- getStart() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the start.
- getStartBlock() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Returns the block start.
- getStartLocation() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
This method reports on the start index of the header.
- getStartPosition() - Method in class com.compomics.util.pdbfinder.das.readers.StartEndPosition
-
Returns the start position.
- getStartProtein() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Returns the protein start.
- getStdDown() - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
Returns the standard deviation to the left of the distribution.
- getStdUp() - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
Returns the standard deviation to the right of the distribution.
- getStoreSpectraFileName() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the name of the file where the binary spectra are to be stored.
- getStringMatching() - Static method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Returns preferences for simple string matching.
- getStringParameter(String) - Method in class com.compomics.util.experiment.ProjectParameters
-
- getStringValue(boolean, boolean, boolean, boolean, boolean, boolean) - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
-
Sets the string value from the stringValue attribute, sets it from the
composition if not set.
- getStyle(ExcelWriter) - Static method in class com.compomics.util.io.export.styles.DefaultStyle
-
Returns the style attached to that writer or create a new one if none
found.
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
In case of a combination of amino acids, returns the comprised amino
acids or amino acid groups represented by their single letter code
including sub combinations.
- getSubAminoAcids(boolean) - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
In case of a combination of amino acids, returns the comprised amino
acids or amino acid groups represented by their single letter code.
- getSubFolder() - Static method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFolder
-
Returns the sub-folder where to write cms files.
- getSubMatrix(int, int, int, int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getSubNumber() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
Returns the number of the fragment in the current amino acid sequence.
- getSubPattern(int, int, boolean) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns a sub pattern of the pattern.
- getSubPattern(int, boolean) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns a sub pattern of the pattern.
- getSubsequence(String, int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getSubsequence(String, int, int) - Method in class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
-
- getSubsequence(String, int, int) - Method in interface com.compomics.util.experiment.io.biology.protein.SequenceProvider
-
Returns the subsequence of the sequence of a given protein.
- getSubstitutedAminoAcid() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Substitution
-
- getSubstitutionAminoAcids(Character) - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
-
Returns the possible substituted amino acids for the given amino acid as
a list of their single letter code.
- getSubstitutionAminoAcids() - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
-
Returns the possible substituted amino acids.
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
-
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
-
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
-
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
-
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the ion subtype.
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
-
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
-
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
- getSubTypeAsString(int) - Static method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
Returns the type of fragment ion as a letter.
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
-
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
-
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
- getSubTypeAsString(int) - Static method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
Returns the type of fragment ion as a letter.
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the subtype as string.
- getSummary(String, FastaParameters, WaitingHandler) - Static method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
-
Gathers summary data on the FASTA file content.
- getSummary(String, FastaParameters, boolean, WaitingHandler) - Static method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
-
Gathers summary data on the FASTA file content.
- getSupportedExtensions() - Static method in interface com.compomics.util.experiment.io.mass_spectrometry.MsFileIterator
-
Returns the supported extensions.
- getTable() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser
-
Returns the JTable containing the items.
- getTable() - Method in interface com.compomics.util.gui.VisibleTableColumnsDialogParent
-
Returns the JTable for which to hide/show the column for.
- getTable() - Method in class com.compomics.util.gui.XYPlottingDialog
-
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.compomics.util.gui.renderers.AlignedTableCellRenderer
-
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.compomics.util.gui.renderers.ByteArrayRenderer
-
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.compomics.util.gui.renderers.FragmentIonTableCellRenderer
-
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer
-
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.compomics.util.gui.renderers.TimestampRenderer
-
- getTableName() - Method in class com.compomics.util.db.DBMetaData
-
This method reports on the tablename.
- getTableTooltips() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser
-
Returns the tooltips used for the column headers.
- getTag() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
-
Returns the tag to annotate.
- getTag() - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
-
Returns the tag of this assumption.
- getTagAssumptionsMap() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Returns the tag assumptions map: advocate id > score > list of
assumptions.
- getTaggedModifiedSequence(ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean, boolean, boolean, HashSet<String>) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the modified sequence as an tagged string with potential
modification sites color coded or with Modification tags, e.g,
<mox>.
- getTaggedModifiedSequence(ModificationParameters, boolean, boolean, boolean, boolean, SequenceMatchingParameters, HashSet<String>) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Returns the modified sequence as an tagged string with potential
modification sites color coded or with modification tags, e.g,
<mox>.
- getTaggedModifiedSequence(ModificationParameters, Tag, boolean, boolean, boolean, boolean, SequenceMatchingParameters, HashSet<String>) - Static method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Returns the modified sequence as an tagged string with potential
modification sites color coded or with modification tags, e.g,
<mox>.
- getTaggedModifiedSequence(ModificationParameters, String, String[], String[], String[], String[], boolean, boolean) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
-
Returns the modified sequence as a tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
- getTaggedModifiedSequence(Peptide, ModificationParameters, String[], String[], String[], String[], String[], String[], boolean, boolean, boolean) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns the modified sequence as an tagged string with potential
modification sites color coded or with Modification tags, e.g,
<mox>.
- getTaggingTimeSeconds() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
Returns the tagging time in seconds as listed in the file.
- getTagLength() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the tag length.
- getTagModificationsAsString(Tag) - Static method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Returns the tag modifications as a string.
- getTagParameter(String) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
Returns the tagging parameter corresponding to a given parameter name.
- getTagsGenerator() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
Returns the tags generator used to create the file.
- getTagsGeneratorVersion() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
Returns the version of the tags generator used to create the file.
- getTagsParametersNames() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
Returns the name of the different parameters names found.
- getTarget() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns the index of the amino acid of interest in the pattern.
- getTargetDecoyFileNameSuffix() - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
-
Returns the target-decoy file name suffix.
- getTargetedAA(int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns the targeted amino acids at a given index in the pattern.
- getTaxonomy(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
- getTaxonomy() - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Returns the taxonomy.
- getTaxonomy(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
-
Returns the taxonomy for the given protein.
- getTaxons() - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
-
Returns the taxons in this map.
- getTaxons() - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
-
Returns the taxons in this map.
- getTermAccession(String) - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
-
Returns the accession of a GO term.
- getTermDomain(String) - Method in class com.compomics.util.experiment.biology.genes.go.GoDomains
-
Returns the description of a GO term.
- getTermName(String) - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
-
Returns the name of a GO term.
- GettersAndSetters - Class in com.compomics.util.db.components
-
This class will generate (and subsequently output upon request) all relevant getters and setters
for a DBAccessor.
- GettersAndSetters() - Constructor for class com.compomics.util.db.components.GettersAndSetters
-
Empty default constructor
- GettersAndSetters(DBMetaData) - Constructor for class com.compomics.util.db.components.GettersAndSetters
-
The constructor takes care of generating all getters and setters,
based on the speicifed metadata.
- getTextOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true if the text output is to be created.
- getTheoreticalFragmentIonsSumOnly() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns true if the theoretical fragment ions are calculated on the sum
in the bin alone.
- getTheoreticMass() - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the theoretic mass, from the atomic composition if available,
from the theoreticMass field otherwise.
- getTheoreticMass() - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
-
- getTheoreticMass() - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
-
- getTheoreticMass(boolean, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
-
Returns the theoretic mass of the tag, eventually without terminal gaps.
- getTheoreticMass() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the theoretic mass of the given assumption.
- getTheoreticMz(Integer) - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the m/z expected for this ion at the given charge.
- getTheoreticMz(boolean, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
-
Returns the theoretic mass of the tag, eventually without terminal gaps.
- getTheoreticMz() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the theoretic m/z.
- getThermoRawFileParserParameters() - Method in class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui.ThermoRawFileParserParametersDialog
-
Returns the parameters as created by the user.
- getTicCutoffPercentage() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the TIC cutoff in percent.
- getTicCutoffPercentage() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns the TicCutoffPercentage.
- getTiesResolution() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns the ties resolution method to use when multiple peaks can be
assigned to an ion.
- getTimeEnd() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
Returns the ending time of the tagging as given in the file.
- getTimeStart() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
-
Returns the starting time of the tagging as given in the file.
- getTip(String, String, ArrayList<String>) - Static method in class com.compomics.util.messages.FeedBack
-
Creates a tip object.
- getTip(String, String) - Static method in class com.compomics.util.messages.FeedBack
-
Creates a general tip with no key word.
- getTitle() - Method in interface com.compomics.util.interfaces.Modification
-
This method returns the title of the modification,
eg.
- getTitle() - Method in interface com.compomics.util.io.export.ExportFeature
-
Returns the column title of the feature.
- getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsAnnotationFeature
-
- getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
-
- getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
-
- getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
-
- getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
-
- getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
-
- getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
-
- getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
-
- getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
-
- getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
-
- getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
-
- getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
-
- getTitle() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
-
- getTitle() - Method in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
-
- getTitle() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
-
- getTitle() - Method in class com.compomics.util.messages.FeedBack
-
Returns the title.
- getTitle() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
-
Returns the title.
- getTitle() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
Returns the title.
- getTitle() - Method in class com.compomics.util.protein.Enzyme
-
Simple getter for the title (name) of the Enzyme.
- getTitle() - Method in class com.compomics.util.protein.ModificationImplementation
-
This method returns the title of the modification,
eg.
- getTitle() - Method in class com.compomics.util.protein.ModificationTemplate
-
This method returns the title of the modification,
eg.
- getTooltipMap() - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
-
Returns the default map of icons for the validation levels.
- getTopPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns the top peaks number.
- getTopPeaksWindow() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns the top peaks window size.
- getTotalIntensity() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Returns the total intensity of the peaks above the intensity threshold.
- getTotalIntensity() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
-
Returns the total intensity of the spectrum.
- getTotalIntensity() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
-
Method calculates the total intensity of the peaks
- getTotalIntensity() - Method in interface com.compomics.util.interfaces.SpectrumFile
-
This method returns the total intensity contributed by all the ions
in this spectrum.
- getTotalPartitions() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns total partitions.
- getTotalPeptidesPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the total number of peptides per fraction.
- getTotalSpectrumCounting() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the total spectrum counting.
- getTotalSpectrumCountingMass() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the total spectrum counting masses.
- getTrace() - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getTransformedScore() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the log transformed score.
- getTrimMs1Peaks() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns true if Ms1 peaks are to be trimmed.
- getTrimMsMsPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns true if MsMs peaks are to be trimmed.
- getTruncatedSequence(int, int) - Method in class com.compomics.util.protein.AASequenceImpl
-
This method will return an AASequenceImpl that represents
an internal truncation of the current sequence.
- getTruncationPosition() - Method in class com.compomics.util.protein.Protein
-
This method reports on the position of the truncation.
- getTrypsinExample() - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Returns the trypsin example as amino acid pattern.
- getType() - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the ion type.
- getType() - Method in class com.compomics.util.experiment.identification.Advocate
-
Returns the type of advocate.
- getType() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Return the type of the filter.
- getType() - Method in class com.compomics.util.experiment.identification.IdentificationMatch
-
Returns the type of match.
- getType() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
- getType() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
- getType() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
- getType() - Method in class com.compomics.util.experiment.io.parameters.DummyParameters
-
- getType() - Method in interface com.compomics.util.experiment.io.parameters.MarshallableParameter
-
Returns the type of marshalled parameter from an unmarshalled object.
- getType() - Method in class com.compomics.util.experiment.patient.PatientInformation
-
Returns the type of information.
- getType() - Method in class com.compomics.util.messages.FeedBack
-
Returns the feedback type.
- getType() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
- getType() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
- getType() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the type.
- getType() - Method in class com.compomics.util.pride.prideobjects.webservice.query.PrideFilter
-
Returns the filter type.
- getTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the type of ion as string.
- getTypeAsString(Ion.IonType) - Static method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the type of ion as string.
- getTypeAsString() - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
-
Returns a string with the different database types found.
- getTypeCategory() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the type category.
- getTypeForGenomeDivision(EnsemblGenomesSpecies.EnsemblGenomeDivision) - Method in class com.compomics.util.gui.genes.SpeciesDialog
-
Deprecated.
Returns the display name of an Ensembl genome division.
- getTypeId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the type ID.
- getTypeReference() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the type reference.
- getTypesAsString() - Static method in enum com.compomics.util.experiment.biology.modifications.ModificationType
-
Returns all of the modification type options as a string.
- getTypeSubparts() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the type subparts.
- getTypeSuperparts() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns the type super parts.
- getUnevenRowColor() - Method in class com.compomics.util.AlternateRowColoursJTable
-
This method returns the Color used for the uneven numbered rows, or 'null' if the
default JTable background color is maintained for these rows.
- getUniModAccessionLink(String) - Method in class com.compomics.util.gui.modification.ModificationsDialog
-
Returns a web link to the given Unimod CV term at http://www.unimod.org.
- getUnimodCvTerm() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns the Unimod CV term associated with this modification.
- getUniprotTaxonomy() - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns the UniProt taxonomy mapping.
- getUniprotTaxonomyFile(String) - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Returns the UniProt taxonomy file.
- getUniqueAminoAcids() - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns a char array of the one letter code of amino acids without
combinations of amino acids.
- getUniqueIndex(char) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns an index for the amino acid excluding combinations.
- getUnit() - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
-
Returns the unit used for normalization.
- getUpperClearMzRange() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Returns the upper mass value for the clear mz range.
- getUpperPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Returns the upper precursor mass.
- getUrlOfZippedVersion(URL, String, boolean) - Static method in class com.compomics.software.autoupdater.WebDAO
-
Gets the first zip file from a URL, in case of a Maven repo deploy this
should be the only zip in the folder.
- getUrParam(UrParameter) - Method in class com.compomics.util.experiment.personalization.ExperimentObject
-
Returns the refinement parameter of the same type than the one provided.
- getUrParams() - Method in class com.compomics.util.experiment.personalization.ExperimentObject
-
Returns the user parameters map.
- getUseDeltaScore() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns true of delta score is to be used.
- getUseFlankingPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true if flanking peaks are to be used.
- getUseGeneMapping() - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
-
Returns a boolean indicating whether gene mappings should be used.
- getUseNeutralLossPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns true if the neutral loss peaks are to be used.
- getUseProvidedPrecursorInfo() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns true of the provided precursor info is to be used.
- getUserAdvocates() - Static method in class com.compomics.util.experiment.identification.Advocate
-
Returns the map of user advocates imported.
- getUserModifications() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns the names of the user defined modifications.
- getUserModificationsOrdered() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Returns the alphabetically (case insensitive) ordered names of the user
defined modifications.
- getUserParametersFile() - Static method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the user preferences file to be used.
- getUserParametersFolder() - Static method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns the user preferences file to be used.
- getUserSelectedFile(Component, String, String, String, String, String, boolean) - Static method in class com.compomics.util.gui.file_handling.FileChooserUtil
-
Returns the file selected by the user, or null if no file was selected.
- getUserSelectedFile(Component, String[], String[], String, String, String, boolean, boolean, boolean, int) - Static method in class com.compomics.util.gui.file_handling.FileChooserUtil
-
Returns the file selected by the user, or null if no file was selected.
- getUserSelectedFolder(Component, String, String, String, String, boolean) - Static method in class com.compomics.util.gui.file_handling.FileChooserUtil
-
Returns the folder selected by the user, or null if no folder was
selected.
- getUseSmartPlusThreeModel() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Returns true if the UseSmartPlusThreeModel is to be used.
- getUseSparseMatrix() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
- getUtilitiesEnzyme(String) - Method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
-
Returns the enzyme associated to the given cvTerm.
- getUtilitiesModificationName(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Tries to convert a modification name to a utilities modification
name.
- getUtilitiesModificationName(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns the name of the modification indexed by the given index.
- getUtilitiesPtmName(String) - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
-
Returns the utilities PTM name corresponding to the given Novor PTM
short name.
- getUtilitiesPtmName(String) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Returns the utilities PTM name corresponding to the given PepNovo PTM
name.
- getUtilitiesPtmName(Character) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Returns the utilities PTM name corresponding to the given pNovo PTM
character.
- getUtilitiesUserParameters() - Method in interface com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent
-
Returns the utilities user preferences.
- getValidatedPeptidesPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the number of validated peptides per fraction.
- getValidatedProteinList() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Returns a list of validated proteins.
- getValidatedProteins(FilterParameters) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the list of validated protein keys.
- getValidatedProteins(WaitingHandler, FilterParameters) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the list of validated protein keys.
- getValidatedSequenceCoverage(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Returns the sequence coverage of the protein of interest.
- getValidatedSpectraPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Returns the number of validated spectra per fraction.
- getValidatedTargetProteinKeys() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Returns the keys of the validated target protein matches.
- getValidationLevelIndexes() - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
-
Returns an array of the validation level indexes in ascending order of
confidence.
- getValidationLevels() - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
-
Returns the implemented validation levels.
- getValidationLevelsNames() - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
-
Returns a list of the names of the implemented validation levels.
- getValidationQCParameters() - Method in class com.compomics.util.gui.parameters.identification.advanced.ValidationQCParametersDialog
-
Returns the validation QC preferences as set by the user.
- getValidationQCParameters() - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
-
Returns the validation QC preferences.
- getValue(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Returns the value used for comparison for a given filtering item.
- getValue(int) - Method in class com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters
-
Returns the value set for a given filter.
- getValue() - Method in interface com.compomics.util.interfaces.TableValueWrapper
-
This method returns the Object that this instance wraps around.
- getValue() - Method in class com.compomics.util.pride.CvTerm
-
Returns the value.
- getValue() - Method in class com.compomics.util.pride.prideobjects.webservice.query.PrideFilter
-
Returns the filter value.
- getValue() - Method in class com.compomics.util.sun.SwingWorker
-
Get the value produced by the worker thread, or null if it
hasn't been constructed yet.
- getValueAt(int, int) - Method in class com.compomics.util.db.DBResultSet
-
Returns the value for the cell at columnIndex
and
rowIndex
.
- getValueAt(int, int) - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
-
- getValueAt(int, int) - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
-
- getValueAt(int, int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
Returns the value of the matrix at given indexes.
- getValueAt(double) - Method in class com.compomics.util.math.roc.DataRoc
-
- getValueAt(double) - Method in class com.compomics.util.math.roc.DistributionRoc
-
- getValueAt(double) - Method in interface com.compomics.util.math.statistics.ROC
-
Returns the sensitivity at a given 1-specificity, i.e., 1-type 2 error,
the number of true healthy for a given type 1 error, the number of false
healthy.
- getValueAt(int, int) - Method in class com.compomics.util.sun.TableMap
-
- getValueAt(int, int) - Method in class com.compomics.util.sun.TableSorter
-
- getValueAtCumulativeProbability(double) - Method in interface com.compomics.util.math.statistics.Distribution
-
The value after which the cumulative density function will be smaller
than p.
- getValueAtCumulativeProbability(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
-
- getValueAtCumulativeProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
- getValueAtCumulativeProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- getValueAtDescendingCumulativeProbability(double) - Method in interface com.compomics.util.math.statistics.Distribution
-
The value after which the cumulative density function will be smaller
than p when starting from high values.
- getValueAtDescendingCumulativeProbability(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
-
- getValueAtDescendingCumulativeProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
-
- getValueAtDescendingCumulativeProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns the van der Waals volume in Ã…3.
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
-
- getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
-
- getVariableModifications() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
Getter for the modifications carried by this sequence in a map: aa number
> modification matches.
- getVariableModifications() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the variable modifications.
- getVariableModifications() - Method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
-
Returns eventual modifications found.
- getVariableModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
-
Returns the expected variable modification names included in this
profile.
- getVariableModificationsAsString(ModificationMatch[]) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns the peptide modifications as a string.
- getVariableModificationsAsString(Peptide) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns the peptide modifications as a string.
- getVariantMatches() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns the sequence variant matches of this peptide indexed by protein
accession and peptide start.
- getVariantMatches() - Method in class com.compomics.util.experiment.identification.matches.PeptideVariantMatches
-
Returns the map of variants indexed by 0 based position on the peptide.
- getVariantMatches(ArrayList<PeptideProteinMapping>) - Static method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
-
Returns the variant matches summarized in a map indexed by protein
accession and peptide index on the protein sequence.
- getVariantType() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Returns whether the specific variant count limitations should be used.
- getVennDiagramPanel() - Method in class com.compomics.util.gui.VennDiagramDialog
-
Returns the Venn diagram panel.
- getVerbosity() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Returns the verbosity type of progress output.
- getVersion() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
-
Returns the version of the features used to create the map.
- getVersion() - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
-
Returns the database version.
- getVersion() - Static method in class com.compomics.util.Util
-
Retrieves the version number set in the pom file.
- getVersionNumber() - Method in class com.compomics.software.autoupdater.MavenJarFile
-
Returns the version number.
- getViewIndex(int) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
-
Returns the view index of the given row.
- getVisibleColumns() - Method in interface com.compomics.util.gui.VisibleTableColumnsDialogParent
-
Returns the list of visible columns.
- getVisibleColumns() - Method in class com.compomics.util.gui.XYPlottingDialog
-
- getWaitingIcon() - Method in class com.compomics.util.gui.VennDiagramDialog
-
- getWaitingIcon() - Method in class com.compomics.util.gui.XYPlottingDialog
-
- getWarning(String, String) - Static method in class com.compomics.util.messages.FeedBack
-
Creates a warning object.
- getWindowIndexes(Spectrum, double, double) - Static method in class com.compomics.util.experiment.mass_spectrometry.spectra.SpectrumUtil
-
Returns the start (inclusive) and end (exclusive) indexes of the peaks between mzMin (inclusive) and mzMax (exclusive).
- getWindowWidthThomsons() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns the window width in Thomson.
- getWorkbook() - Method in class com.compomics.util.io.export.writers.ExcelWriter
-
Return the workBook.
- getWorkbookStyle() - Method in class com.compomics.util.io.export.writers.ExcelWriter
-
Returns the workbook style.
- getWriteMzId() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns true if mzId output is to be created.
- getWritePepXml() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Returns true if pepXML output is to be created.
- getWriter() - Method in class com.compomics.util.io.flat.SimpleFileWriter
-
Returns the underlying buffered writer.
- getX() - Method in class com.compomics.util.XYZDataPoint
-
Returns the x value.
- getXAxisData() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the x-axis data.
- getXAxisZoomRangeLowerValue() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the lower range for the current zoom range.
- getXAxisZoomRangeUpperValue() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the upper range for the current zoom range.
- getXTandemFormat() - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
-
Get the X!Tandem enzyme format.
- getxYValues() - Method in class com.compomics.util.math.roc.DataRoc
-
- getxYValues() - Method in class com.compomics.util.math.roc.DistributionRoc
-
- getxYValues() - Method in interface com.compomics.util.math.statistics.ROC
-
Returns xy values to draw the curve.
- getY() - Method in class com.compomics.util.XYZDataPoint
-
Returns the y value.
- getYAxisData() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the y-axis data.
- getZ() - Method in class com.compomics.util.XYZDataPoint
-
Returns the z value.
- gif - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
-
- GIF - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
-
- GLUTAMIC_ACID - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
Glutamic acid immonium ion.
- GlutamicAcid - Class in com.compomics.util.experiment.biology.aminoacids.impl
-
Glutamic Acid.
- GlutamicAcid() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
-
Constructor.
- Glutamine - Class in com.compomics.util.experiment.biology.aminoacids.impl
-
Glutamine.
- Glutamine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
-
Constructor.
- GLUTAMINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
Glutamine immonium ion.
- Glycan - Class in com.compomics.util.experiment.biology.ions.impl
-
This class represents a glycan.
- Glycan() - Constructor for class com.compomics.util.experiment.biology.ions.impl.Glycan
-
Empty default constructor
- Glycan(String, String) - Constructor for class com.compomics.util.experiment.biology.ions.impl.Glycan
-
Constructor for a glycan.
- Glycine - Class in com.compomics.util.experiment.biology.aminoacids.impl
-
Glycine.
- Glycine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
-
Constructor.
- GLYCINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
Glycine immonium ion.
- GO_MAPPING_FILE_SUFFIX - Static variable in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
The suffix to use for files containing GO mappings.
- GoDomains - Class in com.compomics.util.experiment.biology.genes.go
-
Class parsing go domains and storing them in a map.
- GoDomains() - Constructor for class com.compomics.util.experiment.biology.genes.go.GoDomains
-
Constructor.
- GoMapping - Class in com.compomics.util.experiment.biology.genes.go
-
Class parsing BioMart protein go mappings and storing them in maps.
- GoMapping() - Constructor for class com.compomics.util.experiment.biology.genes.go.GoMapping
-
Constructor.
- GraphicsPanel - Class in com.compomics.util.gui.spectrum
-
This class presents a JPanel that will hold and display a mass spectrum or a
chromatogram.
- GraphicsPanel() - Constructor for class com.compomics.util.gui.spectrum.GraphicsPanel
-
Empty default constructor
- GraphicsPanel.DrawingStyle - Enum in com.compomics.util.gui.spectrum
-
An enumerator of the possible GraphicsPanel types.
- GraphicsPanel.GraphicsPanelType - Enum in com.compomics.util.gui.spectrum
-
An enumerator of the possible GraphicsPanel types.
- GraphicsPanelTableCellRenderer - Class in com.compomics.util.gui.renderers
-
A table cell renderer for GraphicsPanels.
- GraphicsPanelTableCellRenderer() - Constructor for class com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer
-
Empty default constructor
- GraphicsPanelTableCellRenderer(double, double) - Constructor for class com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer
-
Create a new GraphicsPanelTableCellRenderer with a given x-axis range
to ensure that all spectra in the column have the same range.
