- G - Static variable in class com.compomics.util.experiment.biology.AminoAcid
-
- GATHER_FILES_FOR_PICKUP - Static variable in class com.compomics.util.io.FolderMonitor
-
- GENE_MAPPING_FILE_SUFFIX - Static variable in class com.compomics.util.preferences.GenePreferences
-
The suffix to use for files containing gene mappings.
- GENE_MAPPING_FOLDER - Static variable in class com.compomics.util.preferences.GenePreferences
-
The folder where gene mapping related info is stored.
- GeneDetailsDialog - Class in com.compomics.util.gui
-
This dialog displays the gene details associated to a protein match.
- GeneDetailsDialog(Frame, String) - Constructor for class com.compomics.util.gui.GeneDetailsDialog
-
Creates a new GeneDetailsDialog.
- GeneFactory - Class in com.compomics.util.experiment.annotation.gene
-
The gene factory provides gene information for protein accessions.
- GenePreferences - Class in com.compomics.util.preferences
-
Contains methods for downloading gene and GO mappings.
- GenePreferences() - Constructor for class com.compomics.util.preferences.GenePreferences
-
Create a new GenePreferences object.
- GenePreferences(GenePreferences) - Constructor for class com.compomics.util.preferences.GenePreferences
-
Creates new gene preferences based on a GenePreferences object.
- generateQuery() - Method in class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters
-
Returns a boolean indicating whether a blast query shall be generated.
- generateQuery() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- generateTargetDecoyDatabase(File, ProgressDialogX) - Method in class com.compomics.util.gui.protein.SequenceDbDetailsDialog
-
Appends decoy sequences to the given target database file.
- GeneratorException - Exception in com.compomics.util.db
-
This class wraps all exception that can occur while generating code.
- 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.
- get() - Method in class com.compomics.util.sun.SwingWorker
-
Return the value created by the construct
method.
- getAaExcluded() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the map of excluded amino acids.
- getAAOccurrences(JProgressBar) - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the occurrence of every amino acid in the database.
- getAaTargeted() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the map of targeted amino acids.
- getAbbreviatedFASTAHeader() - Method in class com.compomics.util.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.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.protein.Header
-
This method returns an abbreviated version of the Header, suitable for
inclusion in FASTA formatted files.
- getAbsoluteError(boolean) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Get the absolute matching error in Da.
- getAbsoluteError() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Get the absolute matching error in Da without 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.Protein
-
Getter for the protein accession.
- getAccession() - Method in class com.compomics.util.pride.CvTerm
-
- getAccession() - Method in class com.compomics.util.protein.Header
-
- getAccessions(String) - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Returns the protein accessions linked to a GO accession number.
- getAccessions(String) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Returns a list of accessions from the given key.
- getAccessions() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node
-
Returns the accessions attribute.
- getAccessions() - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the sequences present in the database.
- getAccountedNeutralLosses(ArrayList<NeutralLoss>) - Static method in class com.compomics.util.experiment.biology.IonFactory
-
Convenience method returning the possible neutral losses combination as
accounted by the factory, i.e., for now up to two neutral losses per
peak.
- getAccountedNeutralLosses() - Method in class com.compomics.util.experiment.identification.NeutralLossesMap
-
Returns an arraylist of implemented neutral losses.
- getAddenda() - Method in class com.compomics.util.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 enum com.compomics.util.experiment.identification.Advocate
-
Returns the advocate corresponding to the given index.
- getAdvocate() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
-
- getAdvocate() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Get the used advocate.
- getAdvocates() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Returns all advocates used referenced by their index.
- getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
- getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters
-
- getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
- getAlgorithm() - Method in interface com.compomics.util.experiment.identification.IdentificationAlgorithmParameter
-
Returns the identification algorithm.
- getAlgorithms() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the algorithms for which specific parameters are stored.
- getAlgorithmSpecificParameters() - Method in class com.compomics.util.experiment.identification.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
-
- getAllAlignments() - Method in class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerAlingmentReader
-
Get all alingment in the xml string.
- getAllAssumptions(int) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Return all assumptions for the specified search engine indexed by their
e-value.
- getAllAssumptions() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Return all assumptions for all identification algorithms as a list.