- gson - Variable in class com.compomics.util.io.json.JsonMarshaller
-
GSON parser instance to convert JSON to Java objects and back.
- guiDefaultOption - Static variable in enum com.compomics.util.io.export.ExportFormat
-
The default export format to use for GUI exports.
- GUIFileDAO - Class in com.compomics.software.autoupdater
-
GUIFileDAO.
- GUIFileDAO() - Constructor for class com.compomics.software.autoupdater.GUIFileDAO
-
- GuiUtilities - Class in com.compomics.util.gui
-
A class containing simple GUI helper methods.
- GuiUtilities() - Constructor for class com.compomics.util.gui.GuiUtilities
-
- gunzipFile(File, boolean) - Static method in class com.compomics.util.io.compression.GzUtils
-
Uncompresses the given gz file to the given destination file.
- gunzipFile(File, File, boolean) - Static method in class com.compomics.util.io.compression.GzUtils
-
Uncompresses the given gz file to the given destination file.
- GZ_EXTENSION - Static variable in class com.compomics.util.io.compression.GzUtils
-
The extension to use for gz files.
- gzFile(File, boolean) - Static method in class com.compomics.util.io.compression.GzUtils
-
Gzip a file.If the gz file already exists it will be silently
overwritten.
- gzFile(File, File, boolean) - Static method in class com.compomics.util.io.compression.GzUtils
-
Gzip a file.If the gz file already exists it will be silently
overwritten.
- gzipTemp - Variable in class com.compomics.util.io.compression.SectionGzWriter.WriterBySection
-
If true, temp files are gzipped.
- GzUtils - Class in com.compomics.util.io.compression
-
Convenience methods to work with gzipped files.
- GzUtils() - Constructor for class com.compomics.util.io.compression.GzUtils
-
- I - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
- I - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
-
The Iodine atom.
- iAnnotations - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The Vector that holds a set of Annotation instances.
- iAnnotationsMirroredSpectra - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The Vector that holds a set of Annotation instances for the mirrored
spectra.
- iAnnotationYAxisThreshold - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The percent non-inclusive, minimal y-axis value (compared to the highest
point in the spectrum) a point should have before being eligible for
annotation.
- iAreaUnderCurveColor - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Colors in which the chromatogram polyline is rendered.
- iAreaUnderCurveColorMirroredSpectra - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Colors in which the chromatogram polyline is rendered for the mirrored
spectra.
- iArtifact - Variable in class com.compomics.util.protein.ModificationTemplate
-
Boolean to indicate whether this modification is an artifact.
- iBase64String - Variable in class com.compomics.util.BinaryArrayImpl
-
Represents the binary contents of the array as an array of bytes.
- iCleavables - Variable in class com.compomics.util.protein.Enzyme
-
Lookup cache for the cleavable residues.
- iCleavage - Variable in class com.compomics.util.protein.Enzyme
-
This char[] holds the residues after which cleavage will occur.
- iClicked - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Boolean that indicates whether a point has been marked by clicking.
- iClickedDataSetIndex - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Int that indicates which dataset contains the clicked point.
- iClickedDataSetIndexMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Int that indicates which dataset contains the clicked point in the
mirrored spectra.
- iClickedIndex - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Int that indicates which point was clicked.
- iClickedIndexMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Int that indicates which point was clicked in the mirrored spectra.
- iClickedList - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The Vector that holds all points clicked up to now.
- iClickedListDatasetIndices - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The Vector that holds the dataset indices of all points clicked up to
now.
- iClickedListDatasetIndicesMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The Vector that holds the dataset indices of all points clicked up to now
in the mirrored spectra.
- iClickedListMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The Vector that holds all points clicked up to now in the mirrored
spectra.
- iClickedMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Boolean that indicates whether a point has been marked by clicking in the
mirrored spectra.
- iCode - Variable in class com.compomics.util.protein.ModificationTemplate
-
The code for this modification (eg., Mox).
- iCurrentDrawStyle - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This variable holds the current drawing style.
- id - Variable in enum com.compomics.cli.enzymes.EnzymesCLIParams
-
Short Id for the CLI parameter.
- id - Variable in enum com.compomics.cli.fasta.FastaParametersCLIParams
-
Short id for the CLI parameter.
- id - Variable in enum com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
-
Short Id for the CLI parameter.
- id - Variable in enum com.compomics.cli.modifications.ModificationsCLIParams
-
Short Id for the CLI parameter.
- id - Variable in enum com.compomics.cli.paths.PathSettingsCLIParams
-
The id of the command line option.
- id - Variable in enum com.compomics.util.parameters.searchgui.OutputParameters
-
The index of the option.
- iDataEndian - Variable in class com.compomics.util.BinaryArrayImpl
-
Represents the endian value of the binary array (mzData element
.../data/endian).
- iDataLength - Variable in class com.compomics.util.BinaryArrayImpl
-
Represents the length of the binary array (mzData element
.../data/length).
- iDataPointAndLineColor - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Colors in which the data points and peaks are rendered.
- iDataPointAndLineColorMirroredSpectra - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Colors in which the data points and peaks are rendered for the mirrored
spectra.
- iDataPrecision - Variable in class com.compomics.util.BinaryArrayImpl
-
Represents the precision of the binary array (mzData element
.../data/precision).
- Identification - Class in com.compomics.util.experiment.identification
-
This class interacts with the back-end database to manage identification
objects.
- Identification() - Constructor for class com.compomics.util.experiment.identification.Identification
-
Empty default constructor
- Identification(ObjectsDB) - Constructor for class com.compomics.util.experiment.identification.Identification
-
Constructor.
- IdentificationAlgorithmParameter - Interface in com.compomics.util.gui.parameters.identification
-
Interface for the algorithm specific parameters.
- identificationCharge - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
The charge used for identification.
- IdentificationFeaturesCache - Class in com.compomics.util.experiment.identification.features
-
This class caches the identification features calculated by the
IdentificationFeaturesGenerator for later reuse.
- IdentificationFeaturesCache() - Constructor for class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Constructor.
- IdentificationFeaturesCache.ObjectType - Enum in com.compomics.util.experiment.identification.features
-
An enumerator of the supported object types.
- IdentificationFeaturesGenerator - Class in com.compomics.util.experiment.identification.features
-
This class provides identification features and stores them in cache.
- IdentificationFeaturesGenerator() - Constructor for class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Empty default constructor.
- IdentificationFeaturesGenerator(Identification, IdentificationParameters, SequenceProvider, SpectrumProvider, Metrics, SpectrumCountingParameters) - Constructor for class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Constructor.
- identificationFile - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
The identification file.
- IdentificationKeys - Class in com.compomics.util.experiment.identification
-
Placeholder for the keys of the objects in the identification.
- IdentificationKeys() - Constructor for class com.compomics.util.experiment.identification.IdentificationKeys
-
- IdentificationMatch - Class in com.compomics.util.experiment.identification
-
This is an abstract class for an identification match.
- IdentificationMatch() - Constructor for class com.compomics.util.experiment.identification.IdentificationMatch
-
Empty default constructor
- IdentificationMatch.MatchType - Enum in com.compomics.util.experiment.identification
-
The type of match.
- IdentificationMethod - Class in com.compomics.util.experiment.identification
-
This class will contain all methods used to obtain identifications.
- IdentificationMethod() - Constructor for class com.compomics.util.experiment.identification.IdentificationMethod
-
Empty default constructor
- IdentificationMethod(int) - Constructor for class com.compomics.util.experiment.identification.IdentificationMethod
-
Constructor for the identification method
- IdentificationParameters - Class in com.compomics.util.parameters.identification
-
Generic class grouping the parameters used for protein identification.
- IdentificationParameters() - Constructor for class com.compomics.util.parameters.identification.IdentificationParameters
-
Creates empty identification parameters.
- IdentificationParameters(SearchParameters) - Constructor for class com.compomics.util.parameters.identification.IdentificationParameters
-
Creates default identification parameters from the given search
parameters.
- IdentificationParameters(String, String, SearchParameters, AnnotationParameters, SequenceMatchingParameters, PeptideVariantsParameters, GeneParameters, PsmScoringParameters, PeptideAssumptionFilter, ModificationLocalizationParameters, ProteinInferenceParameters, IdMatchValidationParameters, FractionParameters, FastaParameters) - Constructor for class com.compomics.util.parameters.identification.IdentificationParameters
-
Constructor.
- IdentificationParametersCLI - Class in com.compomics.cli.identification_parameters
-
The IdentificationParametersCLI allows creating search parameters files using
command line arguments.
- IdentificationParametersCLI(String[]) - Constructor for class com.compomics.cli.identification_parameters.IdentificationParametersCLI
-
Construct a new IdentificationParametersCLI runnable from a list of
arguments.
- IdentificationParametersCLIParams - Enum in com.compomics.cli.identification_parameters
-
Enum class specifying the SearchParameter command line option parameters to
create a SearchParameters object
- IdentificationParametersEditionDialog - Class in com.compomics.util.gui.parameters.identification
-
IdentificationParametersEditionDialog.
- IdentificationParametersEditionDialog() - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
-
Empty default constructor
- IdentificationParametersEditionDialog(Frame, IdentificationParameters, Image, Image, LastSelectedFolder, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
-
Creates a new IdentificationParametersEditionDialog with a frame as
owner.
- IdentificationParametersEditionDialog(Dialog, Frame, IdentificationParameters, Image, Image, LastSelectedFolder, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
-
Creates a new IdentificationParametersEditionDialog with a dialog as
owner.
- IdentificationParametersFactory - Class in com.compomics.util.experiment.identification.identification_parameters
-
Factory for the identification parameters.
- IdentificationParametersInputBean - Class in com.compomics.cli.identification_parameters
-
This class parses the parameters from a command line and stores them in a
SearchParameters object.
- IdentificationParametersInputBean(CommandLine) - Constructor for class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
-
Takes all the arguments from a command line.
- IdentificationParametersMarshaller - Class in com.compomics.util.io.json.marshallers
-
This class is a convenience class to have a DefaultJsonConverter with the
identification parameters interfaces.
- IdentificationParametersMarshaller() - Constructor for class com.compomics.util.io.json.marshallers.IdentificationParametersMarshaller
-
Constructor.
- IdentificationParametersNameDialog - Class in com.compomics.util.gui.parameters.identification
-
- IdentificationParametersNameDialog() - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersNameDialog
-
Empty default constructor
- IdentificationParametersNameDialog(Frame, IdentificationParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersNameDialog
-
Creates a new IdentificationParametersNameDialog with a frame as owner.
- IdentificationParametersNameDialog(Dialog, Frame, IdentificationParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersNameDialog
-
Creates a new IdentificationParametersNameDialog with a dialog as owner.
- IdentificationParametersOverviewDialog - Class in com.compomics.util.gui.parameters.identification
-
IdentificationParametersOverviewDialog.
- IdentificationParametersOverviewDialog() - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersOverviewDialog
-
Empty default constructor
- IdentificationParametersOverviewDialog(Dialog) - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersOverviewDialog
-
Constructor with a dialog as owner.
- IdentificationParametersOverviewDialog(Frame) - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersOverviewDialog
-
Constructor with a frame as owner.
- identiPy - Static variable in class com.compomics.util.experiment.identification.Advocate
-
The IdentiPy search engine.
- IdfileReader - Interface in com.compomics.util.experiment.io.identification
-
Generic interface for the parser of a file containing PSMs.
- IdfileReaderFactory - Class in com.compomics.util.experiment.io.identification
-
This factory will provide the appropriate identification file reader for each
type of file.
- IdMatchValidationParameters - Class in com.compomics.util.parameters.identification.advanced
-
Generic class grouping the identification matches validation preferences.
- IdMatchValidationParameters() - Constructor for class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
-
Constructor for default settings.
- IdMatchValidationParameters(IdMatchValidationParameters) - Constructor for class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
-
Creates a new IdMatchValidationPreferences based on the values of the
given IdMatchValidationPreferences.
- iDotRadius - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This variable holds the dot radius; only used when drawing style is DOTS
style.
- iDragged - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This boolean is set to 'true' when dragging is performed.
- iDragXLoc - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The current dragging location.
- iEndXLoc - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
When the mouse is dragged, this represents the X-coordinate of the ending
location.
- iFilename - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The spectrum or chromatogram filename.
- iFilenameColor - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This is the color the filename should be presented in.
- iFilenameMirrorredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The spectrum or chromatogram filename for the mirrored spectrum or
chromatogram.
- ignoreExceptions - Variable in class com.compomics.util.exceptions.ExceptionHandler
-
If true exceptions will be ignored.
- iHighLight - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Boolean that will be 'true' when a point needs highlighting.
- iHighLightDatasetIndex - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Index of the dataset containing the point that needs to be highlighted.
- iHighLightDatasetIndexMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Index of the dataset containing the point that needs to be highlighted in
the mirrored spectra.
- iHighLightIndex - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Index of the point that needs to be highlighted.
- iHighLightIndexMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Index of the point that needs to be highlighted in the mirrored spectra.
- iHighLightMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Boolean that will be 'true' when a point needs highlighting in the
mirrored spectra.
- iKnownMassDeltas - Static variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This HashMap instance holds all the known mass deltas (if any).
- iLocation - Variable in class com.compomics.util.protein.ModificationImplementation
-
The location for the modification in the parent sequence.
- ImageType - Enum in com.compomics.util.enumeration
-
Enumerator for supported export plot file types.
- iMassDeltas - Variable in class com.compomics.util.protein.ModificationTemplate
-
This HashMap will contain the following 'key-value' mappings: (key > value)
(residue > double[]{MONOISOTOPIC_DELTA, AVERAGE_DELTA})
- iMinDrag - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Minimal dragging distance in pixels.
- iMiscleavages - Variable in class com.compomics.util.protein.Enzyme
-
This variable holds the number of supported missed cleavages.
- ImmoniumIon - Class in com.compomics.util.experiment.biology.ions.impl
-
Represents an immonium ion.
- ImmoniumIon() - Constructor for class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
Empty default constructor
- ImmoniumIonAnnotator - Class in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators
-
Annotator for immonium and related ions.
- ImmoniumIonAnnotator() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ImmoniumIonAnnotator
-
Empty default constructor
- ImmoniumIonAnnotator(char[]) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ImmoniumIonAnnotator
-
Constructor.
- ImmoniumIonAnnotator(char[], boolean, boolean) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ImmoniumIonAnnotator
-
Constructor.
- implementations - Static variable in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature
-
Array of the implemented features.
- implementedForwardIons - Static variable in class com.compomics.util.parameters.identification.search.SearchParameters
-
Convenience array for forward ion type selection.
- implementedRewindIons - Static variable in class com.compomics.util.parameters.identification.search.SearchParameters
-
Convenience array for rewind ion type selection.
- importFromFile(File, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
-
Reads go mappings from a BioMart file.
- importMaps(GeneMapping) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Imports the gene maps from a gene Mapping.
- importMethods(File) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
-
Imports the methods from an XML file.
- iMSLevel - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The ms level of the current spectrum.
- inBackend(long) - Method in class com.compomics.util.db.object.ObjectsDB
-
Indicates whether an object is loaded in the backend.
- inCache(long) - Method in class com.compomics.util.db.object.ObjectsCache
-
Check if key in cache.
- inCache(long) - Method in class com.compomics.util.db.object.ObjectsDB
-
Indicates whether an object is loaded in cache.
- include(RowFilter.Entry<? extends DefaultTableModel, ? extends Integer>) - Method in class com.compomics.util.gui.XYPlottingDialog.SelectedValuesTableFilter
-
- increaseDepth() - Method in class com.compomics.util.io.export.ExportWriter
-
Notifies the writer that data of a higher hierarchical depth will be
written, e.g.
- increaseDepth() - Method in class com.compomics.util.io.export.writers.ExcelWriter
-
- increaseDepth() - Method in class com.compomics.util.io.export.writers.TextWriter
-
- increaseIndent() - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
-
Increases the indent counter.
- increaseMissedCleavages() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Increases the number of missed cleavages.
- increaseNX() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Increases the number of Xs already considered in this draft.
- increasePrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- increasePrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- increasePrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- increasePrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- increasePrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- increasePrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- increasePrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- increasePrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- increasePrimaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
-
Increase the primary progress counter by one "counter".
- increasePrimaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
-
Increase the primary progress counter by the given increment.
- increaseSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- increaseSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- increaseSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Increase the secondary progress bar value by one "counter".
- increaseSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- increaseSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- increaseSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- increaseSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- increaseSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- increaseSecondaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
-
Increase the secondary progress counter by one "counter".
- increaseSecondaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
-
Increase the secondary progress counter by the given value.
- increasing - Variable in enum com.compomics.util.experiment.identification.psm_scoring.PsmScore
-
Indicates whether the score increases with the quality of the match.
- inDB - Variable in class com.compomics.util.db.object.ObjectsCache.ObjectsCacheElement
-
The database state.
- inDB(long) - Method in class com.compomics.util.db.object.ObjectsDB
-
Indicates whether an object is in the cache or the database.
- indentCounter - Variable in class com.compomics.util.io.export.xml.SimpleXmlWriter
-
Integer keeping track of the number of indents to include at the
beginning of each line.
- index - Variable in enum com.compomics.util.experiment.biology.ions.Ion.IonType
-
The index of the type.
- index - Variable in enum com.compomics.util.experiment.biology.modifications.ModificationType
-
The index of the type, must be the index in the values array.
- index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureAbsolute
-
The index of this ms2pip feature.
- index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureRelative
-
The index of this ms2pip feature.
- index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureAbsolute
-
The index of this ms2pip feature.
- index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureRelative
-
The index of this ms2pip feature.
- index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
-
The index of this ms2pip feature.
- index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonAminoAcidFeature
-
The index of this ms2pip feature.
- index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonFeature
-
The index of this ms2pip feature.
- index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonAminoAcidFeature
-
The index of this ms2pip feature.
- index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonFeature
-
The index of this ms2pip feature.
- index - Variable in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature.Property
-
The index of the option.
- index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
-
The index of this ms2pip feature.
- index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideAminoAcidFeature
-
The index of this ms2pip feature.
- index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
-
The index of this ms2pip feature.
- index - Variable in enum com.compomics.util.experiment.identification.peptide_fragmentation.PeptideFragmentationModel
-
The index of the option.
- index - Variable in enum com.compomics.util.experiment.identification.psm_scoring.PsmScore
-
The index of the score of interest.
- index - Variable in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
-
The index of the format.
- index - Variable in enum com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserOutputFormat
-
The index of the format.
- index - Variable in enum com.compomics.util.io.export.ExportFormat
-
The index of the format.
- index - Variable in enum com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters.MatchingType
-
The index of the type as integer.
- index - Variable in enum com.compomics.util.parameters.identification.search.DigestionParameters.CleavageParameter
-
The index.
- index - Variable in enum com.compomics.util.parameters.identification.search.DigestionParameters.Specificity
-
The index.
- index - Variable in enum com.compomics.util.parameters.peptide_shaker.ProjectType
-
The index of the option.
- IndexedMgfReader - Class in com.compomics.util.experiment.io.mass_spectrometry.mgf
-
Reader for mgf files based on random access.
- IndexedMgfReader() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mgf.IndexedMgfReader
-
General constructor for an mgf reader.
- indexes - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MassIndexMap
-
- indexStringLengths - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
Length of the indexed string (all concatenated protein sequences).
- inDoubleRange(String, String, double, double) - Static method in class com.compomics.software.cli.CommandParameter
-
Returns true if the input is a double value inside the given range.
- inferParameters(String, WaitingHandler) - Static method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
-
Infers the parameters used to parse the file.
- inIntegerRange(String, String, int, int) - Static method in class com.compomics.software.cli.CommandParameter
-
Returns true if the input is an integer value inside the given range.
- init(String, String, String, String, String, String, String) - Method in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
-
Initializes the writing of the file.
- init() - Method in class com.compomics.util.io.json.JsonMarshaller
-
Initializes the marshaller with (custom) type adapters.
- init() - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
-
- initialize(String) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
Initializes the factory.
- initiate(String[]) - Method in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
-
Initiates the IdentificationParametersCli.
- initiate(String) - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
-
Initiates the factory using the files of the static fields.
- initiateSorter() - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
-
Initiates the sorter to the current order of the table.
- insert(int, AminoAcidSequence) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
Inserts another sequence in this sequence.
- insert(int, String) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
Inserts another sequence in this sequence.
- Insertion - Class in com.compomics.util.experiment.biology.variants.amino_acids
-
Class representing an amino acid insertion.
- Insertion() - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Insertion
-
Empty default constructor
- Insertion(char) - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Insertion
-
Constructor.
- insertObject(long, Object) - Method in class com.compomics.util.db.object.ObjectsDB
-
Stores an object in the desired table.
- insertObjects(HashMap<Long, Object>, WaitingHandler, boolean) - Method in class com.compomics.util.db.object.ObjectsDB
-
Inserts a set of objects in the given table.
- installEscapeCloseOperation(JDialog) - Static method in class com.compomics.util.gui.GuiUtilities
-
Close a dialog using the escape key.
- InstanceVariables - Class in com.compomics.util.db.components
-
This class represents the instance variables for a generated DBAccessor.
- InstanceVariables() - Constructor for class com.compomics.util.db.components.InstanceVariables
-
Empty default constructor
- InstanceVariables(DBMetaData) - Constructor for class com.compomics.util.db.components.InstanceVariables
-
This constructor will create all the code for the instance variables from the given
DBMetaData.
- Instrument - Class in com.compomics.util.pride.prideobjects
-
An object for storing Instrument details.
- Instrument() - Constructor for class com.compomics.util.pride.prideobjects.Instrument
-
Empty default constructor
- Instrument(String, CvTerm, CvTerm, ArrayList<CvTerm>) - Constructor for class com.compomics.util.pride.prideobjects.Instrument
-
Create a new Instrument object.
- IntDecoder - Class in com.compomics.util.experiment.io.mass_spectrometry.mzml
-
Decodes ints from the half bytes in bytes.
- IntDecoder(byte[], int) - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mzml.IntDecoder
-
Constructor.
- intensity - Variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
-
The intensity of the peak.
- intensity - Variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
-
The measured intensity of the precursor.
- intensity - Variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
-
The array of the intensities of the peaks.
- intensityArray - Variable in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
The mz array of the spectrum.
- IntensityHistogram - Class in com.compomics.util.gui.spectrum
-
Creates an IntensityHistogram plot.
- IntensityHistogram() - Constructor for class com.compomics.util.gui.spectrum.IntensityHistogram
-
Empty default constructor
- IntensityHistogram(IonMatch[], Spectrum, double) - Constructor for class com.compomics.util.gui.spectrum.IntensityHistogram
-
Creates an IntensityHistogram plot
- intensityLimit - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
The intensity limit to use.
- intensityLimit - Variable in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
The intensity limit used for the index.
- INTERACTIVE_STATUS - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This status indicates that no annotation will be displayed, but the user
will have a fully functional interface (point clicking, selecting,
sequencing etc.)
- InterfaceAdapter<T> - Class in com.compomics.util.io.json.adapter
-
A generic adapter to parse used interfaces in a class.
- InterfaceAdapter() - Constructor for class com.compomics.util.io.json.adapter.InterfaceAdapter
-
Empty default constructor.
- interrupt() - Method in class com.compomics.util.sun.SwingWorker
-
A new method that interrupts the worker thread.
- Iodine - Class in com.compomics.util.experiment.biology.atoms.impl
-
Iodine.
- Iodine() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Iodine
-
Constructor.
- iodoTMT_126 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT 126.
- iodoTMT_126_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT 126 with ETD fragmentation.
- iodoTMT_127 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT 127.
- iodoTMT_127_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT 127 with ETD fragmentation.
- iodoTMT_128 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT 128.
- iodoTMT_128_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT 128 with ETD fragmentation.
- iodoTMT_129 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT 128.
- iodoTMT_129_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT 128 with ETD fragmentation.
- iodoTMT_130 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT 130.
- iodoTMT_130_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT 130 with ETD fragmentation.
- iodoTMT_131 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT 131.
- iodoTMT_131_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT 131 with ETD fragmentation.
- iodoTMT_zero - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT zero.
- iodoTMT_zero_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iodoTMT zero with ETD fragmentation.
- Ion - Class in com.compomics.util.experiment.biology.ions
-
This class models an ion.
- Ion() - Constructor for class com.compomics.util.experiment.biology.ions.Ion
-
Empty default constructor
- ion - Variable in class com.compomics.util.experiment.identification.matches.IonMatch
-
The matching ion.
- Ion.IonType - Enum in com.compomics.util.experiment.biology.ions
-
An enumerator of the supported ion types.
- IonFactory - Class in com.compomics.util.experiment.biology.ions
-
This factory generates the expected ions from a peptide.
- IonFeature - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic
-
Feature based on a property of an ion.
- IonFeature() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature
-
Empty default constructor
- IonFeature.Property - Enum in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic
-
Enum for the possible features.
- IonLabelColorTableModel - Class in com.compomics.util.gui.spectrum
-
A table model to use for the ion label annotation colors.
- IonLabelColorTableModel(HashMap<Ion.IonType, HashSet<Integer>>, HashSet<String>) - Constructor for class com.compomics.util.gui.spectrum.IonLabelColorTableModel
-
Constructor which sets a new table.
- IonLabelColorTableModel() - Constructor for class com.compomics.util.gui.spectrum.IonLabelColorTableModel
-
Constructor which sets a new empty table.
- IonMatch - Class in com.compomics.util.experiment.identification.matches
-
This class represents the assignment of a peak to a theoretical ion.
- IonMatch() - Constructor for class com.compomics.util.experiment.identification.matches.IonMatch
-
Empty default constructor
- IonMatch(double, double, Ion, int) - Constructor for class com.compomics.util.experiment.identification.matches.IonMatch
-
Constructor for an ion match.
- IonMatch.MzErrorType - Enum in com.compomics.util.experiment.identification.matches
-
Enum of the supported error types.
- IonMatchKeysCache - Class in com.compomics.util.experiment.identification.spectrum_annotation
-
Cache for the keys of the ions.
- IonMatchKeysCache() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.IonMatchKeysCache
-
Constructor.
- ionMatchKeysCache - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
The cache to use for the ion match keys.
- IoUtil - Class in com.compomics.util.io
-
Utils for I/O and file handling.
- IoUtil() - Constructor for class com.compomics.util.io.IoUtil
-
- iPointDetectionTolerance - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The deviation (both left and right) allowed for point highlighting
detection.
- iPointSize - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Size for the point on a polygon.
- iPosition - Variable in class com.compomics.util.protein.Enzyme
-
This integer holds the position marker for the cleavage direction for
this Enzyme.
- iPrecursorCharge - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This String holds the charge for the precursor.
- iPrecursorChargeMirorredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This String holds the charge for the precursor for the mirrored spectrum.
- iPrecursorMZ - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This variable holds the precursor M/Z.
- iPrecursorMZMirroredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This variable holds the precursor M/Z for the mirrored spectrum.
- iReport - Variable in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
The report to append.
- iRestrict - Variable in class com.compomics.util.protein.Enzyme
-
This char[] holds the residues that will restrict cleavage when present
after a cleavable residue.
- iRestrictors - Variable in class com.compomics.util.protein.Enzyme
-
Lookup cache for the restricting residues.
- Iron - Class in com.compomics.util.experiment.biology.atoms.impl
-
The iron atom.
- Iron() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Iron
-
Constructor.
- is64BitJava() - Static method in class com.compomics.software.CompomicsWrapper
-
Returns if the Java version used is 64 bit.
- isAa(char) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns a boolean indicating whether the given character is a supported
amino acid.
- isAa(int) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns a boolean indicating whether the given character is a supported
amino acid.
- isAboveXAxis() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Returns true if the reference area is added above the x-axis, false adds
the reference are below the x-axis
- isAccounted(NeutralLossesMap, NeutralLoss, Ion) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Returns a boolean indicating whether the neutral loss should be accounted
for.
- isActive() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Indicates whether the filter is active.
- isAdditionalOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Returns if additional output is to be included.
- isAdjustPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Returns if the precursor mass is to be adjusted.
- isAdvanced() - Method in interface com.compomics.util.io.export.ExportFeature
-
Indicates whether a feature is for advanced user only.
- isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsAnnotationFeature
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
-
- isAdvanced() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
-
- isAnnotateHighestPeak() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns true if the most intense of possible peaks to annotate is to be
selected, false if the most accurate is to be selected.
- isArtifact() - Method in interface com.compomics.util.interfaces.Modification
-
This method indicates whether this modification is considered an artifact.
- isArtifact() - Method in class com.compomics.util.protein.ModificationImplementation
-
This method indicates whether this modification is considered an artifact.
- isArtifact() - Method in class com.compomics.util.protein.ModificationTemplate
-
This method indicates whether this modification is considered an artifact.
- isAutomaticAnnotation() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns whether the annotation settings should be automatically inferred.
- isAutoUpdate() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Indicates whether the tools should use the auto update function.
- isBooleanInput(String, String) - Static method in class com.compomics.software.cli.CommandParameter
-
Returns true of the input is 0 or 1.
- isCacheEmpty() - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
-
Indicates whether all caches are empty.
- isCanceled() - Method in class com.compomics.software.settings.gui.PathParametersDialog
-
Indicates whether the action was canceled by the user.
- isCanceled() - Method in class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui.ThermoRawFileParserParametersDialog
-
Indicates whether the editing was canceled by the user.
- isCanceled() - Method in class com.compomics.util.gui.AminoAcidPatternDialog
-
indicates whether the changes have been canceled
- isCanceled() - Method in class com.compomics.util.gui.atoms.AtomChainDialog
-
Indicates whether the edition has been canceled by the user.
- isCanceled() - Method in class com.compomics.util.gui.enzymes.NewEnzymeDialog
-
Indicates whether the dialog was canceled by the user.
- isCanceled() - Method in class com.compomics.util.gui.ExportFormatSelectionDialog
-
Returns true of the user canceled the dialog.
- isCanceled() - Method in class com.compomics.util.gui.file_handling.FileSelectionDialog
-
Indicates whether the user canceled the dialog.
- isCanceled() - Method in class com.compomics.util.gui.filtering.FilterDialog
-
Indicates whether the editing was canceled by the user.
- isCanceled() - Method in class com.compomics.util.gui.genes.SpeciesDialog
-
Deprecated.
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.modification.ModificationDialog
-
Indicates whether the edition was canceled by the user.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.AnnotationParametersDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.BackgroundSpeciesDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.FractionParametersDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.GeneParametersDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.MatchesImportParametersDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.ModificationLocalizationParametersDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.PeptideVariantsParametersDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.ProteinInferenceParametersDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.PsmScoringParametersDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.SequenceMatchingParametersDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.ValidationParametersDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.ValidationQCParametersDialog
-
Indicates whether the preference edition was canceled by the user.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersNameDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog
-
Indicates whether the cancel button was pressed by the user.
- isCanceled() - Method in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
-
Returns a boolean indicating whether the database selection was canceled
by the user.
- isCanceled() - Method in class com.compomics.util.gui.parameters.proteowizard.MsConvertParametersDialog
-
Indicates whether the editing was canceled by the user.
- isCanceled() - Method in class com.compomics.util.gui.parameters.tools.ProcessingParametersDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.protein.FastaParametersDialog
-
Indicates whether the user canceled the editing.
- isCanceled() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser
-
Returns a boolean indicating whether the selection was canceled by the
user.
- isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.AndromedaParametersDialog
-
- isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.CometParametersDialog
-
- isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.DirecTagParametersDialog
-
- isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MetaMorpheusParametersDialog
-
- isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsAmandaParametersDialog
-
- isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsgfParametersDialog
-
- isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MyriMatchParametersDialog
-
- isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.NovorParametersDialog
-
- isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.OmssaParametersDialog
-
- isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.PepNovoParametersDialog
-
- isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.PNovoParametersDialog
-
- isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.TideParametersDialog
-
- isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
-
- isCancelled() - Method in interface com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog
-
Indicates whether the user canceled the editing.
- isCellEditable(int, int) - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
-
- isCellEditable(int, int) - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
-
- isCellEditable(int, int) - Method in class com.compomics.util.sun.TableMap
-
- isChanged() - Method in interface com.compomics.util.db.interfaces.DBElement
-
This method signals whether the DBElement has changes that should be persisted.
- isCheckSpectrumCharges() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Returns whether the spectra are to be checked for missing charges.
- isCleavageSite(String, String) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
-
Returns a boolean indicating whether the given amino acids represent a
cleavage site.
- isCleavageSite(char, char) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
-
Returns a boolean indicating whether the given amino acids represent a
cleavage site.
- isCleavageSiteNoCombination(Character, Character) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
-
Returns a boolean indicating whether the given amino acids represent a
cleavage site.
- isCleaveNterMethionine() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Indicates whether N-terminal methionines should be cleaved.
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Indicates whether the amino acid object refers to a combination of amino
acids like B, J, Z or X.
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
-
- iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
-
- isConfidentModificationSite(int, String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
-
Indicates whether a site is already registered as confident modification
site.
- isConnectionActive() - Static method in class com.compomics.util.db.object.ObjectsDB
-
Indicates whether the connection to the DB is active.
- isConnectionActive() - Method in class com.compomics.util.experiment.identification.Identification
-
Indicates whether the connection to the DB is active.
- isCorrectPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Returns a boolean indicating whether the precursor mass shall be
corrected (TagDB setting).
- isCTerm() - Method in enum com.compomics.util.experiment.biology.modifications.ModificationType
-
Returns a boolean indicating whether the modification type targets the
C-terminus of a protein or of a peptide.
- isCterm(Peptide, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Indicates whether a peptide is at the C-terminus of a protein.
- isCterm(Peptide, String, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Indicates whether a peptide is at the C-terminus of a given protein.
- isDbSize() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Indicates whether the database size should be checked.
- isDecoy() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Returns a boolean indicating whether the given match is decoy.
- isDecoy(Peptide, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns a boolean indicating whether the peptide matches a decoy
sequence.
- isDecoy(String, FastaParameters) - Static method in class com.compomics.util.experiment.identification.utils.ProteinUtils
-
Returns a boolean indicating whether the given accession corresponds to a
decoy sequence according to the given FASTA parameters.
- isDecoy(String, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.ProteinUtils
-
Returns a boolean indicating whether the given accession corresponds to a
decoy sequence according to the given sequence provider.
- isDecoySuffix() - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
-
Returns a boolean indicating whether the decoy flag is a suffix or a
prefix.
- isDeleted() - Method in interface com.compomics.util.db.interfaces.DBElement
-
This method signals whether the DBElement has been deleted in the persistent
store.
- isDependentLosses() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns whether neutral losses should be sequence dependent.
- isDetermineChargePlusOneAlgorithmically() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Indicates whether charge plus one should be determined algorithmically.
- isDialogCanceled() - Method in class com.compomics.software.dialogs.PeptideShakerSetupDialog
-
Returns true of the dialog was canceled by the user.
- isDialogCanceled() - Method in class com.compomics.software.dialogs.ProteoWizardSetupDialog
-
Returns true of the dialog was canceled by the user.
- isDialogCanceled() - Method in class com.compomics.software.dialogs.ReporterSetupDialog
-
Returns true of the dialog was canceled by the user.
- isDialogCanceled() - Method in class com.compomics.software.dialogs.SearchGuiSetupDialog
-
Returns true of the dialog was canceled by the user.
- isDouble(String, String) - Static method in class com.compomics.software.cli.CommandParameter
-
Returns true if the argument can be parsed as a double value.
- isDuplicateSpectra() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Indicates whether to use duplicate spectra option.
- isEditable() - Method in class com.compomics.util.io.export.ExportScheme
-
Indicates whether the scheme is editable.
- isElement(String) - Method in class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
-
Method that checks if a given string is an element we can calculate an isotopic distribution for
- isElement(String) - Method in class com.compomics.util.gui.spectrum.IsotopicDistributionPanel
-
Method that checks if a given string is an element we can calculate an isotopic distribution for
- isEmpiricalCorrection() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Indicates whether empirical correction should be used.
- isEmpty() - Method in class com.compomics.util.db.object.ObjectsCache
-
Indicates whether the cache is empty.
- isEmpty() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
-
Returns a boolean indicating if the mapping is empty.
- isEnding(AminoAcidPattern, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Indicates whether the given amino acid sequence ends with the pattern.
- isEnding(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Indicates whether the given amino acid sequence ends with the pattern.
- isEnzymatic(Peptide, String, String, ArrayList<Enzyme>) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns a boolean indicating whether the peptide is enzymatic using one
of the given enzymes.
- isEnzymatic(Peptide, SequenceProvider, ArrayList<Enzyme>) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns a boolean indicating whether the peptide is enzymatic in at least
one protein using one of the given enzymes.
- isEnzymaticProduct(String, int, int) - Method in class com.compomics.util.protein.DualEnzyme
-
This method reports on the possibility that the presented subsequence
(represented by the start and end location in the parent) is the result
of enzymatic activity.
- isEnzymaticProduct(String, String) - Method in class com.compomics.util.protein.Enzyme
-
This method reports on the possibility that the presented subsequence is
the result of enzymatic activity.
- isEnzymaticProduct(String, int, int) - Method in class com.compomics.util.protein.Enzyme
-
This method reports on the possibility that the presented subsequence
(represented by the start and end location in the parent) is the result
of enzymatic activity.
- isEnzymaticProduct(String, String) - Method in class com.compomics.util.protein.RegExEnzyme
-
- isEnzymaticProduct(String, int, int) - Method in class com.compomics.util.protein.RegExEnzyme
-
- isEnzymaticTagsOnly() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Returns true if tags should only be mapped to enzymatic peptides.
- isEqualIL() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Indicates whether I and L should be considered indistinguishable.
- isEstimateCharge() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Indicates whether the precursor charge shall be estimated for OMSSA.
- isEstimateCharge() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Indicates whether the precursor charge shall be estimated for PepNovo.
- isFiltered() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Indicates whether the protein list is filtered.
- isFirstDecoy() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Indicates whether the number of hits before the first decoy should be
checked.
- isFixed() - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
-
Returns a boolean indicating whether the neutral loss is fixed or not.
- isForward(int) - Static method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
Indicates whether the given subtype refers to a forward or a rewind ion.
- isFragmentAll() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Indicates whether the fragment all option should be used.
- isFragmentIonPpm() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Indicates whether the fragment ion accuracy is in ppm.
- isFragmentIonPpm() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Indicates whether the fragment ion accuracy is in ppm.
- isGzip() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Indicates whether identification files should be gzipped.
- isHeader() - Method in class com.compomics.util.io.export.ExportScheme
-
Indicates whether column header shall be used.
- isHigherCharge() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Indicates whether higher charge should be considered.
- isIncludeAmmonia() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns a boolean indicating whether ammonia losses should be accounted
for.
- isIncludeDateInOutputName() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Indicates whether the date should be included in the SearchGUI output
name.
- isIncludeDecoy() - Method in class com.compomics.util.io.export.ExportScheme
-
Indicates whether decoy hits should be included.
- isIncludeSectionTitles() - Method in class com.compomics.util.io.export.ExportScheme
-
Indicates whether section titles shall be used.
- isIncludeWater() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Returns a boolean indicating whether water losses should be accounted
for.
- isIndeterminate() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
-
This method signals whether the progressdialog is currently in
indeterminate ('true') or determinate ('false') mode.
- isIndexes() - Method in class com.compomics.util.io.export.ExportScheme
-
Indicates whether lines shall be indexed.
- isInList(String, String, String[]) - Static method in class com.compomics.software.cli.CommandParameter
-
Returns true of the input is in the provided list.
- isInList(String, String, List<String>) - Static method in class com.compomics.software.cli.CommandParameter
-
Returns true of the input is in the provided list.
- isInteger(String, String) - Static method in class com.compomics.software.cli.CommandParameter
-
Returns true if the argument can be parsed as an integer value.
- isIsPpm() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Indicates whether the mass tolerance is in ppm (true) or Dalton (false).
- isList() - Method in class com.compomics.cli.enzymes.EnzymesCLIInputBean
-
Returns a boolean indicating whether the list of implemented enzymes
should be printed.
- isList() - Method in class com.compomics.cli.modifications.ModificationsCLIInputBean
-
Returns a boolean indicating whether the list of implemented enzymes
should be printed.
- isListEnzymes() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
-
Indicates whether the enzymes should be printed.
- isListMods() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
-
Indicates whether the modifications should be printed.
- isLowMemoryMode() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
- isMemoryMappedSequenceLibraries() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Indicates whether sequence libraries should be mapped in memory.
- isMiniature() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns true if the graphics panel is to be drawn in a miniature form.
- isModificationRefinement() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Returns whether the protein mapping should be refined based on terminal and pattern modifications.
- isMonoIsotopic() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns whether monoisotopic mass values shall be used (in contrast to
average mass values).
- isNeutralLossesAuto() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Indicates whether neutral losses should be automatically selected.
- isNTerm() - Method in enum com.compomics.util.experiment.biology.modifications.ModificationType
-
Returns a boolean indicating whether the modification type targets the
N-terminus of a protein or of a peptide.
- isNterm(Peptide, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Indicates whether a peptide is at the N-terminus of a protein.
- isNterm(Peptide, String, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Indicates whether a peptide is at the N-terminus of a given protein.
- isNumber() - Method in interface com.compomics.util.experiment.filtering.FilterItem
-
Indicates whether the item expects a number as threshold.
- isNumber() - Method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
-
- isNumber() - Method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
-
- isNumber() - Method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
-
- isNumber() - Method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
-
- Isoleucine - Class in com.compomics.util.experiment.biology.aminoacids.impl
-
Isoleucine.
- Isoleucine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
-
Constructor.
- ISOLEUCINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
Isoleucine immonium ion.
- isOne(int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
-
Returns true if the value is equal to one.
- isOneInt(int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
-
Returns true if the value is equal to one.
- IsotopeDistributionGui - Class in com.compomics.util.gui.isotopic_calculator
-
This class is a GUI that visualizes the isotopic calculator.
- IsotopeDistributionGui(boolean) - Constructor for class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
-
The constructor
- isotopeMap - Variable in class com.compomics.util.experiment.biology.atoms.Atom
-
Map of the isotope masses relative to the monoisotopic peak (+1 for
carbon 13).
- IsotopicDistribution - Class in com.compomics.util.general
-
This class calculates the isotopic distribution based on a molecular formula.
- IsotopicDistribution(MolecularFormula) - Constructor for class com.compomics.util.general.IsotopicDistribution
-
Constructor
- IsotopicDistribution(MolecularFormula, int) - Constructor for class com.compomics.util.general.IsotopicDistribution
-
Constructor
- IsotopicDistribution(int, int, int, int, int) - Constructor for class com.compomics.util.general.IsotopicDistribution
-
This will calculate the isotopic distribution pattern for the given elements.
- IsotopicDistributionPanel - Class in com.compomics.util.gui.spectrum
-
This class provides a JPanel that can display a peptide isotopic distribution.
- IsotopicDistributionPanel() - Constructor for class com.compomics.util.gui.spectrum.IsotopicDistributionPanel
-
Empty default constructor
- IsotopicDistributionPanel(String, Integer, boolean, int) - Constructor for class com.compomics.util.gui.spectrum.IsotopicDistributionPanel
-
This constructor creates an IsotopicDistributionPanel based on the passed parameters.
- IsotopicDistributionSpectrum - Class in com.compomics.util.general
-
This class is an implementation of the SpectrumFile specific for the isotopic distribution
Created by IntelliJ IDEA.
- IsotopicDistributionSpectrum() - Constructor for class com.compomics.util.general.IsotopicDistributionSpectrum
-
- IsotopicElement - Class in com.compomics.util.general
-
This class represents the isotopically different element with the occurrence
and the dalton difference between this and the natural variant.
- isOutputHistograms() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Indicates whether histograms should be written in the result file.
- isOutputProteins() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Indicates whether the protein bloc should be included in the export.
- isOutputSequences() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns whether the protein sequences should be included in the protein
block of the export.
- isOutputSpectra() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Indicate whether the spectra should be exported in the result file.
- isPeackPicking() - Method in class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserParameters
-
Returns true if peak picking is to be performed.
- isPeakPicked() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns true if the indexed file seems to contain only peak picked
spectra.
- iSpecPanelListeners - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The list of SpectrumPanelListeners.
- isPerformDeisotoping() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Returns whether deisotoping is to be performed.
- isPerFraction() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
-
Returns true if the feature is to be exported per fraction.
- isPositiveDouble(String, String, boolean) - Static method in class com.compomics.software.cli.CommandParameter
-
Returns true if the argument can be parsed as a positive double value.
- isPositiveInteger(String, String, boolean) - Static method in class com.compomics.software.cli.CommandParameter
-
Returns true if the argument can be parsed as a positive integer value.
- isPotentialModificationsForFullRefinment() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Indicates whether the refinement modifications should be used for the
full refinement.
- isPpm - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Boolean indicating whether the tolerance is in ppm (true) or in Dalton
(false).
- isPrecursorAccuracyTypePpm() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Returns true if the current precursor accuracy type is ppm.
- isPrecursorChargesMissing() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Returns true if the at least one spectrum is missing the precursor
charge.
- isProbabilisticScoreCalculation() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Indicates whether a probabilistic modification score is required.
- isProbabilisticScoreNeutralLosses() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Indicates whether the neutral losses shall be taken into account for
spectrum annotation when calculating the probabilistic score.
- isProgressBarValid() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
-
This method reports on whether this instance can be controlled in a
multithreaded environment.
- isProteinQuickAcetyl() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Indicates whether the protein quick acetylation option should be
triggered.
- isQcPassed(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Indicates whether the given QC check was passed.
- isQuickPyrolidone() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns whether the quick pyrolidone option should be triggered.
- isRefine() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns whether the second pass search should be triggered.
- isRefinePointMutations() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Indicates whether point mutations should be looked for during the
refinement process.
- isRefineSemi() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Indicates whether the semi enzymatic option of the second pass search
should be triggered.
- isRefineSnaps() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether snAPs should be used during the refinement process.
- isRefineSpectrumSynthesis() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Indicates whether the spectrum synthesis option should be used during the
refinement process.
- isRefineUnanticipatedCleavages() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns whether the unanticipated cleavages option should be used during
the refinement process.
- isRemovePrecursor() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Indicates whether the precursor shall be removed for OMSSA.
- isReport() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- isReport() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- isReport() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- isReport() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- isReport() - Method in interface com.compomics.util.waiting.WaitingHandler
-
Indicates whether this waiting handler supports reports.
- isRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- isRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- isRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- isRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- isRunCanceled() - Method in interface com.compomics.util.waiting.WaitingHandler
-
Returns true if the run is canceled.
- isRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- isRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- isRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- isRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- isRunFinished() - Method in interface com.compomics.util.waiting.WaitingHandler
-
Returns true if the process is finished.
- isRunning() - Method in class com.compomics.util.io.file.FolderMonitor
-
This method can be consulted to find out whether the monitor is running.
- isSameAs(AminoAcidPattern, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Indicates whether another AminoAcidPattern targets the same pattern.
- isSameAs(AminoAcidSequence, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
Indicates whether another sequence has a matching sequence.
- isSameAs(TagComponent, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
- isSameAs(AtomImpl) - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
-
Indicates whether another atom is the same as this one.
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
-
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
-
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
-
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
-
- isSameAs(RelatedIon) - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
-
Compares the current related ion with another one based on their
composition.
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
-
- isSameAs(ReporterIon) - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Compares the current reporter ion with another one based on their masses.
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
-
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns a boolean indicating whether the ion is the same as another ion.
- isSameAs(NeutralLoss) - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
-
Method indicating whether another neutral loss is the same as the one
considered.
- isSameAs(Modification) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns true if the modification is the same as another one.
- isSameAs(AaSubstitutionMatrix) - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
-
Indicates whether the given AaSubstitutionMatrix is the same as this one.
- isSameAs(Filter) - Method in interface com.compomics.util.experiment.filtering.Filter
-
Indicates whether another filter is the same as the current filter.
- isSameAs(TagComponent, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.MassGap
-
- isSameAs(Tag, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Indicates whether this tag is the same as another tag.
- isSameAs(TagComponent, SequenceMatchingParameters) - Method in interface com.compomics.util.experiment.identification.amino_acid_tags.TagComponent
-
Indicates whether another component is the same as the component of
interest.
- isSameAs(Filter) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
- isSameAs(PeptideAssumptionFilter) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Indicates whether this filter is the same as another one.
- isSameAs(ModificationMatch) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Indicates whether this modification match is the same of another one.
- isSameAs(AnnotationParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns a boolean indicating whether the given annotation settings are
the same as these ones.
- isSameAs(FastaParameters) - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
-
Returns a boolean indicating whether the parsing parameters are the same
as the given parameters.
- isSameAs(Peak) - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
-
Returns true if the peak has the same mz and intensity.
- isSameAs(Precursor) - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
-
Returns a boolean indicating whether the precursor is identical to the
other precursor.
- isSameAs(Spectrum) - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
-
Returns a boolean indicating whether the spectrum is identical to the
other spectrum.
- isSameAs(UnitOfMeasurement) - Method in class com.compomics.util.experiment.units.UnitOfMeasurement
-
Indicates whether the given unit of measurement is the same as another.
- isSameAs(FractionParameters) - Method in class com.compomics.util.parameters.identification.advanced.FractionParameters
-
Returns a boolean indicating whether other given settings are the same as
these.
- isSameAs(PeptideVariantsParameters) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Indicates whether another peptide variant preferences is the same as this
one.
- isSameAs(SequenceMatchingParameters) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Indicates whether another sequence matching preferences is the same as
this one.
- isSameAs(ValidationQcParameters) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Returns true if the two ValidationQCPreferences are the same.
- isSameAs(DigestionParameters) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
-
Returns a boolean indicating whether these digestion parameters are the
same as the given other parameters.
- isSameAs(SpectrumCountingParameters) - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
-
Compares two spectrum counting preferences.
- isSameAtomicComposition(Modification) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns true if the atomic composition of the modification is the same as
another one.
- isSameCompositionAs(AtomChain) - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
-
Indicates whether two atom chains are of the same composition by
comparing their string and type.
- isSameModificationStatus(Peptide) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Indicates whether another peptide has the same variable modifications as
this peptide.
- isSamePattern(Modification) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Returns true if the targeted pattern of the modification is the same as
another one.
- isSameSequence(Peptide, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Returns a boolean indicating whether another peptide has the same
sequence as the given peptide
- isSameSequenceAndModificationStatus(Peptide, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Indicates whether another peptide has the same sequence and modification
status without accounting for modification localization.
- isSameSequenceAndModificationStatusAs(AminoAcidSequence, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
Indicates whether another sequence targets the same sequence without
accounting for PTM localization.
- isSameSequenceAndModificationStatusAs(TagComponent, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
- isSameSequenceAndModificationStatusAs(TagComponent, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.MassGap
-
- isSameSequenceAndModificationStatusAs(Tag, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Indicates whether this tag is the same as another tag without accounting
for modification localization.