- 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
- getAllMappings() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node
-
Returns all the protein mapping of the node.
- getAllModifications() - Method in class com.compomics.util.preferences.ModificationProfile
-
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.preferences.ModificationProfile
-
Returns a list of all searched modifications but the fixed ones.
- getAllPossibleSequences() - Method in class com.compomics.util.experiment.biology.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.
- 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.
- getAllSpecies() - Method in class com.compomics.util.preferences.GenePreferences
-
Return the species lists.
- getAllSpeciesMap() - Method in class com.compomics.util.preferences.GenePreferences
-
Returns the species map.
- getAllSpectrumMatches(WaitingHandler) - Method in interface com.compomics.util.experiment.io.identifications.IdfileReader
-
This methods retrieves all the identifications from an identification
file as a list of spectrum matches It is very important to close the file
reader after creation.
- getAllSpectrumMatches(WaitingHandler) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader
-
- 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
-
- 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.
- getAminoAcid(String) - Static method in class com.compomics.util.experiment.biology.AminoAcid
-
Returns the amino acid corresponding to the letter given, null if not
implemented.
- getAminoAcid(char) - Static method in class com.compomics.util.experiment.biology.AminoAcid
-
Returns the amino acid corresponding to the letter given, null if not
implemented.
- getAminoAcidAfter() - Method in class com.compomics.util.experiment.biology.Enzyme
-
Getter for the amino acids potentially following the cleavage.
- getAminoAcidBefore() - Method in class com.compomics.util.experiment.biology.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.
- getAminoAcids() - Static method in class com.compomics.util.experiment.biology.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.AminoAcidPattern
-
Returns the targeted amino acids at position "target".
- getAminoAcidsList() - Static method in class com.compomics.util.experiment.biology.AminoAcid
-
Convenience method returning an arrayList of all implemented amino acids.
- getAnalysisSet(Sample) - Method in class com.compomics.util.experiment.MsExperiment
-
Returns the analysis set corresponding to a sample.
- getAnnotationIntensityLimit() - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Returns the intensity limit.
- 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.
- getArtifactId() - Method in class com.compomics.software.autoupdater.MavenJarFile
-
Returns the artifact id.
- getAscii(String) - Method in class com.compomics.util.io.FTP
-
GET a file from the FTP server in Ascii mode.
- getAScore(Peptide, ArrayList<PTM>, MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, ArrayList<Integer>, int, double, AminoAcidPattern.MatchingType) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.AScore
-
Returns the A-score for the best PTM location without accounting for
neutral losses.
- getAScore(Peptide, ArrayList<PTM>, MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, double, AminoAcidPattern.MatchingType) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.AScore
-
Returns the A-score for the best PTM location accounting for neutral
losses.
- getAScore(Peptide, ArrayList<PTM>, MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, double, boolean, AminoAcidPattern.MatchingType) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.AScore
-
Returns the A-score for the best PTM location.
- getAScorePeptideScore(Peptide, MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, double, boolean) - Static method in class com.compomics.util.experiment.identification.scoring.PsmScores
-
Returns a PSM score like the peptide score calculated for the A-score.
- getAsStringPattern() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the amino acid pattern as case insensitive pattern for String
matching using default single letter code of amino acids.
- getAsStringPattern(AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the amino acid pattern as case insensitive pattern for String
matching.
- 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.
- getBackedUpPtms() - Method in class com.compomics.util.preferences.ModificationProfile
-
Returns the names of the backed-up PTMs.
- getBackedUpPtmsMap() - Method in class com.compomics.util.preferences.ModificationProfile
-
Returns the PTMs backed-up as a map.
- getBackgroundPeakWidth() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the current width of the background peaks.
- getBase64String() - Method in class com.compomics.util.BinaryArrayImpl
-
- getBatchSize() - Method in class com.compomics.util.db.ObjectsCache
-
Returns the batch size in number of objects.
- getBestPeptideAssumption() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Getter for the best peptide assumption.
- getBinary(String) - Method in class com.compomics.util.io.FTP
-
GET a file from the FTP server in Binary mode.
- getBlock() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- getBlocks() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
- getBlockSequence(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- 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.
- getBStart(NeutralLoss) - Method in class com.compomics.util.experiment.identification.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).