- isSameSequenceAndModificationStatusAs(TagComponent, SequenceMatchingParameters) - Method in interface com.compomics.util.experiment.identification.amino_acid_tags.TagComponent
-
Indicates whether another component is the same as the component of
interest.
- isScalePrecursor() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Indicates whether the precursor shall be scaled for OMSSA.
- isScoringNeeded(int) - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
-
Indicates whether a score computation is needed for the given advocate.
- isScoringNeeded(ArrayList<Integer>) - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
-
Indicates whether a score computation is needed for the given advocates.
- isScrolling - Variable in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
-
When true this indicates that the user is currently scrolling in the
table and that the table should not update.
- isScrolling() - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
-
Indicates whether the table is currently being scrolled.
- isSearchForwardFragmentFirst() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Indicates whether forward ions (b1) should be searched first.
- isSearchPositiveIons() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Indicates whether positive ions are searched.
- isSearchRewindFragments() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Indicates whether C-terminal fragments should be searched.
- isSelfUpdating() - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
-
Indicates whether the table is in self update mode.
- isSequenceMatchingType(String, String) - Static method in class com.compomics.software.cli.CommandParameter
-
Returns true of the input is in the provided list.
- isSquare() - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- isStandAlone() - Method in class com.compomics.util.gui.FlamableJFrame
-
Returns true if frame is stand alone.
- isStandardSearch() - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Indicates whether a modification can be searched with standard search
engines, i.e., true if it targets a single amino acid position, false if
it targets a complex pattern.
- isStarting(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Indicates whether the given amino acid sequence starts with the pattern.
- isStarting(AminoAcidPattern, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Indicates whether the given amino acid sequence starts with the pattern.
- isStpBias() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Returns whether the stP bias should be triggered.
- isSubscriptAnnotationNumbers() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns true if the numbers in the peak annotations are to be
subscripted.
- issueCommand(String) - Method in class com.compomics.util.io.ftp.FTP
-
This method allows the caller to issue a command to the server.
- issueCommandCheck(String) - Method in class com.compomics.util.io.ftp.FTP
-
This method will issue the specified command and throw an exception
whenever the reply is not equal to success! It basically converts an
FTP error code into an FtpProtocolException.
- isTargetDecoy() - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
-
Returns a boolean indicating whether the FASTA file should be processed
as target-decoy or only target.
- isTargetDecoyNeededForPsmScoring(ArrayList<Integer>) - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
-
Indicates whether target decoy databases are needed for PSM scoring.
- isTargeted(Character, int, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Indicates whether the given amino acid at the given index of the pattern
is targeted without accounting for mutations.
- iStartXLoc - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
When the mouse is dragged, this represents the X-coordinate of the
starting location.
- iStartYLoc - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
When the mouse is dragged, this represents the Y-coordinate of the
starting location.
- isToBeDeleted() - Method in interface com.compomics.util.db.interfaces.DBElement
-
This method signals whether the DBElement is marked for deletion.
- iStoredSequence - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The Vector that holds a set of stored points from a previously
established list.
- iStoredSequenceDatasetIndices - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The Vector that holds the dataset indices of stored points from a
previously established list.
- iStoredSequenceDatasetIndicesMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The Vector that holds the dataset indices of stored points from a
previously established list in the mirrored spectra.
- iStoredSequenceMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The Vector that holds a set of stored points from a previously
established list in the mirrored spectra.
- isTruncated() - Method in class com.compomics.util.protein.Protein
-
This method reports on the 'truncatedness' of the protein.
- isUniqueAa(char) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Returns a boolean indicating whether the given character is a supported
amino acid excluding combinations.
- isUseChargeStateFromMS() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Indicates whether the charge state from the spectrum should be used.
- isUseCorrelationCorrectionScore() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Indicates whether the correlation correction score should be used.
- isUseNoiseSuppression() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Indicates whether noise suppression should be used when importing
spectra.
- isUserDefined(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Convenience method returning a boolean indicating whether a Modification
is user defined or default.
- isValid() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
Returns true if valid.
- isValidated(String, FilterItemComparator, Object, long, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider) - Method in class com.compomics.util.experiment.identification.filtering.AssumptionFilter
-
- isValidated(long, String, String, PeptideAssumption, Identification, SequenceProvider, SpectrumProvider, IdentificationFeaturesGenerator, IdentificationParameters) - Method in class com.compomics.util.experiment.identification.filtering.AssumptionFilter
-
Tests whether a match is validated by this filter.
- isValidated(String, FilterItemComparator, Object, long, String, String, PeptideAssumption, Identification, SequenceProvider, SpectrumProvider, IdentificationFeaturesGenerator, IdentificationParameters) - Method in class com.compomics.util.experiment.identification.filtering.AssumptionFilter
-
Indicates whether the match designated by the match key validates the
given item using the given comparator and value threshold.
- isValidated(long, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Tests whether a match is validated by this filter.
- isValidated(String, FilterItemComparator, Object, long, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Indicates whether the match designated by the match key validates the
given item using the given comparator and value threshold.
- isValidated(String, FilterItemComparator, Object, long, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider) - Method in class com.compomics.util.experiment.identification.filtering.PeptideFilter
-
- isValidated(String, FilterItemComparator, Object, long, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider) - Method in class com.compomics.util.experiment.identification.filtering.ProteinFilter
-
- isValidated(String, FilterItemComparator, Object, long, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider) - Method in class com.compomics.util.experiment.identification.filtering.PsmFilter
-
- isValidated() - Method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
-
Indicates whether this level is considered as validated.
- isValidatedOnly() - Method in class com.compomics.util.io.export.ExportScheme
-
Indicates whether only validated results should be exported.
- isValidModifications(CommandLine) - Static method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
-
Verifies that modifications are correctly recognized.
- isValidStartup(CommandLine) - Static method in class com.compomics.cli.enzymes.EnzymesCLIInputBean
-
Verifies the command line start parameters.
- isValidStartup(CommandLine) - Static method in class com.compomics.cli.fasta.FastaParametersInputBean
-
Verifies the command line start parameters.
- isValidStartup(CommandLine, boolean) - Static method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
-
Verifies the command line start parameters.
- isValidStartup(CommandLine) - Static method in class com.compomics.cli.modifications.ModificationsCLIInputBean
-
Verifies the command line start parameters.
- isVariant(Peptide, String) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
-
Returns a boolean indicating whether the peptide needs variants to be
mapped to the given protein.
- iTemplate - Variable in class com.compomics.util.protein.ModificationImplementation
-
The ModificationTemplate which holds all the shared information for a modification.
- items - Variable in class com.compomics.util.gui.utils.user_choice.ListChooser
-
The list of items the user will choose from.
- IteratorFactory - Class in com.compomics.util.experiment.identification.protein_sequences.digestion
-
The iterator goes through a sequence and lists possible peptides with their
fixed modifications.
- IteratorFactory() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.IteratorFactory
-
Empty default constructor
- IteratorFactory(ArrayList<String>, Integer) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.IteratorFactory
-
Constructor.
- IteratorFactory(ArrayList<String>) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.IteratorFactory
-
Constructor with 2 Xs allowed.
- iTitle - Variable in class com.compomics.util.protein.Enzyme
-
This String holds the title (or name) for the enzyme.
- iTitle - Variable in class com.compomics.util.protein.ModificationTemplate
-
The title for this modification (eg., Oxidation Met).
- iTopPadding - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Effective distance from the panel top border to 5 pixels above the top of
the highest point (or y-tick mark).
- iTRAQ4Plex_114 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ 4Plex 114.
- iTRAQ4Plex_115 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ 4Plex 115.
- iTRAQ4Plex_116 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ 4Plex 116.
- iTRAQ4Plex_117 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ 4Plex 117.
- iTRAQ8Plex_113 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ 8Plex 113.
- iTRAQ8Plex_114 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ 8Plex 114.
- iTRAQ8Plex_115 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ 8Plex 115.
- iTRAQ8Plex_116 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ 8Plex 116.
- iTRAQ8Plex_117 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ 8Plex 117.
- iTRAQ8Plex_118 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ 8Plex 118.
- iTRAQ8Plex_119 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ 8Plex 119.
- iTRAQ8Plex_121 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ 8Plex 121.
- iTRAQ_145 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ (reporter + balancer).
- iTRAQ_305 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Standard reporter ion iTRAQ (reporter + balancer).
- iXAxisData - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
All the x-axis data points.
- iXAxisDataInPixels - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This array will hold the x-coordinates in pixels for all the x-axis
values.
- iXAxisDataInPixelsMirroredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This array will hold the x-coordinates in pixels for all the x-axis
values of the mirrored spectrum.
- iXAxisDataMirroredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
All the x-axis data points for the mirrored spectrum.
- iXAxisLabel - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The label (and unit between brackets, if available) for the x-axis.
- iXAxisMax - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The maximum x-axis value to display.
- iXAxisMin - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The minimum x-axis value to display.
- iXAxisStartAtZero - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This boolean is set to 'true' if the x-axis should start at zero.
- iXPadding - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Effective distance from the x-axis to the panel border.
- iXScaleUnit - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Scale unit for the X axis.
- iXUnit - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Graphical unit for the X axis.
- iYAxisData - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
All the y-axis values.
- iYAxisDataInPixels - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This array will hold the y-coordinates in pixels for all the y-axis
values.
- iYAxisDataInPixelsMirroredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This array will hold the y-coordinates in pixels for all the y-axis
values of the mirrored spectrum.
- iYAxisDataMirroredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
All the y-axis values for the mirrored spectra.
- iYAxisLabel - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The label (and unit between brackets, if available) for the y-axis.
- iYAxisMax - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The maximum y-axis value to display.
- iYAxisMin - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The minimum y-axis value to display.
- iYScaleUnit - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Scale unit for the Y axis.
- iYUnit - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Graphical unit for the Y axis.
- S - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
- S - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
-
The sulfur atom.
- sameLists(ArrayList<?>, ArrayList<?>) - Static method in class com.compomics.util.Util
-
Convenience methods indicating whether the content of two lists have the
same content.
- sameModificationsAs(Peptide, ArrayList<String>) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Indicates whether another peptide has the same variable modifications at
the same localization as this peptide.
- sameModificationsAs(Peptide) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Indicates whether another peptide has the same modifications at the same
localization as this peptide.
- Sample - Class in com.compomics.util.pride.prideobjects
-
An object for storing Sample details.
- Sample() - Constructor for class com.compomics.util.pride.prideobjects.Sample
-
Empty default constructor
- Sample(String, ArrayList<CvTerm>) - Constructor for class com.compomics.util.pride.prideobjects.Sample
-
Create a new Sample object.
- SAMPLE_BATCH_SIZE - Static variable in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
-
The batch size of proteins to sample.
- SampleSelection - Class in com.compomics.util.gui
-
Class which allows the selection of the right identification.
- SampleSelection(Frame, boolean, String[], String) - Constructor for class com.compomics.util.gui.SampleSelection
-
Constructor.
- save(Connection) - Method in interface com.compomics.util.db.interfaces.DBElement
-
This method can be called when changes need to be persisted.
- saveCache(WaitingHandler, boolean) - Method in class com.compomics.util.db.object.ObjectsCache
-
Saves the cache content in the database.
- saveFactory() - Method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
-
Saves the factory in the user folder.
- saveFactory() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Saves the factory in the user folder.
- saveFile(File) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
-
Save to file.
- saveIdentificationParameters(IdentificationParameters, File) - Static method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Saves the identification parameters to a file.
- saveIdentificationParameters(SearchParameters, File) - Static method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Saves the identification parameters to a serialized file.
- saveIdentificationParametersAsTextFile(File) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Saves the identification parameters as a human readable text file.
- saveMapping(File) - Method in class com.compomics.util.experiment.biology.genes.go.GoDomains
-
Saves the mapping to the given file.
- saveObjects(int) - Method in class com.compomics.util.db.object.ObjectsCache
-
Saves an entry in the database if modified and clears it from the cache.
- saveObjects(int, WaitingHandler, boolean) - Method in class com.compomics.util.db.object.ObjectsCache
-
Saves an entry in the database if modified.
- saveObjectToJson(Object, File) - Method in class com.compomics.util.io.json.JsonMarshaller
-
Save an object to JSON.
- saveSummary(String, FastaSummary) - Static method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
-
Saves the summary in the user folder.
- saveToFile(EnzymeFactory, File) - Static method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
-
Saves en enzyme factory to a file.
- saveToFile(ModificationFactory, File) - Static method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Saves a Modification factory to a file.
- saveUrl(File, String, int, String, String, WaitingHandler) - Static method in class com.compomics.util.io.IoUtil
-
Save a file from a URL.
- saveUserParameters(UtilitiesUserParameters) - Static method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Convenience method saving the user parameters.
- scaffold - Static variable in class com.compomics.util.experiment.identification.Advocate
-
The Scaffold multiple search engine data interpretation software.
- scaleToMax(double[]) - Static method in class com.compomics.util.ArrayUtil
-
Scales the given values using the maximum value.
- scaleValues(double[], double) - Static method in class com.compomics.util.ArrayUtil
-
Scales the values using the reference value.
- ScalingFactorsEstimators - Class in com.compomics.util.experiment.quantification.spectrumcounting
-
This class estimates spectrum counting scaling factors.
- ScalingFactorsEstimators() - Constructor for class com.compomics.util.experiment.quantification.spectrumcounting.ScalingFactorsEstimators
-
Empty default constructor
- ScalingFactorsEstimators(SpectrumCountingParameters) - Constructor for class com.compomics.util.experiment.quantification.spectrumcounting.ScalingFactorsEstimators
-
Constructor.
- score - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
The (advocate specific) score used to rank this assumption.
- SCORE_1_ROW_INDEX - Static variable in class com.compomics.util.gui.protein.ModificationProfile
-
The score above the sequence row index.
- SCORE_2_ROW_INDEX - Static variable in class com.compomics.util.gui.protein.ModificationProfile
-
The score under the sequence row index.
- Se - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
-
The selenium atom.
- searchDecoyDatabase() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Returns whether MS-GF+ is to create and search a decoy database.
- SEARCHGUI_FASTA_FILE_OPTION - Static variable in class com.compomics.software.ToolFactory
-
The command line argument for FASTA file for SearchGUI.
- SEARCHGUI_PARAMETERS_FILE_OPTION - Static variable in class com.compomics.software.ToolFactory
-
The command line argument for a parameters file for SearchGUI.
- SEARCHGUI_RAW_FILE_OPTION - Static variable in class com.compomics.software.ToolFactory
-
The command line argument for raw files for SearchGUI.
- SEARCHGUI_SPECTRUM_FILE_OPTION - Static variable in class com.compomics.software.ToolFactory
-
The command line argument for mgf files for SearchGUI.
- SearchGuiSetupDialog - Class in com.compomics.software.dialogs
-
A dialog used to set up the connection between PeptideShaker and SearchGUI.
- SearchGuiSetupDialog(JFrame, boolean) - Constructor for class com.compomics.software.dialogs.SearchGuiSetupDialog
-
Creates a new SearchGuiSetupDialog.
- SearchGuiSetupDialog(JDialog, boolean) - Constructor for class com.compomics.software.dialogs.SearchGuiSetupDialog
-
Creates a new SearchGuiSetupDialog.
- SearchParameters - Class in com.compomics.util.parameters.identification.search
-
This class groups the parameters used for identification.
- SearchParameters() - Constructor for class com.compomics.util.parameters.identification.search.SearchParameters
-
Constructor.
- SearchParameters(SearchParameters) - Constructor for class com.compomics.util.parameters.identification.search.SearchParameters
-
Constructor.
- SearchParameters.MassAccuracyType - Enum in com.compomics.util.parameters.identification.search
-
Possible mass accuracy types.
- SearchParametersDialog - Class in com.compomics.util.gui.parameters.identification.search
-
The search settings dialog.
- SearchParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog
-
Empty default constructor
- SearchParametersDialog(Frame, SearchParameters, Image, Image, boolean, boolean, LastSelectedFolder, String, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog
-
Creates a new SearchSettingsDialog with a frame as owner.
- SearchParametersDialog(Dialog, Frame, SearchParameters, Image, Image, boolean, boolean, LastSelectedFolder, String, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog
-
Creates a new SearchSettingsDialog with a dialog as owner.
- sectionCompleted(String) - Method in class com.compomics.util.io.compression.SectionGzWriter.WriterBySection
-
Registers a section as completed and transfers its content to the main
file.
- select(int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
-
Inverse function to the rank function: given the i'th occurrence of a character
in the tree, it provides its position
- SELECT_SPECIES_TAG - Static variable in class com.compomics.util.gui.genes.SpeciesDialog
-
Deprecated.
The text to use to tell the user to please select a species in the list.
- selectDB(boolean) - Method in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
-
Allows the user to select a FASTA file, loads its information, and
returns a boolean indicating whether the process loading was successful.
- SelectedValuesTableFilter() - Constructor for class com.compomics.util.gui.XYPlottingDialog.SelectedValuesTableFilter
-
- Selenium - Class in com.compomics.util.experiment.biology.atoms.impl
-
Selenium.
- Selenium() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Selenium
-
Constructor.
- Selenocysteine - Class in com.compomics.util.experiment.biology.aminoacids.impl
-
SeC (U) (Mascot)-
- Selenocysteine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
-
Constructor.
- SELENOCYSTEINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
Selenocysteine immonium ion.
- SELFDEFINED - Static variable in class com.compomics.util.general.MassCalc
-
Value for the self-defined masses.
- SelfUpdatingTableModel - Class in com.compomics.util.gui.tablemodels
-
These table models include a self updating function.
- SelfUpdatingTableModel() - Constructor for class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
-
- sendBinaryFile(String) - Method in class com.compomics.util.io.ftp.FTPClient
-
This method sends a binary file to the default FTP location on the server.
- sendFiles(String[], boolean[]) - Method in class com.compomics.util.io.ftp.FTPClient
-
This method sends a group of files to the default FTP location on the server.
- sendFiles(String[], boolean) - Method in class com.compomics.util.io.ftp.FTPClient
-
This method sends a group of files to the default FTP location on the server.
- sendGAUpdate(String, String, String) - Static method in class com.compomics.util.Util
-
Function for sending event requests to Google analytics.
- sendIncoming(Object) - Method in interface com.compomics.util.interfaces.PickUp
-
This method should be called by the notifier when appropriate.
- sendServer(String) - Method in class com.compomics.util.io.ftp.FTP
-
Sends command cmd to the server.
- sendTextFile(String) - Method in class com.compomics.util.io.ftp.FTPClient
-
This method sends a text file to the default FTP location on the server.
- SENTINEL - Static variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
Sentinel character necessary for computation of the suffix array.
- SEPARATOR - Static variable in class com.compomics.software.cli.CommandLineUtils
-
The command line argument separator.
- separator - Static variable in class com.compomics.software.settings.UtilitiesPathParameters
-
The separator between a path ID and a path.
- SEPARATOR - Static variable in class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
-
The separator used to separate line contents.
- SEPARATOR - Static variable in class com.compomics.util.experiment.biology.genes.go.GoDomains
-
The separator used to separate line contents.
- SEPARATOR - Static variable in class com.compomics.util.experiment.biology.genes.go.GoMapping
-
The separator used to separate line contents.
- SEPARATOR - Static variable in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
The separator used to separate line contents.
- SEPARATOR - Static variable in class com.compomics.util.experiment.biology.taxonomy.mappings.BiomartMapping
-
The separator used to separate line contents.
- SEPARATOR - Static variable in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
-
The separator used to separate line contents.
- SEPARATOR - Static variable in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
-
The separator used to separate line contents.
- SEPARATOR - Static variable in class com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
-
The separator used to separate line contents.
- SEPARATOR - Static variable in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
The separator used to separate locations in the modification location
key.
- separator - Static variable in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
-
The columns separator.
- Sequence - Interface in com.compomics.util.interfaces
-
This interface defines the default behavior of any kind of
sequence with a certain mass - be it DNA, protein or something
else.
- sequenceCoverageInCache(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Indicates whether the sequence coverage is in cache.
- SequenceDbDetailsDialog - Class in com.compomics.util.gui.parameters.identification.search
-
This dialog displays information about a sequence database.
- SequenceDbDetailsDialog(Dialog, Frame, String, FastaParameters, LastSelectedFolder, boolean, Image, Image) - Constructor for class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
-
Creates a new SequenceDbDetailsDialog with a dialog as owner.
- SequenceDbDetailsDialog(Frame, String, FastaParameters, LastSelectedFolder, boolean, Image, Image) - Constructor for class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
-
Creates a new SequenceDbDetailsDialog.
- SequenceFragmentationPanel - Class in com.compomics.util.gui.spectrum
-
This class was imported from the Peptizer and MascotDatfile parser, and was
developed to display fragmentation information on the modified sequence as
inspired by X!Tandem.
- SequenceFragmentationPanel() - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
-
Empty default constructor
- SequenceFragmentationPanel(String, IonMatch[], boolean, boolean, ModificationParameters, int, int) - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
-
Creates a new SequenceFragmentationPanel working with B and Y ions.
- SequenceFragmentationPanel(String, IonMatch[], boolean, ModificationParameters, int, int) - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
-
Creates a new SequenceFragmentationPanel working with B and Y ions.
- SequenceIterator - Interface in com.compomics.util.experiment.identification.protein_sequences.digestion
-
Interface for an iterator returning peptides along a protein sequence.
- SequenceMatchingParameters - Class in com.compomics.util.parameters.identification.advanced
-
The sequence matching options.
- SequenceMatchingParameters() - Constructor for class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Constructor for empty preferences.
- SequenceMatchingParameters.MatchingType - Enum in com.compomics.util.parameters.identification.advanced
-
The different types of amino acid matching.
- SequenceMatchingParametersDialog - Class in com.compomics.util.gui.parameters.identification.advanced
-
Dialog for the edition of the sequence matching settings.
- SequenceMatchingParametersDialog(Frame, SequenceMatchingParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.SequenceMatchingParametersDialog
-
Creates a new SequenceMatchingSettingsDialog with a frame as owner.
- SequenceMatchingParametersDialog(Dialog, Frame, SequenceMatchingParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.SequenceMatchingParametersDialog
-
Creates a new SequenceMatchingSettingsDialog with a dialog as owner.
- SequenceModificationPanel - Class in com.compomics.util.gui.protein
-
A panel for displaying modification profiles.
- SequenceModificationPanel() - Constructor for class com.compomics.util.gui.protein.SequenceModificationPanel
-
Empty default constructor
- SequenceModificationPanel(String, ArrayList<ModificationProfile>, boolean, String, String) - Constructor for class com.compomics.util.gui.protein.SequenceModificationPanel
-
Creates a new SequenceFragmentationPanel.
- SequenceProvider - Interface in com.compomics.util.experiment.io.biology.protein
-
Interface for a class able to retrieve the sequence of a given protein.
- sequest - Static variable in class com.compomics.util.experiment.identification.Advocate
-
The Sequest search engine.
- SequestFragmentationModel - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models
-
Fragmentation model originally described in the Sequest algorithm
(https://www.ncbi.nlm.nih.gov/pubmed/24226387) adapted to utilities objects.
- SequestFragmentationModel() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.SequestFragmentationModel
-
Empty default constructor
- SequestParamsFileFilter - Class in com.compomics.util.io.file.filefilters
-
File filter for sequest.params files.
- SequestParamsFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.SequestParamsFileFilter
-
Empty default constructor
- SerializationUtils - Class in com.compomics.util.io.file
-
This class implements convenience methods for serialization and
deserialization.
- SerializationUtils() - Constructor for class com.compomics.util.io.file.SerializationUtils
-
Empty default constructor
- serialize(T, Type, JsonSerializationContext) - Method in class com.compomics.util.io.json.adapter.InterfaceAdapter
-
- serialVersionUID - Static variable in interface com.compomics.util.io.export.ExportFeature
-
Serial number for backward compatibility.
- Serine - Class in com.compomics.util.experiment.biology.aminoacids.impl
-
Serine.
- Serine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Serine
-
Constructor.
- SERINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
-
Serine immonium ion.
- serverInput - Variable in class com.compomics.util.io.ftp.FTP
-
Buffered stream for reading replies from server.
- serverIsOpen() - Method in class com.compomics.util.io.ftp.FTP
-
Return server connection status
- serverOutput - Variable in class com.compomics.util.io.ftp.FTP
-
Stream for printing to the server.
- serverResponse - Variable in class com.compomics.util.io.ftp.FTP
-
Array of strings (usually 1 entry) for the last reply from the server.
- setAaAtIndex(int, char) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
replaces the amino acid at the given position by the given amino acid
represented by its single letter code.
- setAaIndex(int) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAIdentityFeature
-
Sets the index on the sequence.
- setAaIndex(int) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAPropertyFeature
-
Sets the index on the sequence.
- setAaSubstitutionMatrix(AaSubstitutionMatrix) - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
-
Sets the substitution matrix to display.
- setAaSubstitutionMatrix(AaSubstitutionMatrix) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Sets the amino acid substitution matrix to use.
- setAboveXAxis(boolean) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set if the reference area is to be added above the x-axis, false adds the
reference are below the x-axis
- setAccession(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the accession.
- setAccession(String) - Method in class com.compomics.util.pride.CvTerm
-
Sets the accession.
- setAccessions(String[]) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Sets the accessions of the proteins in this group.
- setActicationType(String) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Sets the activation type.
- setActive(boolean) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Sets whether the filter is active.
- setAdditionalOutput(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Set if additional output is to be included.
- setAdjustPrecursorMass(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Set if the precursor mass is to be adjusted.
- setAdvocate(int) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Sets the advocate id.