- getCacheSize() - Method in class com.compomics.util.db.ObjectsCache
-
Returns the cache size in number of objects.
- getCacheSize() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
-
Returns the size of the cache used for peptide mappings (note that there
are two of them).
- getCacheSize() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the spectrum cache size.
- 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() - Method in class com.compomics.util.experiment.massspectrometry.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.
- getChromosomeForGeneName(String) - Method in class com.compomics.util.experiment.annotation.gene.GeneFactory
-
Returns the chromosome for a given gene.
- getChromosomeFromGeneId(String) - Method in class com.compomics.util.experiment.annotation.gene.GeneFactory
-
Returns the chromosome where a gene can be located, null if not found.
- getChromosomeFromGeneName(String) - Method in class com.compomics.util.experiment.annotation.gene.GeneFactory
-
Returns the chromosome where a gene can be located, null if not found.
- 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
-
- 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.PTMFactory
-
Returns the color used to code the given modification.
- 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.preferences.ModificationProfile
-
Returns the color used to code the given modification.
- getColors() - Method in class com.compomics.util.preferences.ModificationProfile
-
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.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.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.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.
- getCombinations() - Method in class com.compomics.util.experiment.biology.AminoAcid
-
Returns the amino acids combinations which might represent this amino
acid.
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Alanine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Arginine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Asparagine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.AsparticAcid
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.B
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Cysteine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.GlutamicAcid
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Glutamine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Glycine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Histidine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Isoleucine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.J
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Leucine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Lysine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Methionine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Phenylalanine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Proline
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Pyrrolysine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Selenocysteine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Serine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Threonine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Tryptophan
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Tyrosine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Valine
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.X
-
- getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.Z
-
- getCommandLineArgument(ArrayList<File>) - Static method in class com.compomics.software.CommandLineUtils
-
Returns the list of file as argument for the command line.
- getCommandLineArgument(File) - Static method in class com.compomics.software.CommandLineUtils
-
Returns the file as argument for the command line.
- getCommandLineOptions() - Static method in enum com.compomics.util.experiment.identification.ptm.PtmScore
-
Returns the different implemented scores as list of command line option.
- getCommonProteins(String, String) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Returns the common proteins between two protein groups.
- getConsecutiveIonProbability() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.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 labelled 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.
- getCoreHeader() - Method in class com.compomics.util.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.
- getCoveredAminoAcids(HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, MSnSpectrum, Peptide, double, double, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
- getCTerminal() - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the C-terminal of the peptide as a String.
- getCTerminal(boolean) - Method in class com.compomics.util.experiment.identification.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.tags.Tag
-
Returns the C-terminal gap of the tag.
- 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.NonSymmetricalNormalDistribution
-
- getCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- getCurrentAnnotation(MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>) - Method in class com.compomics.util.experiment.identification.spectrum_annotators.PeptideSpectrumAnnotator
-
- getCurrentAnnotation(MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>) - Method in class com.compomics.util.experiment.identification.spectrum_annotators.TagSpectrumAnnotator
-
- getCurrentAnnotation(MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Returns the currently matched ions with the given settings.
- getCurrentEnsemblVersion(String) - Method in class com.compomics.util.experiment.annotation.gene.GeneFactory
-
Returns the current Ensembl version number.
- getCurrentFastaFile() - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the currently loaded fasta file.
- getCurrentFastaIndex() - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the FASTA index of the currently loaded file.
- getCurrentlyLoadedPeptide() - Method in class com.compomics.util.experiment.identification.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the currently inspected peptide.
- getCurrentlyLoadedSpectrumKey() - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Returns the spectrum currently inspected.
- getCurrentPrecursorCharge() - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Returns the current precursor charge.
- getCurrentSpecies() - Method in class com.compomics.util.preferences.GenePreferences
-
Returns the current species.
- getCurrentSpeciesType() - Method in class com.compomics.util.preferences.GenePreferences
-
Returns the current species type.
- getCurrentVennDiagramType() - Method in class com.compomics.util.gui.VennDiagramPanel
-
Returns the current Venn diagram type.
- 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.
- getDatabaseType() - Method in class com.compomics.util.experiment.biology.Protein
-
Getter for the protein database type.
- getDatabaseType() - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Indicates the database type.