- setAlgorithmDeltaPEP(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Sets the difference in identification algorithm level PEP with the next
best peptide assumption with sequence difference for the given search
engine.
- setAlignNonConfidentModifications(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Sets whether the non confidently localized modifications should be
aligned on the confident sites.
- setAllPathsIn(String) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
-
Sets all the paths inside a given folder.
- setAlpha(float) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set the alpha level (transparency).
- setAlphaLevel(float) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Sets the alpha level
- setAminoAcid(char) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAIdentityFeature
-
Sets the amino acid targeted represented as single letter code.
- setAminoAcidFeature1(AAPropertyFeature) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
-
Sets the first amino acid feature.
- setAminoAcidFeature2(AAPropertyFeature) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
-
Sets the second amino acid feature.
- setAminoAcidProperty(AminoAcid.Property) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAPropertyFeature
-
- setAminoAcidProperty(AminoAcid.Property) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature
-
- setAminoAcidProperty(AminoAcid.Property) - Method in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.SingleAAPropertyFeature
-
Sets the amino acid property to consider.
- setAminoAcidScores(ArrayList<double[]>) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Set the amino acid scores.
- setAnnotateHighestPeak(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set if the most intense of possible peaks to annotate is to be selected,
false if the most accurate is to be selected.
- setAnnotationParameters(AnnotationParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the annotation parameters used for identification.
- setAnnotations(List<SpectrumAnnotation>, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This method sets all the annotations on this instance.
- setAnnotations(List<SpectrumAnnotation>) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This method sets all the annotations on this instance.
- setAnnotationsMirrored(List<SpectrumAnnotation>, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This method sets all the annotations for the mirrored spectra.
- setAnnotationsMirrored(List<SpectrumAnnotation>) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This method sets all the annotations for the mirrored spectra.
- setAnnotationYAxisThreshold(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This method allows the caller to set the minimal non-inclusive y-axis
value threshold in percent (compared to the highest point in the spectrum
or chromatogram) a point must pass before being eligible for annotation.
- setAreaColor(Color) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set the area color.
- setAreaUnderCurveColor(Color, int) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Sets the color of the area under the curve for profile chromatograms and
spectra for the dataset with the given dataset index.
- setAtomChainAdded(AtomChain) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Sets the atom chain added.
- setAtomChainRemoved(AtomChain) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Sets the atom chain removed.
- setAtomicComposition(AtomChain) - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Returns the atomic composition.
- setAtomSymbol(String) - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
-
Sets the atom symbol as specified in the Atom class.
- setAutomaticAnnotation(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Sets whether the annotation settings should be automatically inferred.
- setAutoUpdate(Boolean) - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
-
Sets whether the gene mappings should be automatically updated.
- setAutoUpdate(Boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Sets whether the tools should use the auto update function.
- setBackgroundPeakWidth(float) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set the backgroundPeakWidth peak width.
- setBackgroundSpecies(Integer) - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
-
Sets the taxon of the species selected as background species.
- setBackgroundSpeciesFromFastaSummary(FastaSummary) - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
-
Set the background species to the most common species in the FASTA file.
- setBatchSize(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the batch size.
- setBestPeak(double[], double[], int[], IonMatch) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Returns the peak to retain of the matched peaks according to the ties
resolution setting.
- setBestPeptideAssumption(PeptideAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Setter for the best peptide assumption.
- setBestTagAssumption(TagAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Setter for the best tag assumption.
- setBinMax(Integer) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Sets the highest bin in index.
- setBinMin(Integer) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Sets the lowest bin in index.
- setBlob(byte[]) - Method in class com.compomics.util.db.object.objects.BlobObject
-
Sets the byte representation of the object.
- setBlock(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Sets the block.
- setBlocks(PdbBlock[]) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
Set the blocks.
- setBoldFont(boolean) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set if the label is to be in bold.
- setBorderColor(Color) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set the border color.
- setBorderWidth(float) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set the border width.
- setCategory(ModificationCategory) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Set the modification category.
- setCharge(int) - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
-
Setter for the charge
- setCharge(int) - Method in interface com.compomics.util.interfaces.SpectrumFile
-
This method sets the charge of the precursor ion.
- setCheckDuplicateTitles(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set if the spectra should be checked for duplicate titles or not.
- setCheckMgfSize(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set if the mgf should be checked for size.
- setCheckPeakPicking(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set if the spectra should be checked for peak picking or not.
- setCheckSpectrumCharges(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set if the spectra are to be checked for missing charges.
- setClassSizeMultiplier(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Set the intensity class size multiplier.
- setCleavage(char[]) - Method in class com.compomics.util.protein.DualEnzyme
-
This method allows the caller to specify the cleavable residues.
- setCleavage(String) - Method in class com.compomics.util.protein.DualEnzyme
-
This method allows the caller to specify the cleavable residues.
- setCleavage(char[], int) - Method in class com.compomics.util.protein.DualEnzyme
-
This method allows the caller to specify the cleavable residues.
- setCleavage(String, int) - Method in class com.compomics.util.protein.DualEnzyme
-
This method allows the caller to specify the cleavable residus.
- setCleavage(char[]) - Method in class com.compomics.util.protein.Enzyme
-
This method allows the caller to specify the cleavable residues.
- setCleavage(String) - Method in class com.compomics.util.protein.Enzyme
-
This method allows the caller to specify the cleavable residues.
- setCleavage(String) - Method in class com.compomics.util.protein.RegExEnzyme
-
This method can be used to set the cleavage pattern for this RegExEnzyme.
- setCleavage(char[]) - Method in class com.compomics.util.protein.RegExEnzyme
-
- setCleavageParameter(DigestionParameters.CleavageParameter) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
-
Sets the cleavage parameters.
- setCleaveNterMethionine(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets whether N-terminal methionines should be cleaved.
- setClipNtermMethionine(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if the starting methionine peptides will be included both with and
without the starting M.
- setCloseDialogWhenImportCompletes(boolean, boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Set if the value for if the dialog is to be closed when completed and if
the option is enabled or not.
- setColor(String, int) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Sets a new color for the given expected modification.
- setColor(Color) - Method in class com.compomics.util.gui.protein.ModificationProfile
-
Sets the PTM color.
- setColor(String, int) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
-
Sets a new color for the given expected modification.
- setColumn(int, ArrayList<Double>) - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- setComparatorForItem(String, FilterItemComparator) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Sets the comparator for a given item.
- setComplementMzTolerance(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Sets the complement m/z tolerance.
- setComplementScoreWeight(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Set the complement score weight.
- setComposition(AtomChain) - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
-
Sets the composition of the neutral loss.
- setComputeExactPValues(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if the exact p-values are to be computed.
- setComputeSpScore(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if the SP score is to be computed.
- setComputeXCorr(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Sets if a Sequest-like cross correlation score will be calculated for the
top ranking hits in each spectrum’s result set.
- setConcatenatTargetDecoy(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if the target and decoy results are to be concatenated.
- setCondition(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Sets the description of the condition to meet.
- setConfidenceMargin(Double) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Sets the margin to the threshold to use as factor of the resolution.
- setConfidenceThreshold(double) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Sets the confidence below which a peptide is considered absent.
- setConfident(boolean) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Sets whether the modification is confidently localized on the sequence.
- setConsecutiveIonProbability(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Set the consecutive ion probability.
- setContacts(ArrayList<Contact>) - Method in class com.compomics.util.pride.prideobjects.ContactGroup
-
Set the contacts.
- setContent(ArrayList<TagComponent>) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
-
Sets the content for the given tag.
- setContinueReading(boolean) - Method in class com.compomics.util.io.StreamGobbler
-
Set if the reading is to continue or not.
- setControlSamples(ArrayList<String>) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
Sets the indexes of the samples labeled as control.
- setCorrectPrecursorMass(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Sets whether the precursor mass shall be corrected (TagDB setting).
- setCreationTime(Date) - Method in class com.compomics.util.experiment.ProjectParameters
-
- setcTermModification(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Sets the C-term modification.
- setCurrentPeptideKey(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Sets the current peptide key.
- setCurrentProteinKey(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Sets the current protein key.
- setCvTerm(CvTerm) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
-
Sets the CV term associated with this enzyme.
- setCvTerms(ArrayList<CvTerm>) - Method in class com.compomics.util.pride.prideobjects.Instrument
-
Set the CV terms.
- setCvTerms(ArrayList<CvTerm>) - Method in class com.compomics.util.pride.prideobjects.Protocol
-
Set the CV terms.
- setCvTerms(ArrayList<CvTerm>) - Method in class com.compomics.util.pride.prideobjects.Sample
-
Set the CV terms.
- setDatabaseType(ProteinDatabase) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the database type.
- setDataFilters(HashMap<String, String>) - Method in class com.compomics.util.gui.XYPlottingDialog
-
Set the data filters.
- setDataPointAndLineColor(Color, int) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Sets the color of data points and line for the dataset with the given
dataset index.
- setDateTimeFormat(String) - Method in class com.compomics.util.gui.JTableForDB
-
This method allows the setting of the date /time format.
- setDbFolder(File) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Sets the last used database folder.
- setDbSize(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Sets whether the database size should be checked.
- setDebugInteractions(boolean) - Static method in class com.compomics.util.db.object.ObjectsDB
-
Turn the debugging of interactions on or off.
- setDeconvolutionIntensityRatio(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the deconvolution intensity ratio.
- setDeconvolutionMassTolerance(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the deconvolution mass tolerance.
- setDeconvolutionMassToleranceType(MetaMorpheusParameters.MetaMorpheusToleranceType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the deconvolution mass tolerance type.
- setDecoy(boolean) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Sets whether the given match is decoy
- setDecoyFlag(String) - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
-
Sets the decoy flag.
- setDecoyFormat(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the decoy format.
- setDecoyMode(AndromedaParameters.AndromedaDecoyMode) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Set the decoy mode.
- setDecoySeed(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the decoy seed.
- setDecoysInFirstBin(Integer) - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
-
Sets the minimal number of decoys to include in a bin to set the bin size
of the score histogram.
- setDecoySuffix(boolean) - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
-
Sets whether the decoy flag is a suffix or a prefix.
- setDecoyType(MetaMorpheusParameters.MetaMorpheusDecoyType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the decoy type.
- setDefaultAdvancedSettings() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Set the advanced settings to the default values.
- setDefaultAdvancedSettings(SearchParameters) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Set the advanced settings to the values in the given search parameters
object or to the default values of the advanced settings are not set for
a given advocate.
- setDefaultEnzymes() - Static method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
-
Sets the instance to only contain the default enzymes.
- setDefaultPeptideFDR(double) - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
-
Sets the default peptide FDR.
- setDefaultProteinFDR(double) - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
-
Sets the default protein FDR.
- setDefaultPsmFDR(double) - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
-
Sets the default PSM FDR.
- setDeisotopingMode(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Sets the deisotoping flag value.
- setDeltaMassWindow(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set the size of the window to use when searching for matches in the known
masses list when the user hovers over a second data point after clicking
a previous data point.
- setDeltaPEP(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Sets the difference in identification algorithm level PEP with the next
best peptide assumption with sequence difference across all search
engines.
- setDeltaScore(int, double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Sets the delta score at a given site.
- setDeNovoCharge(int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Set the charge to use for the fragment ions in the de novo sequencing
- setDeNovoGuiPath(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the path to the DeNovoGUI installation.
- setDependentLosses(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets whether neutral losses should be sequence dependent.
- setDescription(String) - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
-
Sets the description of this substitution matrix.
- setDescription(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Sets the description of the filter.
- setDescription(String) - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
-
Sets the description for this database.
- setDescription(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the description.
- setDescription(String) - Method in class com.compomics.util.experiment.patient.PatientInformation
-
Sets the description of the information.
- setDescription(String, boolean) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the description of the parameters.
- setDescriptionProteinName(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the protein name.
- setDescriptionShort(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the short description.
- setDestinationFile(String) - Method in class com.compomics.util.io.ftp.FTP
-
This method allows the specification of the destinationfile.
- setDetector(CvTerm) - Method in class com.compomics.util.pride.prideobjects.Instrument
-
Set the instrument detector.
- setDeterminate(int, int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
-
This method sets the progressbar to determinate mode, with the specified
minimum and maximum values.
- setDetermineChargePlusOneAlgorithmically(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets whether charge plus one should be determined algorithmically.
- setDigestionParameters(DigestionParameters) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Sets the digestion preferences.
- setDigestionType(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the enzyme digestion type.
- setDiscardLowQualitySpectra(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Sets whether low quality spectra shall be discarded.
- setDisplayedTips(ArrayList<String>) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the list of displayed tips.
- setDisplayProgress(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- setDisplayProgress(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- setDisplayProgress(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setDisplayProgress(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- setDisplayProgress(boolean) - Method in interface com.compomics.util.waiting.WaitingHandler
-
Set if the waiting handler is to show the progress for the current
process or not.
- setDissociationType(MetaMorpheusParameters.MetaMorpheusDissociationType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the dissociation type.
- setDoi(String) - Method in class com.compomics.util.pride.prideobjects.Reference
-
Set the Digital Object Identifier (DOI) of the reference.
- setDoPrecursorDeconvolution(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set whether precursor deconvolution is to be carried out.
- setDoubleChargeWindow(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the window size for doubly charged ions.
- setDrawLabel(boolean) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set to true if the label is to be drawn, false otherwise.
- setDrawOnTop(boolean) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set to true if the area is to be drawn in front of the data, false
otherwise.
- setDScoreThreshold(double) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Sets the D-score threshold.
- setDuplicateSpectra(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Sets whether to use duplicate spectra option.
- setDynamicRange(double) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets the dynamic range for spectrum filtering.
- setEditable(boolean) - Method in class com.compomics.util.io.export.ExportScheme
-
Sets whether the scheme is editable.
- setEMail(String) - Method in class com.compomics.util.pride.prideobjects.Contact
-
Set the contact e-mail.
- setEmpiricalCorrection(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets whether empirical correction should be used.
- setEnd(double) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set the end value.
- setEndBlock(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Set the block end.
- setEndProtein(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Set the protein end.
- setEnsemblVersionsMap(HashMap<String, String>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Sets the Ensembl version map.
- setEnzymaticTagsOnly(boolean) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Sets whether tags should only be mapped to enzymatic peptides.
- setEnzymes(ArrayList<Enzyme>) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
-
Sets the enzymes used for digestion.
- setEnzymeType(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the enzyme type.
- setEqualIL(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets whether I and L should be considered indistinguishable.
- setEstimateCharge(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets whether the precursor charge shall be estimated for OMSSA.
- setEstimateCharge(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Sets whether the precursor charge shall be estimated for PepNovo.
- setEvenRowColor(Color) - Method in class com.compomics.util.AlternateRowColoursJTable
-
Sets the colour of the even numbered rows; by default, the LIGHT_AQUA background color will be used..
- setExceptions(HashSet<Long>) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Sets the excepted matches.
- setExcluded(int, ArrayList<Character>) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Excludes the given amino acids from the targeted amino acids at the given
index.
- setExperiment_type(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
Set the experiment type.
- setExportFeatures(String, ArrayList<ExportFeature>) - Method in class com.compomics.util.io.export.ExportScheme
-
Sets the export features of a given section.
- setFastaParameters(FastaParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the ASTA processing parameters.
- setFastIndexFolderName(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the name of the FASTA index folder.
- setFeature(IonFeature.Property) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature
-
Sets the peptide feature.
- setFile(File) - Method in class com.compomics.util.gui.file_handling.FileAndFileFilter
-
Set the file.
- setFileFilter(FileFilter) - Method in class com.compomics.util.gui.file_handling.FileAndFileFilter
-
Set the file filter.
- SetFileMode(int) - Method in class com.compomics.util.io.ftp.FTP
-
This method sets the file transfer mode.
- setFilename(String) - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
-
Setter for the filename
- setFilename(String) - Method in interface com.compomics.util.interfaces.SpectrumFile
-
This method sets the filename for the file.
- setFilename(String) - Method in class com.compomics.util.io.ftp.FTP
-
This method sets the name of the file to up- or download.
- setFileName(String) - Method in class com.compomics.util.io.PklFile
-
- setFilenameColor(Color) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This method sets the display color for the filename on the panel.
- setFilter() - Method in class com.compomics.util.gui.filtering.FilterDialog
-
/**
Modifies the filter according to the user selection.
- setFiltered(boolean) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Sets whether the protein list is filtered.
- setFilterFromSearchParameters(SearchParameters) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Updates the filter based on the search parameters.
- setFilterItem(String, FilterItemComparator, Object) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Sets an item to the filter.
- setFirstDecoy(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Sets whether the number of hits before the first decoy should be checked.
- setFixed(boolean) - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
-
Sets whether the loss is fixed or not.
- setFixedAaModifications(HashMap<Integer, String>) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Sets the modifications at specific amino acids.
- setFixedVariants(HashMap<String, ArrayList<SNPElement>>) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
sets the fixed variants
- setFlanking(boolean) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Set whether the flanking amino acids of a mapped peptide are to be
reported.
- setFontColor(Color) - Method in class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
-
Set the color for the font of the peptide sequence.
- setFontSize(int) - Method in class com.compomics.util.gui.VennDiagramPanel
-
Set the font size.
- setFontSizeLegend(int) - Method in class com.compomics.util.gui.VennDiagramPanel
-
Set the font size of the legend.
- setForeignAccession(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the foreign accession.
- setForeignDescription(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the foreign description.
- setForeignID(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the foreign ID.
- setForwardIons(ArrayList<Integer>) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Sets the forward ions searched as list of integers as indexed in the
FragmentIon class.
- setFoundModifications(TreeSet<String>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Sets the list of variable modifications found in the dataset.
- setFractionMolecularWeightRanges(HashMap<String, XYDataPoint>) - Method in class com.compomics.util.parameters.identification.advanced.FractionParameters
-
Set the user provided molecular weight ranges for the fractions.
- setFractionOfPeaksForChargeEstimation(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the fraction of peaks to be retained for charge >1 estimation.
- setFractionParameters(FractionParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the fraction parameters.
- setFractionPEP(String, Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Sets the fraction confidence.
- setFractionPEP(HashMap<String, Double>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
- setFractionPsmMatches(HashMap<String, ArrayList<Long>>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Set the fraction PSM matches.
- setFractions(ArrayList<String>) - Method in class com.compomics.util.experiment.identification.Identification
-
Sets the fractions.
- setFractionScore(String, double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Sets the fraction confidence.
- setFractionScore(HashMap<String, Double>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Sets the fraction score map.
- setFragmentAccuracyType(SearchParameters.MassAccuracyType) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Sets the fragment accuracy type.
- setFragmentAll(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets whether the fragment all option should be used.
- setFragmentationMethod(FragmentationMethod) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets the fragmentation method used.
- setFragmentationMethod(String) - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
-
Set the fragmentation method.
- setFragmentationModel(String) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Sets the name of the fragmentation model.
- setFragmentationRule(String) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Set the fragmentation rule.
- setFragmentationTerminus(MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the fragmentation terminus.
- setFragmentationType(int) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Set the fragmentation ID.
- setFragmentBinOffset(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the fragment ion bin offset.
- setFragmentIonAccuracy(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Sets the fragment ion accuracy.
- setFragmentIonAccuracy(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Sets the fragment ion accuracy.
- setFragmentIonAccuracy(double) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Sets the fragment ion m/z tolerance.
- setFragmentIonPpm(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Sets whether the fragment ion accuracy is in ppm.
- setFragmentIonPpm(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Sets whether the fragment ion accuracy is in ppm.
- setFunction(AASequenceFeature.Function) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature
-
Sets the function used to compare the amino acid properties.
- setGeneMappingFolder(String) - Static method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
-
Sets the folder where gene mappings are saved.
- setGeneName(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Set the gene name.
- setGeneNameToChromosomeMap(HashMap<String, String>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Sets the gene name to chromosome map.
- setGeneNameToEnsemblIdMap(HashMap<String, String>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Sets the gene name to Ensembl ID map.
- setGeneParameters(GeneParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the gene parameters.
- setGenerateDecoyDatabase(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set whether a decoy database shall be created and searched against.
- setGenerateQuery(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Sets a boolean indicating whether a blast query shall be generated.
- setGoAccessionToProteinMap(HashMap<String, HashSet<String>>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Sets the GO to protein accession map.
- setGoNamesMap(HashMap<String, String>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Sets the GO accession to names map.
- setGPtmCategories(ArrayList<ModificationCategory>) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the modification categories to include in the G-PTM search.
- setGroupClass(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
- setGzip(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Sets whether identification files should be gzipped.
- setHeader(Header) - Method in class com.compomics.util.nucleotide.NucleotideSequence
-
This method sets the header.
- setHeader(Header) - Method in class com.compomics.util.protein.Protein
-
Simple setter for the header.
- setHidden(boolean) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Hide/Unhide a match.
- setHigherCharge(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets whether higher charge should be considered.
- setHighIntensityCutOff(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the high intensity cut-off as percentage of the most intense ion
peak.
- setHitListLength(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the length of the hit list for OMSSA.
- setHitListLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Sets the length of the hit list.
- setID(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the ID.
- setId(long) - Method in class com.compomics.util.experiment.personalization.ExperimentObject
-
Sets the id of the object.
- setIdentificationAlgorithmParameter(int, IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Adds identification algorithm specific parameters.
- setIdentificationCharge(int) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Sets the identification charge.
- setIdentificationFeaturesCache(IdentificationFeaturesCache) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Sets the the identification features cache.
- setIdentificationFile(String) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Sets the identification file.
- setIdentificationKeys(IdentificationKeys) - Method in class com.compomics.util.experiment.identification.Identification
-
Sets the identification keys.
- setIdentificationParameters(IdentificationParameters) - Method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
-
Sets the identification parameters.
- setIdentifier(String) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Sets the references identifier.
- setIdValidationParameters(IdMatchValidationParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the identification matches validation parameters.
- setIgnoreExceptions(boolean) - Method in class com.compomics.util.exceptions.ExceptionHandler
-
Sets whether exceptions should be ignored.
- setIncludeAmmonia(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets whether ammonia losses should be accounted for.
- setIncludeDateInOutputName(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Sets whether the date should be included in the SearchGUI output name.
- setIncludeDecoy(Boolean) - Method in class com.compomics.util.io.export.ExportScheme
-
Sets whether decoy hits should be included.
- setIncludeWater(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets whether water losses should be accounted for.
- setIndentString(String) - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
-
Sets the indent string to use, e.g.
- setIndeterminate() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
-
This method makes the progressbar indeterminate.
- setIndexOnProtein(int) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Sets the peptide index on the protein.
- setInferred(boolean) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Sets whether the modification is inferred from another peptide.
- setInitiatorMethionineBehavior(MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the initiator methionine behavior.
- setInstitution(String) - Method in class com.compomics.util.pride.prideobjects.Contact
-
Set the instituttion.
- setInstrumentID(String) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set the instrument ID.
- setInstrumentID(int) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Set the instrument ID.
- setIntegerParameter(String, Integer) - Method in class com.compomics.util.experiment.ProjectParameters
-
- setIntensity(double) - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
-
Setter for the intensity.
- setIntensity(double) - Method in interface com.compomics.util.interfaces.SpectrumFile
-
This method sets the intensity of the precursor ion.
- setIntensityCutOffIncrement(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the intensity cut-off increment.
- setIntensityLimit(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Sets the intensity percentile to consider for annotation.
- setIntensityScoreWeight(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Set the intensity score weight.
- setIntensityThresholdType(AnnotationParameters.IntensityThresholdType) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Sets the intensity threshold type.
- setIntensityValues(double[]) - Method in class com.compomics.util.io.PklFile
-
- setIntermediateScore(Integer, Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Adds an intermediate score.
- setIntermediateScores(HashMap<Integer, Double>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
- setIonColor(Ion, Color) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel
-
Sets an annotation color for the given ion.
- setIonMatches(IonMatch[]) - Method in class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
-
Set the ArrayList with FragmentIon matches.
- setIsotope(Integer) - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
-
Sets the isotope, 0 for monoisotope.
- setIsotopeCorrection(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the isotope correction setting.
- setIsotopeMzTolerance(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Sets the deisotoping m/z tolerance.
- setIsPpm(boolean) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Sets whether the mass tolerance is in ppm (true) or Dalton (false).
- setIsScrolling(boolean) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
-
Set if the user is currently scrolling or not.
- setIterativeReplaceEvalue(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the e-value threshold to use to replace a hit for the iterative
search.
- setIterativeSequenceEvalue(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the e-value threshold to use to consider a sequence for the
iterative search.
- setIterativeSpectrumEvalue(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the e-value threshold to use consider a spectrum for the iterative
search.
- setiXAxisMax(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Sets the maximum value for the x-axis.
- setiXAxisMin(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Sets the minimum value for the x-axis.
- setiYAxisMax(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Sets the maximum value for the y-axis.
- setiYAxisMin(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Sets the minimum value for the y-axis.
- setJavaHome(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the Java Home folder.
- setKeepTerminalAminoAcids(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the option for keeping the terminal amino acids when generating the
decoys
- setKey(long) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Sets the object key.
- setKey(long) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
Sets a new key for the match.
- setKeyWords(ArrayList<String>) - Method in class com.compomics.util.messages.FeedBack
-
Sets the the key words for this report.
- setKnownMassDeltas(HashMap<Double, String>) - Static method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set all the known mass deltas (if any).
- setLabel(String) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Sets the label.
- setLabelColor(Color) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set the label color.
- setLabelDifference(int) - Method in class com.compomics.util.general.IsotopicDistribution
-
This method set the label dalton difference
- setLastSelectedFolder(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Sets the last selected folder.