- getDatabaseType() - Method in class com.compomics.util.protein.Header
-
- getDatabaseTypeAsString(Header.DatabaseType) - Static method in class com.compomics.util.protein.Header
-
Convenience method returning the database name as a String.
- getDatabaseTypesAsString() - Static method in class com.compomics.util.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.
- 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).
- getDbFolder() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Returns the folder where the db in the sequence factory is stored.
- getDbFolder() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the last used database folder.
- getDbFolderName() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Returns the folder name where to store information about the protein
sequence database loaded in the sequence factory.
- getDecodedByteArray() - Method in class com.compomics.util.BinaryArrayImpl
-
Returns the contents of the binary array decoded using the
Base64 algorithm.
- getDecoyAccesions() - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Returns the list of decoy accessions.
- getDecoyTag() - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Returns the decoy tag.
- getDefaultColor(String) - Static method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns a default color based on the modification name.
- getDefaultCVTerm(String) - Static method in class com.compomics.util.pride.PtmToPrideMap
-
Returns the default cvTerm of a modification when it exists.
- getDefaultDecoyAccession(String) - Static method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the default decoy accession for a target accession.
- getDefaultDecoyAccessionSuffix() - Static method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the default suffix for a decoy accession.
- getDefaultDecoyDescription(String) - Static method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the default description for a decoy protein.
- getDefaultExportFolder() - Method in interface com.compomics.util.gui.export.graphics.ExportGraphicsDialogParent
-
Returns the default folder used for the export.
- getDefaultExportFolder() - Method in class com.compomics.util.gui.VennDiagramDialog
-
- getDefaultExportFolder() - Method in class com.compomics.util.gui.XYPlottingDialog
-
- getDefaultInstruments() - Static method in class com.compomics.util.pride.prideobjects.Instrument
-
Returns a list of predefined instruments.
- getDefaultLosses(Peptide, AminoAcidPattern.MatchingType, double) - Static method in class com.compomics.util.experiment.identification.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the possible neutral losses expected by default for a given
peptide.
- getDefaultLosses(Tag, AminoAcidPattern.MatchingType, double) - Static method in class com.compomics.util.experiment.identification.spectrum_annotators.TagSpectrumAnnotator
-
Returns the possible neutral losses expected by default for a given
peptide.
- getDefaultLosses(SpectrumIdentificationAssumption, AminoAcidPattern.MatchingType, double) - Static method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Returns the possible neutral losses expected by default for a given
peptide.
- getDefaultModifications() - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns the names of the default modifications.
- getDefaultModificationsOrdered() - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns the alphabetically ordered names of the default modifications.
- getDefaultNeutralLosses() - Method in class com.compomics.util.experiment.biology.IonFactory
-
Returns the default neutral losses.
- getDefaultOMSSAIndex(String) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns the default OMSSA index of the modification.
- getDefaultProteinTree() - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the default protein tree corresponding to the database loaded in
factory.
- getDefaultProteinTree(WaitingHandler) - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the default protein tree corresponding to the database loaded in
factory.
- getDefaultProteinTree(WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the default protein tree corresponding to the database loaded in
factory
- getDefaultProtocols() - Static method in class com.compomics.util.pride.prideobjects.Protocol
-
Returns a list of default protocols.
- getDefaultReference(String, String, int) - Static method in class com.compomics.util.experiment.identification.Identification
-
Returns the default reference for an identification.
- 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.
- getDefaultShortName(String) - Static method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns a default short name for a given modification.
- getDefaultTargetAccession(String) - Static method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the default target accession of a given decoy protein.
- getDefaultVersion(long) - Static method in class com.compomics.util.experiment.identification.FastaIndex
-
Returns the default version based on the time the file was last modified.
- getDeltaMass(double, boolean, boolean) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the precursor mass error (in ppm or Da).
- getDeltaMass(double, boolean) - 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.
- getDeNovoCharge() - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Returns the charge to use for the fragment ions in the de novo
sequencing.
- getDepth() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node
-
Returns the depth of the node in the tree.
- 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.NonSymmetricalNormalDistribution
-
- getDescendingCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- 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 class com.compomics.util.io.filefilters.DatFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.DtaFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.FastaFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.JpegFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.MgfFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.Ms2FileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.MzDataFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.MzMlFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.MzXmlFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.OmxFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.OutFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.PdfFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.PeffFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.PepXmlFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.PklFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.PklSpoFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.PkxFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.PngFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.ProtXmlFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.SequestParamsFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.SvgFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.TiffFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.filefilters.XmlFileFilter
-
The description of this filter
- getDescription() - Method in class com.compomics.util.io.FilenameExtensionFilter
-
- getDescription() - Method in class com.compomics.util.protein.Header
-
- getDescriptionProteinName() - Method in class com.compomics.util.protein.Header
-
- getDescriptionShort() - Method in class com.compomics.util.protein.Header
-
- getDesignaledPeakList(ArrayList<IonMatch>) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the peak list of this spectrum without matched peaks.
- getDestinationFile() - Method in class com.compomics.util.experiment.identification.search_parameters_cli.IdentificationParametersInputBean
-
Returns the file where to save the identification parameters.
- getDestinationFile() - Method in class com.compomics.util.io.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
-
- getDifference() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- getDifferenceToMonoisotopic(int) - Method in class com.compomics.util.experiment.biology.Atom
-
Returns the mass difference between the given isotope and the
monoisotopic mass.
- getDiscardLowQualitySpectra() - Method in class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters
-
Returns a boolean indicating whether low quality spectra shall be
discarded.
- getDiscardLowQualitySpectra() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- getDisplayedTips() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the list of displayed tips.
- getDoi() - Method in class com.compomics.util.pride.prideobjects.Reference
-
Returns the Digital Object Identifier (DOI) of the reference.
- 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.experiment.identification.identification_parameters.OmssaParameters
-
Returns the window size for doubly charged ions.
- getDoubleListFromString(String, String) - Static method in class com.compomics.software.CommandLineUtils
-
Parses a list of doubles from a command line option.
- getDuplicatedSpectrumTitles() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Returns a map of the duplicated spectrum titles, can be null.
- getDynamicRange() - Method in class com.compomics.util.experiment.identification.identification_parameters.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
-
- getEnd_block() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- getEnd_protein() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- getEndLocation() - Method in class com.compomics.util.protein.Header
-
This method reports on the end index of the header.
- getEndPosition() - Method in class com.compomics.util.pdbfinder.das.readers.StartEndPosition
-
- getEnsemblDatabaseName(String) - Method in class com.compomics.util.preferences.GenePreferences
-
Deprecated.
use the one with the Ensembl type parameter instead
- getEnsemblDatabaseName(String, String) - Method in class com.compomics.util.preferences.GenePreferences
-
Returns the Ensembl database name corresponding to a species name
according to the speciesMap.
- getEnsemblSpeciesVersion(String) - Method in class com.compomics.util.preferences.GenePreferences
-
Deprecated.
use getEnsemblSpeciesVersion(String ensemblType, String
speciesName) instead
- getEnsemblSpeciesVersion(String, String) - Method in class com.compomics.util.preferences.GenePreferences
-
Returns the Ensembl version for the given species name.
- getEnsemblVersion(String) - Method in class com.compomics.util.preferences.GenePreferences
-
Returns the Ensembl version corresponding to the given Ensembl database
according to the ensemblVersionsMap.
- getEnsemblVersionsMap() - Method in class com.compomics.util.preferences.GenePreferences
-
Returns the Ensembl versions 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.EnzymeFactory
-
Returns the enzyme corresponding to the given name.
- getEnzyme() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the enzyme used for digestion.
- getEnzyme() - Method in class com.compomics.util.gui.searchsettings.EnzymeSelectionDialog
-
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.
- getEnzymeFile() - Method in class com.compomics.util.experiment.identification.search_parameters_cli.AbstractIdentificationParametersCli
-
Returns the enzyme file needed to initiate the factory.
- 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.EnzymeFactory
-
Get the imported enzymes.
- getError() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Deprecated.
replaced by getAbsoluteError() and getRelativeError()
- getError(boolean, boolean) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the error.
- 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.
- getEValue() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
-
Deprecated.
use getScore instead
- 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.
- getExceptionType(Exception) - Static method in class com.compomics.util.general.ExceptionHandler
-
Returns the exception type.
- getExcludedAA(int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the excluded amino acids at a given index in the pattern.