- setLastSelectedFolder(String, String) - Method in class com.compomics.util.io.file.LastSelectedFolder
-
Sets the last selected folder of the given use case.
- setLastSelectedFolder(String) - Method in class com.compomics.util.io.file.LastSelectedFolder
-
Sets the last selected folder.
- setLastSelectedFolder(LastSelectedFolder) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Sets the last selected folder.
- setLeadingAccession(String) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Sets the leading accession for this match.
- setLegendDatasetAFourWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
-
Set the legend location of Dataset A in a four way Venn diagram.
- setLegendDatasetAThreeWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
-
Set the legend location of Dataset A in a three way Venn diagram.
- setLegendDatasetBFourWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
-
Set the legend location of Dataset B in a four way Venn diagram.
- setLegendDatasetBThreeWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
-
Set the legend location of Dataset B in a three way Venn diagram.
- setLegendDatasetCFourWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
-
Set the legend location of Dataset C in a four way Venn diagram.
- setLegendDatasetCThreeWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
-
Set the legend location of Dataset C in a three way Venn diagram.
- setLegendDatasetDFourWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
-
Set the legend location of Dataset D in a four way Venn diagram.
- setLimitX(double) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Sets the maximal share of X's a match can contain, range [0.0-1.0].
- setLine(int, ArrayList<Double>) - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- setLocalPrideFolder(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the local PRIDE folder.
- setLocation(int, int) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
This method allows the caller to add information to the header about
location of the sequence in a certain master sequence.
- setLocation(int) - Method in interface com.compomics.util.interfaces.Modification
-
This method allows the setting of the location for this modification.
- setLocation(int) - Method in class com.compomics.util.protein.ModificationImplementation
-
This method allows the setting of the location for this modification.
- setLookAndFeel() - Static method in class com.compomics.util.gui.UtilitiesGUIDefaults
-
Sets the look and feel to the default utilities look and feel.
- setLowerClearMzRange(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the lower mass value for the clear mz range.
- setLowerPrecursorMass(int) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Set the lower precursor mass.
- setLowIntensityCutOff(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the low intensity cut-off as percentage of the most intense ion
peak.
- setLowMemoryMode(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
- setManualValidation(HashSet<Long>) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Sets the list of manually validated keys.
- setManualValidation(boolean) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Sets whether the match validation was manually inspected.
- setMaps(GoMapping) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Imports the GO maps from a GO mapping.
- setMass(double) - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Method to set the mass of the reporter ion.
- setMass(double) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Sets the mass.
- setMass(double) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.MassGap
-
Sets the mass of the gap.
- setMass(double) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Sets the mass.
- setMassAnalyzer(String) - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
-
Set the mass analyzer.
- setMassDiffAcceptorType(MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the mass difference acceptor type.
- setMassErrorDistribution(String, double[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Sets a mass error distribution in the massErrorDistribution map.
- setMassShift(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Sets an m/z shift on all ions.
- setMassShifts(double, double, double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Sets the m/z shifts.
- setMassTolerance(double, boolean, SpectrumAnnotator.TiesResolution) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Sets a new m/z tolerance for peak matching.
- setMatchingKey(long) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Sets the key accounting for sequence matching preferences.
- setMatchValidationLevel(MatchValidationLevel) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Sets the validation level of the match.
- setMatchValidationLevel(Integer) - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
-
Sets the lowest validation level to consider as an integer as indexed in
the MatchValidationLevel enum.
- setMaxCharge(Integer) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Sets the maximum charge in this file.
- setMaxChargeSearched(int) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Sets the maximal charge searched.
- setMaxCombinations(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets the maximal number of combinations.
- setMaxDynamicMods(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Sets the maximum number of dynamic mods.
- setMaxDynamicMods(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Set the maximum number of variable modifications.
- setMaxEValue(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the maximal e-value searched for.
- setMaxEValue(double) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets the maximal e-value searched for.
- setMaxFragmentCharge(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the maximum fragment ion charge.
- setMaxFragmentCharge(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the maximal fragment charge.
- setMaxFragmentPerSeries(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the maximal number of fragments to retain per series.
- setMaxFragmentSize(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the max fragmentation size.
- setMaxHeterozygousVariants(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the max heterozygous variants.
- setMaxHitsPerSpectrumPerCharge(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Set the maximal number of hits searched per spectrum and per charge.
- setMaximumExpectationValueRefinement(double) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets the maximum expectation value to use for refinement.
- setMaxIntensity(Double) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Sets the maximum precursor intensity in this file.
- setMaxIsotopes(Integer) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Sets the maximal number of isotopes allowed (inclusive).
- setMaxIsotopicCorrection(int) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Sets the maximal isotopic correction.
- setMaxIterations(int) - Method in class com.compomics.util.math.clustering.KMeansClustering
-
Set the maximum number of iterations.
- setMaxLoadedProteins(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set the maximum number of proteins loaded into memory.
- setMaxLoadedSpectra(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set the maximum number of spectra loaded into memory.
- setMaxMissedCleavages(Integer) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Set the maximum number of missed cleavages.
- setMaxModificationIsoforms(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the max modification isoforms.
- setMaxModifications(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set the maximum number of modifications per peptide.
- setMaxModificationSites(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set the maximum number of modifications sites per modification per
peptide.
- setMaxModsForPeptide(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the max mods for peptide.
- setMaxMW(Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Sets the molecular weight of the fattest protein in the dataset.
- setMaxMz(Double) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Sets the maximum m/z in this file.
- setMaxMzDeviation(double) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Sets the maximal m/z deviation allowed.
- setMaxMzLadders(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the maximal m/z ladder length.
- setMaxNeutralLosses(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set the maximum number of water and ammonia losses per peptide.
- setMaxNeutralLossesPerModification(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set the maximum number identical modification specific losses per
peptide.
- setMaxNPeptides(Integer) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Sets the maximal number of peptides among the proteins of the dataset.
- setMaxNPsms(Integer) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Sets the the maximal amount of PSMs in the proteins of the dataset.
- setMaxNumberOfModifications(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets the maximal number of modifications.
- setMaxPadding(int) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set the max padding (distance between the axes and the border of the
panel).
- setMaxPeakCount(Integer) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Sets the maximum peak count in this file.
- setMaxPeakCount(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Set the maximum peak count.
- setMaxPeakCount(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Set the max peak count.
- setMaxPepLength(int) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Sets the maximal peptide length allowed.
- setMaxPeptideLength(int) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Sets the maximal peptide length allowed.
- setMaxPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the maximum peptide length.
- setMaxPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set the maximum peptide length.
- setMaxPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Sets the maximal peptide length allowed.
- setMaxPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Sets the maximal peptide length allowed.
- setMaxPeptideLength(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the maximal peptide length allowed.
- setMaxPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Sets the maximal peptide length allowed.
- setMaxPeptideLengthNoEnzyme(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets the maximal peptide length to use when searching with no enzyme.
- setMaxPeptideMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets the maximal peptide mass.
- setMaxPeptidePrecursorErrorDa(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Set the max peptide precursor mass error in Dalton.
- setMaxPeptidePrecursorErrorPpm(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Set the max peptide precursor mass error in ppm.
- setMaxPrecursorAdjustment(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Set the maximum precursor adjustment.
- setMaxPrecursorMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the maximum precursor mass.
- setMaxPrecursorMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Sets the maximum precursor mass.
- setMaxPrecursorMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Sets the maximum precursor mass.
- setMaxPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- setMaxPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- setMaxPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setMaxPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- setMaxPrimaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
-
Set the maximum value for the primary progress counter.
- setMaxProteinAccessionLength(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Sets the max protein accession length.
- setMaxProteinAveragePrecursorIntensity(Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Set the maximum protein average precursor intensity.
- setMaxProteinSummedPrecursorIntensity(Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Set the maximum summed protein precursor intensity.
- setMaxPtmsPerTagPeptide(int) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Sets the maximum number of PTMs to consider when mapping tags to protein
sequences.
- setMaxRank(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set the maximum rank.
- setMaxRT(Double) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Sets the maximal RT in this file.
- setMaxSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- setMaxSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- setMaxSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setMaxSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- setMaxSecondaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
-
Set the maximum value for the secondary progress counter.
- setMaxSpectrumChargeRange(int) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the maximum charge added when the charge is missing for a given
spectrum.
- setMaxSpectrumCount(int) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Sets the maximal amount of PSMs for the peptides in the current peptide
list.
- setMaxSpectrumCounting(Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Sets the maximal spectrum counting value of the proteins of the dataset.
- setMaxSpectrumMz(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the max spectrum m/z to search for.
- setMaxTagCount(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Sets the maximum number of tags per spectrum to be generated.
- setMaxTagPrecursorErrorDa(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Set the max tag precursor mass error in Dalton.
- setMaxTagPrecursorErrorPpm(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Set the max tag precursor mass error in ppm.
- setMaxValidatedPeptidesPerFraction(Integer) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Set the maximum validated peptides at the fraction level.
- setMaxValidatedSpectraPerFraction(Integer) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Set the maximum validated spectra at the fraction level.
- setMaxVariableModifications(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set the maximum number of variable modifications per peptide.
- setMaxVariableModificationsPerPeptide(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the maximum number of variable modifications of allowed on a single
peptide.
- setMaxVariableModificationsPerTypePerPeptide(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the maximum number of variable modifications of each modification
type allowed on a single peptide.
- setMaxVariableMods(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the maximum number of variable modifications per peptide.
- setMemoryMappedSequenceLibraries(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets whether sequence libraries should be mapped in memory.
- setMemoryParameter(int) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Sets the upper memory limit.
- setMemoryShare(double) - Method in class com.compomics.util.db.object.ObjectsCache
-
Sets the share of heap size which can be used before emptying the cache.
- setMessage(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
-
This method allows the caller to set a message on the progressbar.
- setMessage(String) - Method in class com.compomics.util.messages.FeedBack
-
Sets the message.
- setMethod(ReporterMethod) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
Sets the reporter method used.
- setMethodUsed(Quantification.QuantificationMethod) - Method in class com.compomics.util.experiment.quantification.Quantification
-
setter for the method used
- setMgfMaxSize(double) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the max mgf file size before splitting.
- setMgfNSpectra(int) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the max number of spectra in an mgf file.
- setMH(double) - Method in class com.compomics.util.experiment.refinement_parameters.PepnovoAssumptionDetails
-
Sets the PepNovo provided mH.
- setMinAllowedIntensityRatioToBasePeak(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the minimum allowed intensity ratio to base peak.
- setMinAminoAcidScore(int) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Set the minimum amino acid score.
- setMinAnnotatedPeaks(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the minimal number of annotated peaks a peptide should have.
- setMinChargeSearched(int) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Sets the minimal charge searched.
- setMinFragmentMz(double) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets the minimal fragment m/z.
- setMiniature(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set if the graphics panel is to be drawn in a miniature form.
- setMinimalChargeForMultipleChargedFragments(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the minimal precursor charge to account for multiply charged
fragments in OMSSA.
- setMinIsotopes(Integer) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Sets the minimal number of isotopes allowed (inclusive).
- setMinIsotopicCorrection(int) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Sets the minimal isotopic correction.
- setMinMissedCleavages(Integer) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Set the minimum number of missed cleavages.
- setMinPeakIntensity(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the minimum peak intensity.
- setMinPeaks(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the minimum number of peaks.
- setMinPeaks(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the minimal number of peaks a spectrum should contain.
- setMinPeaksPerSpectrum(int) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets the minimal number of peaks per spectrum.
- setMinPepLength(int) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Sets the maximal peptide length allowed.
- setMinPeptideLength(int) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Sets the minimal peptide length allowed.
- setMinPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the minimum peptide length.
- setMinPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set the minimum peptide length.
- setMinPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Sets the minimal peptide length allowed.
- setMinPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Sets the minimal peptide length allowed.
- setMinPeptideLength(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the minimal peptide length allowed.
- setMinPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Sets the minimal peptide length allowed.
- setMinPeptideLengthNoEnzyme(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets the minimal peptide length to use when searching with no enzyme.
- setMinPrecPerSpectrum(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the minimal number of precursors per spectrum.
- setMinPrecursorAdjustment(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Set the minimum precursor adjustment.
- setMinPrecursorMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the minimum precursor mass.
- setMinPrecursorMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Sets the minimum precursor mass.
- setMinPrecursorMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Sets the minimum precursor mass.
- setMinPrecursorMass(double) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets the minimal precursor mass.
- setMinRT(Double) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Sets the minimum RT in this file.
- setMinSpectrumChargeRange(int) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the minimum charge added when the charge is missing for a given
spectrum.
- setMinSpectrumMz(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the min spectrum m/z to search for.
- setMinSpectrumPeaks(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the min number of peaks in a spectrum.
- setMinTagLength(int) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Set the minimum tag length.
- setMinTerminiCleavages(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Set the minimum number of termini cleavages.
- setMinus1(double) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Sets the isotopic correction factor at -1 Da.
- setMinus2(double) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Sets the isotopic correction factor at -2 Da.
- setMinVariantDepth(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the min variant depth.
- setMiscleavages(int) - Method in class com.compomics.util.protein.Enzyme
-
This method allows the caller to specify the number of allowed missed
cleavages for this enzyme.
- setModel(TableModel, boolean) - Method in class com.compomics.util.gui.JTableForDB
-
This method allows you to specify a tablemodel and a boolean
which indicates whether or not the table should be sortable by
clicking the column headers.
- setModel(TableModel) - Method in class com.compomics.util.gui.JTableForDB
-
Sets a TableModel for the table and defaults it to being sortable.
- setModel(TableModel) - Method in class com.compomics.util.sun.TableMap
-
- setModel(TableModel) - Method in class com.compomics.util.sun.TableSorter
-
- setModification(String) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Sets the theoretic PTM.
- setModificationLocalizationParameters(ModificationLocalizationParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the modification localization parameters.
- setModificationParameters(ModificationParameters) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Sets the modification settings.
- setModificationRefinement(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Sets whether the protein mapping should be refined based on terminal and pattern modifications.
- setModifications(ArrayList<String>) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Sets the variable modifications searched.
- setModifications(Vector) - Method in class com.compomics.util.protein.AASequenceImpl
-
Simple setter for the modifications.
- setModPeptidesAreDifferent(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set whether modified peptides are considered different.
- setMonoIsotopic(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set whether monoisotopic mass values shall be used (in contrast to
average mass values).
- setMonoisotopicPrecursor(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if the precursor mass is monoisotopic.
- setMsFormat(ProteoWizardMsFormat) - Method in class com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters
-
Sets the format to convert to.
- setMsFormat(ThermoRawFileParserOutputFormat) - Method in class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserParameters
-
Sets the format to convert to.
- setMzBinOffset(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the m/z bin offset.
- setMzBinWidth(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the m/z bin width.
- setMzFidelityScoreWeight(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Set the mzFidelity score weight.
- setMzidOutput(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if the mzid output is to be created.
- setMzValues(double[]) - Method in class com.compomics.util.io.PklFile
-
- setnAaDeletions(int) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Sets the number of amino acid deletions allowed.
- setnAaInsertions(int) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Sets the number of amino acid insertions allowed.
- setnAaSubstitutions(int) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Sets the number of amino acid substitutions allowed.
- setnAaSwap(int) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Sets the number of amino acid swaps allowed.
- setName(String) - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
-
Setter for the ion name.
- setName(String) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Sets the modification name.
- setName(String) - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
-
Sets the name of this substitution matrix.
- setName(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Sets the name of the filter.
- setName(String) - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
-
Sets a new name for the database.
- setName(String) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Sets the name of the reagent.
- setName(String) - Method in class com.compomics.util.io.export.ExportScheme
-
Sets the name of the scheme.
- setName(String) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the name of the parameters.
- setName(String) - Method in class com.compomics.util.pride.CvTerm
-
Sets the name.
- setName(String) - Method in class com.compomics.util.pride.prideobjects.Contact
-
Set the contact name.
- setName(String) - Method in class com.compomics.util.pride.prideobjects.ContactGroup
-
Set the contact group name.
- setName(String) - Method in class com.compomics.util.pride.prideobjects.Instrument
-
Set the instrument name.
- setName(String) - Method in class com.compomics.util.pride.prideobjects.Protocol
-
Set the protocol name.
- setName(String) - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
-
Set the references group name.
- setName(String) - Method in class com.compomics.util.pride.prideobjects.Sample
-
Set the name of the sample.
- setnAnnotatedMostIntensePeaks(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the minimal number of annotated most intense peaks.
- setnClusters(int) - Method in class com.compomics.util.math.clustering.settings.KMeansClusteringSettings
-
Sets the number of clusters to use.
- setnConfidentProteins(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Sets the number of confident proteins.
- setNeutralLosses(ArrayList<NeutralLoss>) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Sets the neutral losses possibly encountered with this modification.
- setNeutralLossesAuto(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Sets whether neutral losses should be automatically selected.
- setNeutralLossesMap(NeutralLossesMap) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Sets the map of neutral losses to annotate.
- setNeutralLossesSequenceAuto(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Sets whether neutral losses are considered only for amino acids of
interest or not.
- setNeutronThreshold(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the mass after which exact neutron mass should be considered in the
calculation.
- setNewTitle(String) - Method in class com.compomics.util.gui.DummyFrame
-
Update the frame title and return the frame.
- setnMissedCleavages(String, int) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
-
Sets the number of allowed missed cleavages.
- setNoOneHitWonders(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set whether one hit wonders are to be excluded.
- setNoProlineRuleSeries(ArrayList<Integer>) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the id numbers of ion series to apply no product ions at proline
rule at.
- setNormalizationFactors(NormalizationFactors) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
Sets the normalization factors.
- setNormalize(Boolean) - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
-
Sets whether the spectrum counting index should be normalized.
- setNormalizePeaksAcrossAllWindows(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the normalize peaks across all windows.
- setNovorPtmMap(HashMap<String, String>) - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
-
Set the Novor to utilities PTM map.
- setnPeaks(int) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets the number of most intense peaks to consider.
- setnPeaksInDoubleChargeWindow(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the number of peaks in doubly charged windows.
- setnPeaksInSingleChargeWindow(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the number of peaks in singly charged windows.
- setnTermModification(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Sets the N-term modification.
- setnThreads(int) - Method in class com.compomics.util.parameters.tools.ProcessingParameters
-
Sets the number or threads to use.
- setNumberOfBatches(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Set the number of batches per node to strive for when using the MPI-based
parallelization features.
- setNumberOfCandidates(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets the number of candidates.
- setNumberOfModificationsPerPeptide(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Set the maximum number of modifications per peptide.
- setNumberOfPeaksToKeepPerWindow(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the number of peaks to keep per window.
- setNumberOfPeptides(int) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Set the number of peptides to report per spectrum.
- setNumberOfSpectrumMarches(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Set the maximum number of spectrum matches.
- setNumberOfSpectrumMatches(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the maximum number of spectrum matches.
- setNumberOfSpectrumMatches(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Set the maximum number of spectrum matches.
- setNumberOfSpectrumMatches(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the number of PSMs to report per spectrum.
- setNumberOfTasks(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Set the number of tasks.
- setNumberOfWindows(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the number of windows.
- setNumberTolerableTermini(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Set the number of tolerable termini.
- setNumChargeStates(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Sets the number of charge states.
- setNumericParameter(String, Double) - Method in class com.compomics.util.experiment.ProjectParameters
-
- setNumIntensityClasses(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Sets the number of intensity classes.
- setNumIntensityClasses(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Set the number of intensity classes.
- setnValidatedProteins(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Sets the number of validated proteins.
- setnValidatedPsms(int) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Sets the number of validated PSMs for the currently selected peptide.
- setnVariants(int) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Sets the total number of variants allowed.
- setObject(K) - Method in class com.compomics.util.general.BoxedObject
-
Sets the boxed object.
- setObjectCache(ObjectsCache) - Method in class com.compomics.util.db.object.ObjectsDB
-
Sets the object cache to be used by this database.
- setObservedFractionalMassesAll(HashMap<String, ArrayList<Double>>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Set the observed molecular masses for each fraction in kDa.
- setOccurrence(Atom, Integer, Integer) - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
-
Sets the occurrence of a given atom.
- setOntology(String) - Method in class com.compomics.util.pride.CvTerm
-
Sets the ontology.
- setOrganismIdentifier(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the organism identifier.
- setOutputData(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Sets whether data should be copied along with the identification files in
the SearchGUI output.
- setOutputFolder(File) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Sets the last used output folder.
- setOutputFolderName(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the name of the output folder.
- setOutputFormat(String) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set the output format.
- setOutputFormat(String) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Set the output format.
- setOutputHistograms(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether histograms should be written in the result file
- setOutputProteins(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether the protein bloc should be included in the export.
- setOutputResults(String) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Set the output results filter.
- setOutputSequences(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether the protein sequences should be included in the protein
block of the export.
- setOutputSpectra(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether the spectra should be exported in the result file.
- setOutputSuffix(String) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Sets the output tags suffix.
- setParametersFromSearch(SearchParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets identification parameters based on given search parameters.
- setParametersFromSearchParameters(SearchParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Updates the annotation parameters based on search parameters.
- setParentFolder(String) - Static method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
-
Set the parent folder.
- setParentFolder(String) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFolder
-
Sets the parent folder where to write cms files to.
- setParentMonoisotopicMassIsotopeError(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether the parent ion mass tolerance is expanded by opening up
multiple tolerance windows centered on the first and second 13C isotope
peaks for a peptide.
- setPassive(boolean) - Method in class com.compomics.util.io.ftp.FTP
-
Set Passive mode Transfers.
- setPathParameter(UtilitiesPathParameters.UtilitiesPathKey, String) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
-
Sets the path according to the given key and path.
- setPathSettings() - Method in class com.compomics.cli.paths.PathSettingsCLI
-
Sets the path settings according to the pathSettingsCLIInputBean.
- setPattern(AminoAcidPattern) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Sets the amino acid pattern targeted by this modification.
- setPdbaccession(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
Set the PDB accession.
- setPeackPicking(boolean) - Method in class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserParameters
-
Set if peak picking is to be performed.
- setPeakPicked(Boolean) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Set if the indexed file seems to contain only peak picked spectra or not.
- setPeaks(HashMap) - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
-
Setter for the peaks
- setPeaks(HashMap) - Method in interface com.compomics.util.interfaces.SpectrumFile
-
This method sets the peaks on the spectrum.
- setPeakWaterMarkColor(Color) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set the peak water mark color.
- setPeakWidth(float) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set the peak width.
- setPepNovoPtmMap(Map<String, String>) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
-
Set the PepNovo to utilities PTM map.
- setPeptide(Peptide) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
Setter for the peptide.
- setPeptide(Peptide, int, ModificationParameters, SequenceProvider, SequenceMatchingParameters, SpecificAnnotationParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
Sets a new peptide to annotate.
- setPeptide(Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, HashMap<Integer, HashMap<Integer, ArrayList<Ion>>>, int, SpecificAnnotationParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
-
Sets a new peptide to annotate.
- setPeptide(Peptide) - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
-
Returns the peptides.
- setPeptideAssumptionFilter(PeptideAssumptionFilter) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the filter used when importing PSMs.
- setPeptideAssumptionMap(HashMap<Integer, TreeMap<Double, ArrayList<PeptideAssumption>>>) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Sets the peptide assumption map.
- setPeptideFilters(ArrayList<Filter>) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Sets the list of peptide quality filters.
- setPeptideHideFilters(HashMap<String, PeptideFilter>) - Method in class com.compomics.util.gui.filtering.FilterParameters
-
Sets the peptide hide filters.
- setPeptideLengthDistribution(NonSymmetricalNormalDistribution) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Sets the distribution of validated peptide lengths.
- setPeptideList(long[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Sets the current peptide list.
- setPeptideMatchesKeys(long[]) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Sets the peptide keys for this protein match.
- setPeptideSequenceFont(Font) - Method in class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
-
Set the font to use for the peptide sequence.
- setPeptideShakerPath(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the path to the PeptideShaker installation.
- setPeptideStarFilters(HashMap<String, PeptideFilter>) - Method in class com.compomics.util.gui.filtering.FilterParameters
-
Sets the peptide star filters.
- setPeptideVariantsParameters(PeptideVariantsParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the peptide variant parameters.
- setPepXmlOutput(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if the pepxml output is to be created.
- setPercentLength(double) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set the length of the reference area in percent.
- setPerformDeisotoping(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Sets if deisotoping is to be performed.
- setPinOutput(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if the Percolator output is to be created.
- setPlus1(double) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Sets the isotopic correction factor at +1 Da.
- setPlus2(double) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Sets the isotopic correction factor at +2 Da.
- setPmid(String) - Method in class com.compomics.util.pride.prideobjects.Reference
-
Set the PubMed ID of the reference.
- setPNovoPtmMap(HashMap<Character, String>) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Set the pNovo to utilities PTM map.
- setPNovoPtmResiduesMap(HashMap<Character, Character>) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Set the pNovo to original amino acids residue map.
- setPointSize(Integer) - Method in class com.compomics.util.gui.spectrum.ChromatogramPanel
-
This method allows the caller to set the point size for the
profileChromatogram.
- setPosition(int) - Method in class com.compomics.util.protein.Enzyme
-
This method allows the caller to set the cleavage position for the
Enzyme.
- setPotentialModificationsForFullRefinment(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether the refinement modifications should be used for the full
refinement
- setPpm(boolean) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Sets whether the precursor mass tolerance is in ppm.
- setPrecurorCharge(int) - Method in class com.compomics.util.io.PklFile
-
- setPrecursorAccuracy(double) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Sets the precursor tolerance.
- setPrecursorAccuracyType(SearchParameters.MassAccuracyType) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Sets the precursor accuracy type.
- setPrecursorAdjustmentStep(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Set the precursor adjustment step.
- setPrecursorCharge(int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Sets the precursor charge.
- setPrecursorChargesMissing(Boolean) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
-
Set if at least one spectrum is missing the precursor charge.
- setPrecursorIntensity(double) - Method in class com.compomics.util.io.PklFile
-
- setPrecursorIntensityAveragePerFraction(HashMap<String, Double>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Sets the precursor intensity per fraction map.
- setPrecursorIntensityPerFraction(HashMap<String, ArrayList<Double>>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Get the precursor intensity in the given fraction.
- setPrecursorIntensitySummedPerFraction(HashMap<String, Double>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Sets the summed precursor intensity per fraction map.
- setPrecursorMZ(double) - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
-
Setter for the precursor MZ
- setPrecursorMZ(double) - Method in interface com.compomics.util.interfaces.SpectrumFile
-
This method sets the precursor M/Z on the file.
- setPrecursorMz(double) - Method in class com.compomics.util.io.PklFile
-
- setPrideFolder(String) - Static method in class com.compomics.util.pride.PrideObjectsFactory
-
Sets the folder where pride annotation information should be saved.
- setPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- setPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- setPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- setPrimaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
-
Sets the primary progress counter to the given value.
- setPrimaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- setPrimaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- setPrimaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setPrimaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- setPrimaryProgressCounterIndeterminate(boolean) - Method in interface com.compomics.util.waiting.WaitingHandler
-
Sets whether the primary progress counter is indeterminate or not.
- setPrintExpectScore(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set if the export score is to be printed.
- setPrintPeptides(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if a list of the peptides should be printed to the output folder.
- setPrintProgressIndicatorSize(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the progress indicator size.
- setProbabilisticScore(int, double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Sets the probabilistic score at a given site.
- setProbabilisticScoreCalculation(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Sets whether a probabilistic modification score is required.
- setProbabilisticScoreNeutralLosses(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Sets whether the neutral losses shall be taken into account for spectrum
annotation when calculating the probabilistic score.
- setProbabilisticScoreThreshold(double) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Sets the probabilistic score threshold (inclusive).
- setProbability(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Set the probability.
- setProcessingType(ProcessingParameters.ProcessingType) - Method in class com.compomics.util.parameters.tools.ProcessingParameters
-
Sets the processing type.
- setProfile(double[][]) - Method in class com.compomics.util.gui.protein.ModificationProfile
-
Sets the profile.
- setProfileMode(boolean) - Method in class com.compomics.util.gui.spectrum.ChromatogramPanel
-
Set the drawing style to profile or centroid mode.
- setProfileMode(boolean) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
-
Change the drawing type of the spectrum.
- setProgress(int, String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
-
This method allows the caller to set the progress on the progressbar to the specified value,
along with the specified message.
- setProgress(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
-
This method sets the progress to the specified value.
- setProperty(ModificationFeature.Property) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
-
Sets the feature property.
- setProperty(PeptideFeature.Property) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
-
Sets the feature property.
- setProteinConfidenceMwPlots(Double) - Method in class com.compomics.util.parameters.identification.advanced.FractionParameters
-
Sets the protein confidence for inclusion in MW plots.
- setProteinEvidence(Integer) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the protein evidence level.
- setProteinFilters(ArrayList<Filter>) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Sets the list of protein quality filters.
- setProteinHideFilters(HashMap<String, ProteinFilter>) - Method in class com.compomics.util.gui.filtering.FilterParameters
-
Sets the protein hide filters.
- setProteinInferenceClass(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Sets the protein group class.
- setProteinInferenceParameters(ProteinInferenceParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the protein inference parameters.
- setProteinKeys(long[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Sets the ordered protein list.
- setProteinKeys(long[]) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Sets the list of ordered protein keys.
- setProteinList(long[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Sets the protein list.
- setProteinListAfterHiding(long[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Sets the protein list after all hiding filters have been used.
- setProteinMapping(TreeMap<String, int[]>) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Sets the protein mapping as a map of 0-based indexes for every protein
accession.
- setProteinPtmComplexity(double) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Set the proteinPtmComplexity.
- setProteinQuickAcetyl(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether the protein quick acetylation option should be triggered.
- setProteinStarFilters(HashMap<String, ProteinFilter>) - Method in class com.compomics.util.gui.filtering.FilterParameters
-
Sets the protein star filters.
- setProteinToGoMap(HashMap<String, HashSet<String>>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
-
Sets the protein to GO terms accession map.
- setProteoWizardPath(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the path to ProteoWizard.
- setProtocol(int) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Set the protocol ID.
- setPsiModCvTerm(CvTerm) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Set the PSI-MOD CV term associated with this modification.
- setPsmFilters(ArrayList<Filter>) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
-
Sets the list of PSM quality filters.
- setPsmHideFilters(HashMap<String, PsmFilter>) - Method in class com.compomics.util.gui.filtering.FilterParameters
-
Sets the psm hide filters.
- setPsmList(long[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Sets the PSM list.
- setPsmScoringParameters(PsmScoringParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the scoring preferences used when scoring PSMs.
- setPsmStarFilters(HashMap<String, PsmFilter>) - Method in class com.compomics.util.gui.filtering.FilterParameters
-
Sets the psm star filters.
- setPtmIndex(String, int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets the index for a given modification.
- setPtmIndex(String, int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the index for a given modification.
- setPtmIndexes(ModificationParameters) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Set the PTM indexes of the modifications searched.
- setPtmName(String) - Method in class com.compomics.util.gui.protein.ModificationProfile
-
Sets the PTM name.
- setPtmToPrideMap(PtmToPrideMap) - Method in class com.compomics.util.pride.PrideObjectsFactory
-
Sets a new PTM to PRIDE map.
- setQcFilters(HashMap<String, Boolean>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Sets the qc filters.
- setQcResult(String, boolean) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Sets whether the match passed a quality control check.
- setQuickPyrolidone(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether the quick pyrolidone option should be triggered.
- setRank(int) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Set the rank of the PeptideAssumption.
- setRankScore(double) - Method in class com.compomics.util.experiment.refinement_parameters.PepnovoAssumptionDetails
-
Sets the PepNovo rank score.
- setRawHeader(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the entire header.
- setRawScore(double) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Sets the raw score as provided by the identification algorithm.
- setReadOnly(boolean) - Method in class com.compomics.util.db.object.ObjectsCache
-
Sets the cache in read only.
- setReadOnly(boolean) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Sets the cache in read only.
- setReadTweets(ArrayList<String>) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the list of read tweets.
- setRef(double) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Sets the value used as reference for the correction factors.
- setReference(String) - Method in class com.compomics.util.pride.prideobjects.Reference
-
Set the reference.
- setReferenceMass(Double) - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
-
Sets the reference total mass to use for normalization.
- setReferences(ArrayList<Reference>) - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
-
Set the references.
- setRefine(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether the second pass search should be triggered.
- setRefinePointMutations(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether point mutations should be looked for during the refinement
process.
- setRefineSemi(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether the semi enzymatic option of the second pass search should
be triggered.
- setRefineSnaps(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether snAPs should be used during the refinement process.
- setRefineSpectrumSynthesis(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether the spectrum synthesis option should be used during the
refinement process.
- setRefineUnanticipatedCleavages(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether the unanticipated cleavages option should be used during the
refinement process.
- setRefMass(double) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Sets the reference mass used to convert ppm to Da.
- setRefMass(double) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Sets the reference mass for the conversion of the fragment ion tolerance
from ppm to Dalton.
- setRelatedIons(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Sets whether related ions should be annotated by default.
- setRelationship(AAPropertyRelationshipFeature.Relationship) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
-
Sets the relationship between the features.
- setRelimsPath(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the path to the Relims installation.
- setRemoveMethionine(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Sets if n-term methionine is to be removed.
- setRemovePrecursor(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set if the precursor is to be removed.
- setRemovePrecursor(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets whether the precursor shall be removed for OMSSA.
- setRemovePrecursor(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if the precursor peak is to be removed.
- setRemovePrecursorTolerance(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the precursor removal tolerance.
- setRemovePrecursorTolerance(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the tolerance with which to remove the precursor peak.
- setRemoveTempFolders(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if the output and index folders are to be removed when the search has
completed.
- setRemoveUnknownModifications(boolean) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
-
Set whether unknown modifications shall be removed.
- setRenameXTandemFile(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set if the X! Tandem file should be renamed.
- setReportBothBestHitsForTD(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
-
Set if target and decoy are ranked separately or shared.
- setReporterIon(ReporterIon) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
-
Sets the reporter ion to look for in the spectrum.
- setReporterIons(ArrayList<ReporterIon>) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Sets the reporter ions possibly encountered with this modification.
- setReporterIons(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Sets whether reporter ions should be annotated by default.
- setReporterPath(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the path to the PeptideShaker installation.
- setReportFailed(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Sets the report when the filter is not passed.
- setReportPassed(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Sets the report when the filter is passed.
- setRequireVariableMods(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set if at least one variable modification is required per peptide.
- setResolution(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
Set the resolution.
- setRest(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the rest of the header.
- setRestrict(char[]) - Method in class com.compomics.util.protein.Enzyme
-
This method allows the caller to specify the residues that restrict
cleavage.
- setRestrict(String) - Method in class com.compomics.util.protein.Enzyme
-
This method allows the caller to specify the residues which restrict
cleavage.
- setRewindIons(ArrayList<Integer>) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
Sets the rewind ions searched as list of integers as indexed in the
FragmentIon class.
- setRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- setRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- setRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- setRunCanceled() - Method in interface com.compomics.util.waiting.WaitingHandler
-
Set the process as canceled.
- setRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- setRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- setRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- setRunFinished() - Method in interface com.compomics.util.waiting.WaitingHandler
-
Set the process as finished.
- setRunGptm(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set whether the G-PTM search is to be performed.
- setRunNotFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Set the run to not finished.
- setSampleIndex(String, Integer) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
Set the sample index for the given sample.
- setScalePrecursor(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets whether the precursor shall be scaled for OMSSA.
- setScalingFactor(double) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Sets the scaling factor.
- setSchema(URL) - Method in class com.compomics.util.pride.validation.PrideXmlValidator
-
Set the schema.
- setScientificXAxis(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set if the x-axis tags are to be drawn using scientific annotation.
- setScientificXAxis(String) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set if the x-axis tags are to be drawn using scientific annotation.
- setScientificYAxis(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set if the y-axis tags are to be drawn using scientific annotation.
- setScientificYAxis(String) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set if the y-axis tags are to be drawn using scientific annotation.
- setScore(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Set the peptide score.
- setScore(double) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Sets the score.
- setScoreCutoff(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the score cut-off.
- setSearchDecoyDatabase(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
-
Set whether MS-GF+ is to create and search a decoy database.
- setSearchForwardFragmentFirst(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets whether forward ions (b1) should be searched first.
- setSearchGuiOutputParameters(OutputParameters) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Sets how SearchGUI output files should be organized.
- setSearchGuiPath(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the path to the SearchGUI installation.
- setSearchParameters(SearchParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the parameters used for the spectrum matching.
- setSearchPositiveIons(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets whether positive ions are searched.
- setSearchRewindFragments(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets whether C-terminal fragments should be searched.
- setSearchTarget(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set whether target sequences are to be searched.
- setSearchType(MetaMorpheusParameters.MetaMorpheusSearchType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the search type.
- setSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- setSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- setSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- setSecondaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
-
Sets the secondary progress counter to the given value.
- setSecondaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- setSecondaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- setSecondaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setSecondaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- setSecondaryProgressCounterIndeterminate(boolean) - Method in interface com.compomics.util.waiting.WaitingHandler
-
Sets the secondary progress counter to indeterminate or not.
- setSecondaryProgressText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- setSecondaryProgressText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- setSecondaryProgressText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setSecondaryProgressText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- setSecondaryProgressText(String) - Method in interface com.compomics.util.waiting.WaitingHandler
-
Set the secondary progress counter text.
- setSelectedCharges(HashSet<Integer>) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Sets the charges selected for annotation.
- setSelectedExportFolder(LastSelectedFolder) - Method in class com.compomics.util.gui.VennDiagramDialog
-
- setSelectedExportFolder(LastSelectedFolder) - Method in class com.compomics.util.gui.XYPlottingDialog
-
- setSelectedIonsMap(HashMap<Ion.IonType, HashSet<Integer>>) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Sets the map of ions to annotate.
- setSelectedMethod(SpectrumCountingMethod) - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
-
Set the current spectrum counting method.
- setSelectedOutput(String) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the output type, omx, csv or pepXML.
- setSelectedOutputFormat(CometParameters.CometOutputFormat) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Sets the output format.
- setSelectedPositions(Integer[]) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Set the selected positions.
- setSelectedProbabilisticScore(ModificationLocalizationScore) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Sets the selected probabilistic score.
- setSelfUpdating(boolean) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
-
Sets whether the table is in self update mode.
- setSequence(String) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
Sets the sequence.
- setSequence(String) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Sets for the sequence.
- setSequence(char[]) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
-
Sets the sequence.
- setSequence(String, boolean) - Method in class com.compomics.util.gui.protein.SequenceModificationPanel
-
Set the Sequence for the SequenceFragmentationPanel.
- setSequence(String, boolean) - Method in class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
-
Set the Sequence for the SequenceFragmentationPanel.
- setSequence(String) - Method in interface com.compomics.util.interfaces.Sequence
-
This method will set the sequence.
- setSequence(NucleotideSequenceImpl) - Method in class com.compomics.util.nucleotide.NucleotideSequence
-
This method allows the setting of a sequence.
- setSequence(String) - Method in class com.compomics.util.nucleotide.NucleotideSequenceImpl
-
This method will set the sequence.
- setSequence(String) - Method in class com.compomics.util.protein.AASequenceImpl
-
Simple setter for the sequence.
- setSequence(AASequenceImpl) - Method in class com.compomics.util.protein.Protein
-
Simple setter for the sequence.
- setSequenceMatchingParameters(SequenceMatchingParameters) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
-
Sets the sequence matching preferences to use when mapping modifications
on amino acid sequences.
- setSequenceMatchingParameters(SequenceMatchingParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Sets the sequence matching preferences.
- setSequenceMatchingType(SequenceMatchingParameters.MatchingType) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
-
Sets the sequence matching type.
- setSerializationFolder(String) - Static method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
-
Sets the folder where to save the factory.
- setSerializationFolder(String) - Static method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Sets the folder where the factory is saved.
- setShortName(String) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Sets the short modification name.
- setShowAllPeaks(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Set if all peaks or just the annotated ones are to be shown.
- setShowForwardIonDeNovoTags(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Set if the automatic forward ion de novo tags are to be shown.
- setShowLegend(boolean) - Method in class com.compomics.util.gui.VennDiagramPanel
-
Set if the legend is to be shown.
- setShowPrecursorDetails(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set whether the precursor details are to be shown.
- setShowResolution(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set whether the resolution is to be shown.
- setShowRewindIonDeNovoTags(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Set if the automatic rewind ion de novo tags are to be shown.
- setSimplifyGroups(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Sets whether the protein groups should be simplified based on the
PeptideShaker confidence.
- setSimplifyGroupsConfidence(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Sets whether the protein groups should be simplified based on the peptide
confidence level.
- setSimplifyGroupsEnzymaticity(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Sets whether the protein groups should be simplified based on the peptide
enzymaticity.
- setSimplifyGroupsEvidence(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Sets whether the protein groups should be simplified based on the Uniprot
evidence level.
- setSimplifyGroupsVariants(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
-
Sets whether the protein groups should be simplified based on the peptide
variant matching.
- setSingleChargeWindow(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets the window size for singly charged ions.
- setSite(int) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Setter for the modification site, 1 is the first amino acid.
- setSiteConfidence(int, int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
-
Sets the confidence level of a modification site.
- setSkylinePath(String) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets the skyline path.
- setSortPsmsOnRt(Boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set if the PSMs are sorted on retention time, false sorts on PSM score.
- setSource(CvTerm) - Method in class com.compomics.util.pride.prideobjects.Instrument
-
Set the instrument source.
- setSourceFile(String) - Method in class com.compomics.util.io.ftp.FTP
-
This method allows to set the source for the file that is to be
transferred.
- setSparklineColor(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Setter for the sparkline color.
- setSparklineColorDoubtful(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Setter for the doubtful sparkline color.
- setSparklineColorFalsePositives(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Setter for the false positives sparkline color.
- setSparklineColorNonValidated(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Setter for the non-validated sparkline color.
- setSparklineColorNotFound(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Setter for the not found sparkline color.
- setSparklineColorPossible(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Setter for the possible sparkline color.
- setSpecificity(String, DigestionParameters.Specificity) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
-
Sets the expected specificity of the enzyme.
- setSpectrum(String, String, Spectrum, double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Sets a new spectrum to annotate.
- setSpectrumAnnotatedMirroredPeakColor(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the color to use for the annotated mirrored peaks.
- setSpectrumAnnotatedPeakColor(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the color to use for the annotated peaks.
- setSpectrumAnnotatedPeakWidth(float) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the width of the annotated peaks.
- setSpectrumBackgroundPeakColor(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the color to use for the background peaks.
- setSpectrumBackgroundPeakWidth(float) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Set the width of the background peaks.
- setSpectrumCharges(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the spectrum charges to search for.
- setSpectrumCountingPreferences(SpectrumCountingParameters) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Sets the spectrum counting preferences.
- setSpectrumFile(String) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Sets the spectrum file name.
- setSpectrumFile(SpectrumFile) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
-
This method initializes a SpectrumPanel based on the spectrum information
in the specified SpectrumFile.
- setSpectrumFileId(String) - Method in class com.compomics.util.io.PklFile
-
- setSpectrumFolder(File) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Sets the last used spectrum folder.
- setSpectrumMatchesKeys(long[]) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
Sets the spectrum matches keys.
- setSpectrumPeakColor(Color) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
-
Set the default spectrum peak color.
- setSpectrumProfileModeLineColor(Color) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
-
Set the default spectrum profile mode color.
- setSpectrumTitle(String) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Sets the spectrum title.
- setSqtOutput(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if the sqt output is to be created.
- setStarred(boolean) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Star/Unstar a match.
- setStart(double) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set the start value.
- setStartBlock(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Set the block start.
- setStartProtein(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
Set the protein start.
- setStoreSpectraFileName(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the name of the file where the binary spectra are to be stored.
- setStpBias(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether the stP bias should be triggered
- setString(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
Sets the string to display in the progress bar.
- setStringParameter(String, String) - Method in class com.compomics.util.experiment.ProjectParameters
-
- setSubscriptAnnotationNumbers(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set if the numbers in the peak annotations are to be subscripted.
- setTag(Tag, ModificationParameters, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
-
Sets a new tag to match.
- setTag(Tag) - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
-
- setTagAssumptionMap(HashMap<Integer, TreeMap<Double, ArrayList<TagAssumption>>>) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Sets the tag assumption map.
- setTagLength(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Sets the tag length.
- setTarget(Integer) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Sets the index of the amino acid of interest in the pattern.
- setTargetDecoy(boolean) - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
-
Sets whether the FASTA file should be processed as target-decoy or only
target.
- setTargetDecoyFileNameSuffix(String) - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
-
Set the target-decoy file name suffix.
- setTargeted(int, ArrayList<Character>) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Sets the amino acids targeted at a given index.
- setTaxonomy(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
-
Sets the taxonomy.
- setTerminalMassShifts(double, double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Sets the terminal m/z shifts.
- setTextOutput(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if the text output is to be created.
- setTheoreticalFragmentIonsSumOnly(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set if the theoretical fragment ions are calculated on the sum in the bin
alone.
- setTheoreticMass(double) - Method in class com.compomics.util.experiment.biology.ions.Ion
-
Sets a new theoretic mass.
- setTicCutoffPercentage(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Set the TIC cutoff in percent.
- setTicCutoffPercentage(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Set the TicCutoffPercentage.
- setTiesResolution(SpectrumAnnotator.TiesResolution) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Sets the ties resolution method to use when multiple peaks can be
assigned to an ion.
- setTitle(String) - Method in class com.compomics.util.messages.FeedBack
-
Sets the title.
- setTitle(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
Set the title.
- setTitle(String) - Method in class com.compomics.util.protein.Enzyme
-
This method allows the caller to change the title (name) of the Enzyme.
- setToolTips(Vector) - Method in class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer
-
Set the tooltips.
- setTopPeaks(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets the top peaks number.
- setTopPeaksWindow(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
-
Sets the top peaks window size.
- setTotalIntensity(double) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Set the total intensity.
- setTotalPartitions(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the total partitions.
- setTotalPeptidesPerFraction(HashMap<String, Integer>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Set the total number of peptides per fraction.
- setTotalSpectrumCounting(Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Sets the total spectrum counting.
- setTotalSpectrumCountingMass(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Sets the total spectrum counting value.
- setTrimMs1Peaks(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set whether Ms1 peaks are to be trimmed.
- setTrimMsMsPeaks(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set whether MsMs peaks are to be trimmed.
- setType(MatchFilter.FilterType) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Sets the type of the filter.
- setType() - Method in class com.compomics.util.experiment.io.parameters.DummyParameters
-
- setType() - Method in interface com.compomics.util.experiment.io.parameters.MarshallableParameter
-
Sets the parameters type.
- setType(String) - Method in class com.compomics.util.experiment.patient.PatientInformation
-
Sets the type of information.
- setType(FeedBack.FeedBackType) - Method in class com.compomics.util.messages.FeedBack
-
Sets the feedback type.
- setType() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
-
- setType() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
-
- setUnevenRowColor(Color) - Method in class com.compomics.util.AlternateRowColoursJTable
-
Sets the colour of the uneven numbered rows; by default, the default JTable background color will be used..
- setUnimodCvTerm(CvTerm) - Method in class com.compomics.util.experiment.biology.modifications.Modification
-
Set the Unimod CV term associated with this modification.
- setUnit(UnitOfMeasurement) - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
-
Sets the unit used for normalization.
- setUnstoppable(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
Set this to true of the process the progress bar is used for is not
possible to stop, or not possible to stop nicely.
- setUpGUI(Frame, String) - Method in class com.compomics.software.settings.gui.PathParametersDialog
-
Sets up the GUI components.
- setUpGUI() - Method in class com.compomics.util.gui.filtering.FilterDialog
-
Sets up the GUI components.
- setUpperClearMzRange(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
Set the upper mass value for the clear mz range.
- setUpperPrecursorMass(int) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
-
Set the upper precursor mass.
- setUpTable() - Method in class com.compomics.util.gui.filtering.FilterDialog
-
Updates the table content according to the selected filter.
- setUpTable() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser
-
Updates the table content.
- setUrParams(HashMap<Long, UrParameter>) - Method in class com.compomics.util.experiment.personalization.ExperimentObject
-
Sets the user parameters map.
- setUseChargeStateFromMS(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
-
Sets whether the charge state from the spectrum should be used.
- setUseCorrelationCorrectionScore(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
-
Sets whether the correlation correction score should be used.
- setUseDeltaScore(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set whether delta score is to be used.
- setUseFlankingPeaks(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if flanking peaks are to be used.
- setUseGeneMapping(Boolean) - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
-
Sets whether gene mappings should be used.
- setUseMassDeltaCombinations(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
If true, pairs of delta mass annotations are used when doing de novo
sequencing.
- setUseNeutralLossPeaks(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set if the neutral loss peaks are to be used.
- setUseNoiseSuppression(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
-
Sets whether noise suppression should be used when importing spectra.
- setUseProvidedPrecursorInfo(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set whether the provided precursor info is to be used.
- setUserAdvocates(HashMap<Integer, Advocate>) - Static method in class com.compomics.util.experiment.identification.Advocate
-
Returns the map of user advocates imported.
- setUserParametersFolder(String) - Static method in class com.compomics.util.parameters.UtilitiesUserParameters
-
Sets the user preferences file to be used.
- setUseSmartPlusThreeModel(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
-
Sets if the UseSmartPlusThreeModel is to be used.
- setUseSparseMatrix(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
-
- setValidatedOnly(Boolean) - Method in class com.compomics.util.io.export.ExportScheme
-
Sets whether only validated results should be exported.
- setValidatedPeptidesPerFraction(HashMap<String, Integer>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Get the number of validated peptides in the given fraction.
- setValidatedProteinList(long[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
-
Sets the list of validated proteins.
- setValidatedSpectraPepFraction(HashMap<String, Integer>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
-
Get the number of validated spectra in the given fraction.
- setValidatedTargetProteinKeys(long[]) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
-
Sets the keys of the validated target protein matches.
- setValidationQCParameters(ValidationQcParameters) - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
-
Sets the validation QC preferences.
- setValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
Sets the progress bar value.
- setValue(String) - Method in class com.compomics.util.pride.CvTerm
-
Sets the value.
- setValueAt(int, int, Double) - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- setValueAt(Object, int, int) - Method in class com.compomics.util.sun.TableMap
-
- setValueAt(Object, int, int) - Method in class com.compomics.util.sun.TableSorter
-
- setValueForItem(String, Object) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
-
Sets the value for a given item.
- setVariableModifications(ModificationMatch[]) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
-
Sets the variable modifications.
- setVariableModifications(ModificationMatch[]) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Sets the variable modifications.
- setVariantMatches(HashMap<String, HashMap<Integer, PeptideVariantMatches>>) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
-
Sets the sequence variant matches of this peptide.
- setVatiantType(PeptideVariantsParameters.VariantType) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
-
Sets whether the specific variant count limitations should be used.