- getExpectedIons(HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, Peptide) - Method in class com.compomics.util.experiment.identification.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the expected ions in a map indexed by the possible charges.
- getExpectedIons(HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Returns the expected ions in a map indexed by the possible charges.
- getExpectedPTMs(ModificationProfile, Peptide, double, double, AminoAcidPattern.MatchingType) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns the expected modifications based on the modification profile, the
peptide found and the modification details.
- getExpectedPTMs(ModificationProfile, Peptide, String, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns the names of the possibly expected modification based on the name
of the expected modification in a map where the PTM names are indexed by
their potential site on the sequence.
- getExperiment_type() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
-
- getExperiment_type() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
- getExportFeatures(String) - Method in interface com.compomics.util.io.export.ExportFactory
-
Returns the export features implemented for the given section.
- getExportFeatures() - 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.
- getExportScheme(String) - Method in interface com.compomics.util.io.export.ExportFactory
-
Returns the export scheme indexed by the given name.
- getExtension() - Method in enum com.compomics.util.enumeration.ImageType
-
Returns the extension.
- getExtension() - Method in interface com.compomics.util.experiment.io.identifications.IdfileReader
-
This method should return the extension of the file for which this
IdfileReader can be used.
- getExtension() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader
-
- getExtension(File) - Static method in class com.compomics.util.io.filefilters.FileFilterUtils
-
Get the extension of a file.
- getExtension(File) - Static method in class com.compomics.util.Util
-
Returns the extensions of a file.
- getFamilyName() - Method in class com.compomics.util.experiment.identification.TagAssumption
-
- getFamilyName() - Method in interface com.compomics.util.experiment.personalization.UrParameter
-
This method returns the family name of the parameter.
- getFamilyName() - Method in class com.compomics.util.experiment.refinementparameters.MascotScore
-
This method returns the family name of the parameter.
- getFamilyName() - Method in class com.compomics.util.experiment.refinementparameters.PepnovoAssumptionDetails
-
- getFastaFile() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the sequence database file used for identification.
- getFavoriteDBs() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the last used databases.
- getFeatureFamily() - Method in interface com.compomics.util.io.export.ExportFeature
-
Returns the family type of this export feature.
- getFeatureId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- getFeatureLabel() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- 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.
- getFileName() - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Returns the file name of the inspected FASTA file.
- getFileName(String) - Method in class com.compomics.util.experiment.identification.Identification
-
Deprecated.
use the database methods instead
- getFileName() - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the name of the loaded FASTA file.
- getFileName() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Returns the name of the indexed file.
- getFileName() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the file name.
- 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() - 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
-
- getFileName(String) - Static method in class com.compomics.util.Util
-
An OS independent getName alternative.
- getFileName(File) - Static method in class com.compomics.util.Util
-
An OS independent getName alternative.
- getFileReader(File, WaitingHandler) - Method in class com.compomics.util.experiment.io.identifications.IdfileReaderFactory
-
This method returns the proper identification file reader depending on
the format of the provided file.
- getFiles(String, ArrayList<String>) - Static method in class com.compomics.software.CommandLineUtils
-
Returns a list of files as imported from the command line option.
- getFilter() - Method in class com.compomics.util.preferences.gui.ImportSettingsDialog
-
Returns the id filter as set by the user.
- getFirstHit(int) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Returns the first hit obtained using the specified advocate.
- getFixedModifications() - Method in class com.compomics.util.preferences.ModificationProfile
-
Returns the searched fixed modifications names.
- 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.
- getFlrThreshold() - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
Returns the FLR threshold.
- 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.protein.Header
-
- getForeignDescription() - Method in class com.compomics.util.protein.Header
-
- getForeignID() - Method in class com.compomics.util.protein.Header
-
- getForwardIons() - Static method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the list of forward ions.
- getFractionMolecularWeightRanges() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the user provided molecular weight ranges for the fractions.
- getFractionMolecularWeights() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use getFractionMolecularWeightRanges instead
- getFractionOfPeaksForChargeEstimation() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the fraction of peaks to be retained for charge >1 estimation.
- getFragmentAccuracyType() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the fragment accuracy type.
- getFragmentationModel() - Method in class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters
-
Returns the name of the fragmentation model.