- setVerbosity(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
-
Set the verbosity type of progress output.
- setVersion(String) - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
-
Sets the database version.
- setVisible(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- setVisibleColumns(HashMap<Integer, Boolean>) - Method in interface com.compomics.util.gui.VisibleTableColumnsDialogParent
-
Sets the list of visible columns.
- setVisibleColumns(HashMap<Integer, Boolean>) - Method in class com.compomics.util.gui.XYPlottingDialog
-
- setWaitingText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- setWaitingText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
- setWaitingText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setWaitingText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
-
- setWaitingText(String) - Method in interface com.compomics.util.waiting.WaitingHandler
-
Sets the text describing what is currently being waited for.
- setWindowWidthThomsons(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set the window width in Thomson.
- setWorkbookStyle(WorkbookStyle) - Method in class com.compomics.util.io.export.writers.ExcelWriter
-
Sets the workbook style.
- setWriteMzId(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set whether mzId output is to be created.
- setWritePepXml(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
-
Set whether pepXML output is to be created.
- setX(double) - Method in class com.compomics.util.XYZDataPoint
-
Sets the x value.
- setXAxisStartAtZero(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This method sets the start value of the x-axis to zero.
- setY(double) - Method in class com.compomics.util.XYZDataPoint
-
Sets the y value.
- setYAxisZoomExcludesBackgroundPeaks(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Set if the automatic y-axis zoom only considers the annotated peaks.
- setYAxisZoomExcludesBackgroundPeaks(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set if the automatic y-axis zoom only considers the annotated peaks.
- setYDataIsPositive(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set to true of all y data values can be assumed to be positive.
- setZ(double) - Method in class com.compomics.util.XYZDataPoint
-
Sets the z value.
- shortName - Variable in enum com.compomics.util.experiment.biology.modifications.ModificationType
-
The short name of the type.
- showAllPeaks() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
If true, all peaks are shown, false displays the annotated peaks, and the
non-annotated in the background.
- showAllPeaks - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
If false, only the annotated peaks will be shown.
- showAnnotatedPeaksOnly(boolean) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
-
If true only the annotated peaks will be drawn.
- showFileName - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The boolean is set to 'true' if the file name is to be shown in the
panel.
- showForwardIonDeNovoTags() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns true if the automatic forward ion de novo tags are to be shown.
- showLegend() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Show the legend or not.
- showPrecursorDetails - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The boolean is set to 'true' if the precursor details is to be shown in
the panel.
- showPrecursorDetails() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns true of the precursor details are to be shown.
- showResolution - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The boolean is set to 'true' if the resolution is to be shown in the
panel.
- showResolution() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns true if the resolution is to be shown.
- showRewindIonDeNovoTags() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
-
Returns true if the automatic rewind ion de novo tags are to be shown.
- shuttlesort(int[], int[], int, int) - Method in class com.compomics.util.sun.TableSorter
-
- signalStop() - Method in class com.compomics.util.io.file.FolderMonitor
-
This method can be used to signal the monitor to halt its monitoring.
- SIMPLE_DATA_FORMAT - Static variable in interface com.compomics.util.waiting.WaitingHandler
-
Convenience date format.
- SimpleFileReader - Interface in com.compomics.util.io.flat
-
Interface for file readers.
- SimpleFileWriter - Class in com.compomics.util.io.flat
-
Simple gz file writer that is thread safe and throws exceptions as runtime
exceptions.
- SimpleFileWriter(File, boolean) - Constructor for class com.compomics.util.io.flat.SimpleFileWriter
-
Constructor.
- SimpleGzReader - Class in com.compomics.util.io.flat.readers
-
Simple wrapper for a gz file reader.
- SimpleGzReader(File) - Constructor for class com.compomics.util.io.flat.readers.SimpleGzReader
-
Constructor.
- SimpleLinearRegression - Class in com.compomics.util.math.statistics.linear_regression.regressions
-
Performs a simple linear regression.
- SimpleLinearRegression() - Constructor for class com.compomics.util.math.statistics.linear_regression.regressions.SimpleLinearRegression
-
Empty default constructor
- SimpleMzIdentMLExporter - Class in com.compomics.util.experiment.io.identification.writers
-
Simple mzIdentML exporter for PSM-level results.
- SimpleMzIdentMLExporter(String, String, String, File, File, ArrayList<File>, File, HashMap<String, ArrayList<String>>, File, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, ModificationProvider, FastaSummary, String, String, String, String, String, String, String, boolean) - Constructor for class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
-
Constructor.
- SimpleNoiseDistribution - Class in com.compomics.util.experiment.mass_spectrometry
-
This class makes a simple modeling of the noise using a normal distribution
on the log of the peak intensities and returns the associated binned
cumulative probability for a given intensity.
- SimpleNoiseDistribution() - Constructor for class com.compomics.util.experiment.mass_spectrometry.SimpleNoiseDistribution
-
Empty default constructor
- SimpleNoiseDistribution(double[]) - Constructor for class com.compomics.util.experiment.mass_spectrometry.SimpleNoiseDistribution
-
Constructor.
- SimplePeptideAnnotator - Class in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
-
A simple annotator for peptides.
- SimplePeptideAnnotator(Peptide, String[], int, AnnotationParameters) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator
-
Constructor.
- SimplePeptideAnnotator() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator
-
Empty default constructor
- SimplePeptideAnnotator(Peptide, String[], int, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, ReporterIon[]) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator
-
Constructor.
- SimplePeptideAnnotator.IonSeries - Enum in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
-
The type of ion series to annotate.
- SimpleSemaphore - Class in com.compomics.util.threading
-
A simple semaphore where thread interrupted exception are thrown as runtime exception.
- SimpleSemaphore(int, boolean) - Constructor for class com.compomics.util.threading.SimpleSemaphore
-
Constructor.
- SimpleSemaphore(int) - Constructor for class com.compomics.util.threading.SimpleSemaphore
-
Constructor.
- SimpleTextReader - Class in com.compomics.util.io.flat.readers
-
Simple wrapper for a flat file reader.
- SimpleTextReader(File) - Constructor for class com.compomics.util.io.flat.readers.SimpleTextReader
-
Constructor.
- SimpleXmlWriter - Class in com.compomics.util.io.export.xml
-
Simple writer for xml files.
- SimpleXmlWriter() - Constructor for class com.compomics.util.io.export.xml.SimpleXmlWriter
-
Empty default constructor
- SimpleXmlWriter(BufferedWriter) - Constructor for class com.compomics.util.io.export.xml.SimpleXmlWriter
-
Constructor.
- SINGLE_AA_SUFFIX - Static variable in class com.compomics.util.experiment.biology.modifications.ModificationFactory
-
Suffix for the modification clone targeting a single amino acid instead
of a pattern.
- SingleAAPropertyFeature - Interface in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration
-
Interface for the ms2pip features having a single amino acid property.
- singleBaseSubstitution - Static variable in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
-
Substitution matrix allowing for a single base substitution.
- singleLetterCode - Variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
Single letter code of the amino acid.
- SingleProteinSequenceProvider - Class in com.compomics.util.experiment.identification.protein_sequences
-
Sequence provider for a single protein.
- SingleProteinSequenceProvider() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
-
Empty default constructor.
- SingleProteinSequenceProvider(Protein) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
-
Constructor.
- singleRangeQuery(int, int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
-
Returns a new left/right index range for a given character recursively.
- site(String) - Method in class com.compomics.util.io.ftp.FTP
-
Site Command
- size() - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
-
Returns the number of atoms in this atom chain.
- skip(long) - Method in class com.compomics.util.io.file.MonitorableFileInputStream
-
Skips over and discards n
bytes of data from the
input stream.
- skip(long) - Method in class com.compomics.util.io.file.MonitorableInputStream
-
Skips over and discards n
bytes of data from the
input stream.
- SNPElement - Class in com.compomics.util.experiment.identification.protein_inference.fm_index
-
- SNPElement(int, char, char) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.SNPElement
-
- SnrScore - Class in com.compomics.util.experiment.identification.psm_scoring.psm_scores
-
This score uses the intensity distribution of the peaks to evaluate an SNR
score.
- SnrScore() - Constructor for class com.compomics.util.experiment.identification.psm_scoring.psm_scores.SnrScore
-
Constructor.
- Sodium - Class in com.compomics.util.experiment.biology.atoms.impl
-
The sodium atom.
- Sodium() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Sodium
-
Constructor.
- sonar - Static variable in class com.compomics.util.experiment.identification.Advocate
-
The Sonar search engine, integrated in radars.
- sort(int, ProgressDialogX) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
-
Sorts the table according to a given column using the built in sorter.
- sort(Object) - Method in class com.compomics.util.sun.TableSorter
-
- sortByColumn(int) - Method in class com.compomics.util.sun.TableSorter
-
- sortByColumn(int, boolean) - Method in class com.compomics.util.sun.TableSorter
-
- sourceAA - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.SNPElement
-
- SparklineColorsDialog - Class in com.compomics.util.gui.parameters
-
Dialog for user selection of the colors used by the sparklines.
- SparklineColorsDialog(JFrame, UtilitiesUserParameters) - Constructor for class com.compomics.util.gui.parameters.SparklineColorsDialog
-
Creates a new SparklineColorsDialog.
- SparklineColorsDialog(JDialog, UtilitiesUserParameters) - Constructor for class com.compomics.util.gui.parameters.SparklineColorsDialog
-
Creates a new SparklineColorsDialog.
- SPECIES_OPTION - Static variable in class com.compomics.software.ToolFactory
-
The command line argument for the species.
- SPECIES_TYPE_OPTION - Static variable in class com.compomics.software.ToolFactory
-
The command line argument for the species type.
- SpeciesDialog - Class in com.compomics.util.gui.genes
-
- SpeciesDialog(Frame, boolean, Image, Image, Integer) - Constructor for class com.compomics.util.gui.genes.SpeciesDialog
-
Deprecated.
Creates a new SpeciesDialog.
- SpeciesDialog(JDialog, JFrame, boolean, Image, Image, Integer) - Constructor for class com.compomics.util.gui.genes.SpeciesDialog
-
Deprecated.
Creates a new SpeciesDialog.
- SpeciesFactory - Class in com.compomics.util.experiment.biology.taxonomy
-
Class related to the handling of species.
- speciesOccurrence - Variable in class com.compomics.util.experiment.io.biology.protein.FastaSummary
-
The species occurrence in the FASTA file.
- SpecificAnnotationParameters - Class in com.compomics.util.experiment.identification.spectrum_annotation
-
The spectrum annotation preferences specific to a spectrum and an
identification assumption.
- SpecificAnnotationParameters() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
-
Empty default constructor
- specificAnnotationSettings - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
If provided, the annotator will only look for the ions included in the
specific annotation settings.
- SpecificSingleEnzymeCombinationIterator - Class in com.compomics.util.experiment.identification.protein_sequences.digestion.iterators
-
Iterator for enzymatic digestion.
- SpecificSingleEnzymeCombinationIterator() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeCombinationIterator
-
Empty default constructor
- SpecificSingleEnzymeCombinationIterator(ProteinIteratorUtils, String, Enzyme, int, double, double) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeCombinationIterator
-
Constructor.
- SpecificSingleEnzymeIterator - Class in com.compomics.util.experiment.identification.protein_sequences.digestion.iterators
-
Iterator for enzymatic digestion.
- SpecificSingleEnzymeIterator() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeIterator
-
Empty default constructor
- SpecificSingleEnzymeIterator(ProteinIteratorUtils, String, Enzyme, int, double, double) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeIterator
-
Constructor.
- spectraST - Static variable in class com.compomics.util.experiment.identification.Advocate
-
The SpectraST spectral library search engine (TPP).
- spectraTag - Static variable in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
-
Tag for the spectrum file.
- Spectrum - Class in com.compomics.util.experiment.mass_spectrometry.spectra
-
This class models a spectrum.
- Spectrum() - Constructor for class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
-
Empty default constructor.
- Spectrum(Precursor, double[], double[]) - Constructor for class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
-
Constructor.
- SpectrumAnnotation - Interface in com.compomics.util.gui.interfaces
-
This interface describes the behaviour for a spectrum annotation.
- SpectrumAnnotator - Class in com.compomics.util.experiment.identification.spectrum_annotation
-
The spectrum annotator annotates peaks in a spectrum.
- SpectrumAnnotator() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Empty default constructor
- SpectrumAnnotator.TiesResolution - Enum in com.compomics.util.experiment.identification.spectrum_annotation
-
Enum of the possibilities for ties resolution when multiple peaks can be
annotated.
- spectrumCountingInCache(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
-
Indicates whether the default spectrum counting value is in cache for a
protein match.
- SpectrumCountingMethod - Enum in com.compomics.util.experiment.quantification.spectrumcounting
-
Enum of the implemented spectrum counting methods.
- SpectrumCountingParameters - Class in com.compomics.util.parameters.quantification.spectrum_counting
-
This class contains the spectrum counting parameters.
- SpectrumCountingParameters() - Constructor for class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
-
Default constructor.
- SpectrumCountingParameters(SpectrumCountingParameters) - Constructor for class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
-
Creates new preferences based on other spectrum counting preferences.
- spectrumFile - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
The file of the currently loaded spectrum.
- SpectrumFile - Interface in com.compomics.util.interfaces
-
This interface describes the behaviour for a spectrum file
(ie., PKL file, Mascot Generic file, dat file, ...).
- spectrumIdentification - Variable in class com.compomics.util.experiment.identification.IdentificationKeys
-
Map mapping spectra per file.
- SpectrumIdentificationAssumption - Class in com.compomics.util.experiment.identification
-
Spectrum identification assumption made by an identification algorithm.
- SpectrumIdentificationAssumption() - Constructor for class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Empty default constructor.
- SpectrumIndex - Class in com.compomics.util.experiment.mass_spectrometry.indexes
-
This map stores the fragment ions indexed by mass.
- SpectrumIndex() - Constructor for class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Constructor for an empty index.
- SpectrumIndex(double[], double[], double, double, boolean) - Constructor for class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
-
Builds a new index.
- SpectrumMatch - Class in com.compomics.util.experiment.identification.matches
-
This class models a spectrum match.
- SpectrumMatch() - Constructor for class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Constructor for the spectrum match.
- SpectrumMatch(String, String) - Constructor for class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Constructor for the spectrum match.
- SpectrumMatchesIterator - Class in com.compomics.util.experiment.identification.matches_iterators
-
An iterator for spectrum matches.
- SpectrumMatchesIterator() - Constructor for class com.compomics.util.experiment.identification.matches_iterators.SpectrumMatchesIterator
-
Empty default constructor
- SpectrumMatchesIterator(Identification, WaitingHandler, boolean) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.SpectrumMatchesIterator
-
Constructor.
- SpectrumMatchesIterator(long[], Identification, WaitingHandler, boolean) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.SpectrumMatchesIterator
-
Constructor.
- SpectrumMatchesIterator(long[], Identification, WaitingHandler, boolean, String) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.SpectrumMatchesIterator
-
Constructor.
- spectrumMill - Static variable in class com.compomics.util.experiment.identification.Advocate
-
The Spectrum Mill search engine, Agilent.
- SpectrumPanel - Class in com.compomics.util.gui.spectrum
-
This class presents a JPanel that will hold and display a mass spectrum in
centroid or profile mode.
- SpectrumPanel(SpectrumFile) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the spectrum
information in the specified SpectrumFile as an interactive lines plot.
- SpectrumPanel(SpectrumFile, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the spectrum
information in the specified SpectrumFile as a line plot.
- SpectrumPanel(SpectrumFile, GraphicsPanel.DrawingStyle, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the spectrum
information in the specified SpectrumFile with the specified drawing
style.
- SpectrumPanel(SpectrumFile, GraphicsPanel.DrawingStyle, boolean, Color) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the spectrum
information in the specified SpectrumFile with the specified drawing
style.
- SpectrumPanel() - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
Empty default constructor
- SpectrumPanel(SpectrumFile, GraphicsPanel.DrawingStyle, boolean, Color, int, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the spectrum
information in the specified SpectrumFile with the specified drawing
style.
- SpectrumPanel(SpectrumFile, GraphicsPanel.DrawingStyle, boolean, Color, int, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the spectrum
information in the specified SpectrumFile with the specified drawing
style.
- SpectrumPanel(SpectrumFile, GraphicsPanel.DrawingStyle, boolean, Color, int, boolean, boolean, boolean, int) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the spectrum
information in the specified SpectrumFile with the specified drawing
style.
- SpectrumPanel(SpectrumFile, GraphicsPanel.DrawingStyle, boolean, Color, int, boolean, boolean, boolean, int, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the spectrum
information in the specified SpectrumFile with the specified drawing
style.
- SpectrumPanel(double[], double[], double, String, String) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the passed parameters.
- SpectrumPanel(double[], double[], double, String, String, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the passed parameters.
- SpectrumPanel(double[], double[], double, String, String, int, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the passed parameters.
- SpectrumPanel(double[], double[], double, String, String, int, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the passed parameters.
- SpectrumPanel(double[], double[], double, String, String, int, boolean, boolean, boolean, int) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the passed parameters.
- SpectrumPanel(double[], double[], double, String, String, int, boolean, boolean, boolean, int, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
-
This constructor creates a SpectrumPanel based on the passed parameters.
- SpectrumPanelListener - Interface in com.compomics.util.gui.interfaces
-
This interface describes the behaviour for a listener that wants to receive information
about events that occurred on a SpectrumPanel.
- SpectrumProvider - Interface in com.compomics.util.experiment.mass_spectrometry
-
Interface for objects providing spectra.
- spectrumTitle - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
The title of the currently loaded spectrum.
- spectrumTitle - Variable in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap.PrecursorWithTitle
-
The spectrum title
- SpectrumUtil - Class in com.compomics.util.experiment.mass_spectrometry.spectra
-
Utilities functions to handle spectra.
- SpectrumUtil() - Constructor for class com.compomics.util.experiment.mass_spectrometry.spectra.SpectrumUtil
-
- SplashScreen - Class in com.compomics.software
-
Class that takes care of converting an svg file to a png file using the
command line version of apache batik.
- SplashScreen(String[]) - Constructor for class com.compomics.software.SplashScreen
-
Constructor.
- splitFile(File, int, WaitingHandler) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileUtils
-
Splits an mgf file into smaller ones and returns the indexes of the
generated files.
- splitInput(String) - Static method in class com.compomics.software.cli.CommandLineUtils
-
Splits the input of comma separated command line input and returns the
results as an arraylist.
- spo - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
-
- SPO - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
-
- sqid - Static variable in class com.compomics.util.experiment.identification.Advocate
-
The SeQuence IDentfication (SQID) search engine.
- standardGeneticCode - Variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
The standard genetic code.
- StandardMasses - Enum in com.compomics.util.experiment.mass_spectrometry.utils
-
Enum of standard masses.
- StandardUnit - Enum in com.compomics.util.experiment.units
-
The standard units implemented.
- start(String) - Static method in class com.compomics.util.io.StartBrowser
-
Opens the given URL in the default browser.
- start() - Method in class com.compomics.util.sun.SwingWorker
-
Start the worker thread.
- start() - Method in class com.compomics.util.waiting.Duration
-
Sets the start time to the system current time in milliseconds.
- StartBrowser - Class in com.compomics.util.io
-
This class starts a browser for the given URL.
- StartBrowser() - Constructor for class com.compomics.util.io.StartBrowser
-
Empty constructor.
- StartEndPosition - Class in com.compomics.util.pdbfinder.das.readers
-
StartEndPosition.
- StartEndPosition() - Constructor for class com.compomics.util.pdbfinder.das.readers.StartEndPosition
-
Empty default constructor
- StartEndPosition(int, int) - Constructor for class com.compomics.util.pdbfinder.das.readers.StartEndPosition
-
Constructor.
- startGenerator(String, String, String, String) - Method in class com.compomics.util.db.DBAccessorGenerator
-
This method starts the generator for the specified parameters.
- startGenerator(String, String, String, String, String, String, boolean) - Method in class com.compomics.util.db.DBAccessorGenerator
-
This method starts the generator for the specified parameters.
- startNewSection() - Method in class com.compomics.util.io.export.ExportWriter
-
Starts a new section.
- startNewSection(String) - Method in class com.compomics.util.io.export.ExportWriter
-
Starts a new section.
- startNewSection(String, WorkbookStyle) - Method in class com.compomics.util.io.export.ExportWriter
-
Starts a new section.
- startNewSection(String, WorkbookStyle) - Method in class com.compomics.util.io.export.writers.ExcelWriter
-
- startNewSection(String, WorkbookStyle) - Method in class com.compomics.util.io.export.writers.TextWriter
-
- startPeptideShaker(JFrame) - Static method in class com.compomics.software.ToolFactory
-
Starts PeptideShaker from the location of utilities preferences.
- startPeptideShaker(JFrame, File) - Static method in class com.compomics.software.ToolFactory
-
Starts PeptideShaker from the location of utilities preferences and opens
the file given as argument.
- startPeptideShakerFromURL(JFrame, String, String) - Static method in class com.compomics.software.ToolFactory
-
Starts PeptideShaker from the location of utilities preferences and opens
the file given as argument.
- startReporter(JFrame) - Static method in class com.compomics.software.ToolFactory
-
Starts Reporter from the location of utilities preferences.
- startReshake(JFrame, String) - Static method in class com.compomics.software.ToolFactory
-
Starts PeptideShaker from the location of utilities preferences in the
Reshake mode and attempts at selecting the given project.
- startSearchGUI(JFrame) - Static method in class com.compomics.software.ToolFactory
-
Starts SearchGUI from the location of utilities preferences.
- startSearchGUI(JFrame, ArrayList<File>, ArrayList<File>, File, File, File, String, String, String) - Static method in class com.compomics.software.ToolFactory
-
Starts SearchGUI from the location of utilities preferences.
- startShake() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Make the dialog shake when the process has completed.
- std(ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
-
Convenience method returning the standard deviation of a list of doubles.
- StreamGobbler - Class in com.compomics.util.io
-
A stream gobbler.
- StreamGobbler() - Constructor for class com.compomics.util.io.StreamGobbler
-
Empty default constructor
- StreamGobbler(InputStream) - Constructor for class com.compomics.util.io.StreamGobbler
-
Constructor.
- StreamUtil - Class in com.compomics.util
-
Convenience methods to work with lambdas.
- StreamUtil() - Constructor for class com.compomics.util.StreamUtil
-
- strFileNameAndPath - Variable in class com.compomics.util.io.ftp.FTP
-
String to hold the file we are up/downloading
- StringListChooser - Class in com.compomics.util.gui.utils.user_choice.list_choosers
-
Dialog for choosing an item in a list of String.
- StringListChooser() - Constructor for class com.compomics.util.gui.utils.user_choice.list_choosers.StringListChooser
-
Empty default constructor
- StringListChooser(Frame, ArrayList<String>, String, String, String, boolean) - Constructor for class com.compomics.util.gui.utils.user_choice.list_choosers.StringListChooser
-
Constructor.
- StringListChooser(JDialog, ArrayList<String>, String, String, String, boolean) - Constructor for class com.compomics.util.gui.utils.user_choice.list_choosers.StringListChooser
-
Constructor.
- subAminoAcidsWithCombination - Variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
The sub amino acids with combination.
- subAminoAcidsWithoutCombination - Variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
-
The sub amino acids without combination.
- Substitution - Class in com.compomics.util.experiment.biology.variants.amino_acids
-
Class representing an amino acid substitution.
- Substitution() - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Substitution
-
Empty default constructor
- Substitution(char, char) - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Substitution
-
Constructor.
- SUBTRACT_ISOTOPE - Static variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
-
Minimal isotopic correction when matching an ion.
- suffixCharacter(String, int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
-
Forward propagation of the BWT to get the n'th consecutive character
- Sulfur - Class in com.compomics.util.experiment.biology.atoms.impl
-
The sulfur atom.
- Sulfur() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Sulfur
-
Constructor.
- sum(ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
-
Convenience method returning the sum of a list of doubles.
- supportedVersion(File) - Static method in class com.compomics.util.parameters.identification.IdentificationParameters
-
Returns a boolean indicating whether the version of the parameters file
is supported.
- svg - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
-
- SVG - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
-
- SvgFileFilter - Class in com.compomics.util.io.file.filefilters
-
File filter for *.svg files.
- SvgFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.SvgFileFilter
-
Empty default constructor
- Swap - Class in com.compomics.util.experiment.biology.variants.amino_acids
-
Class representing an amino acid swap.
- Swap() - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Swap
-
Empty default constructor
- Swap(char, char) - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Swap
-
Constructor.
- swap(int, int) - Method in class com.compomics.util.sun.TableSorter
-
- swapRows(int, int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
-
Swap two rows in the pattern.
- SwingUtils - Class in com.compomics.util.gui.utils
-
Swing utilities methods.
- SwingUtils() - Constructor for class com.compomics.util.gui.utils.SwingUtils
-
Empty default constructor
- SwingWorker - Class in com.compomics.util.sun
-
This is the 3rd version of SwingWorker (also known as
SwingWorker 3), an abstract class that you subclass to
perform GUI-related work in a dedicated thread.
- SwingWorker() - Constructor for class com.compomics.util.sun.SwingWorker
-
Start a thread that will call the construct
method
and then exit.
- SYMBOL - Variable in enum com.compomics.util.experiment.units.MetricsPrefix
-
The prefix symbol.
- synonymousVariant - Static variable in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
-
Substitution matrix grouping synonymous amino acids.
- syst() - Method in class com.compomics.util.io.ftp.FTP
-
Retrieve the system type from the remote server.