- getFragmentationModel() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- getFragmentIonAccuracy() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the MS2 ion m/z tolerance.
- getFragmentIonAccuracy() - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Returns the fragment ion accuracy.
- getFragmentIons(Peptide) - Method in class com.compomics.util.experiment.biology.IonFactory
-
This method returns the theoretic ions expected from a peptide.
- getFragmentIons(Tag) - Method in class com.compomics.util.experiment.biology.IonFactory
-
This method returns the theoretic ions expected from a tag.
- getFragmentIonTypes() - Method in class com.compomics.util.preferences.AnnotationPreferences
-
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.protein.Header
-
This method reports on the full header, with the addenda (if present).
- getGeneEnsemblId(String) - Method in class com.compomics.util.experiment.annotation.gene.GeneFactory
-
Returns the Ensembl ID of a gene, null if not found.
- getGeneMappingFolder() - Method in class com.compomics.util.preferences.GenePreferences
-
Returns the path to the folder containing the gene mapping files.
- getGeneName(String) - Method in class com.compomics.util.experiment.annotation.gene.GeneFactory
-
Returns the name of a gene, null if not found.
- getGeneName() - Method in class com.compomics.util.protein.Header
-
- getGeneNameForUniProtProtein(String) - Method in class com.compomics.util.experiment.annotation.gene.GeneFactory
-
Returns the gene name attached to a protein.
- 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, ArrayList<NeutralLoss>) - Static method in class com.compomics.util.experiment.biology.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.Ion
-
Convenience method returning a generic ion based on the given ion type
without neutral losses.
- getGlycons() - Method in class com.compomics.util.experiment.biology.GlyconFactory
-
A getter to access the glycons.
- getGoAccessionLink(String) - Method in class com.compomics.util.gui.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.annotation.go.GOFactory
-
Returns the GO accession numbers linked to a given protein accession
number.
- getGoDomainMap() - Method in class com.compomics.util.preferences.GenePreferences
-
Returns the GO domain map, e.g., key: GO term: GO:0007568, element:
biological_process.
- 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.
- getHeader() - Static method in class com.compomics.util.experiment.identification.search_parameters_cli.AbstractIdentificationParametersCli
-
IdentificationParametersCLI header message when printing the usage.
- getHeader(String) - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the desired header for the protein 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
-
- getHeader() - Method in class com.compomics.util.protein.Protein
-
This method reports on the header for the current
protein.
- getHeaderIterator(boolean) - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns an iterator of all the headers in the FASTA file.
- 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.experiment.identification.identification_parameters.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.ptm.PtmtableContent
-
Get histogram.
- getHitListLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the length of the hit list for OMSSA.
- getHitListLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters
-
Returns the length of the hit list.
- getHitListLength() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- getHitListLengthDeNovo() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- getHomeFolder() - Static method in class com.compomics.util.io.FileSystemAccessor
-
Returns the user home folder.
- getId() - Method in class com.compomics.util.experiment.biology.Enzyme
-
Get the enzyme id.
- getId() - Method in enum com.compomics.util.experiment.identification.ptm.PtmScore
-
Returns the id number of the score.
- getId() - Method in class com.compomics.util.experiment.patient.Patient
-
Returns the patient id,
- getID() - Method in class com.compomics.util.protein.Header
-
- getIdentification(int) - Method in class com.compomics.util.experiment.ProteomicAnalysis
-
Returns identification results obtained with an identification method
- getIdentificationAlgorithmParameter(int) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the algorithm specific parameters, null if not found.
- getIdentificationCharge() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
-
- getIdentificationCharge() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the charge used for identification.
- getIdentificationFile() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
-
- getIdentificationFile() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the identification file.
- getIdentificationParameters(File) - Static method in class com.compomics.util.experiment.identification.SearchParameters
-
Loads the identification parameters from a serialized file.
- 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
-
- getImplementedIons() - Static method in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Returns an arraylist of possible subtypes.
- getImplementedIonTypes() - Static method in class com.compomics.util.experiment.biology.Ion
-
Returns the implemented ion types.
- getImplementedIsotopes() - Method in class com.compomics.util.experiment.biology.Atom
-
returns a list of isotopes for which a mass is available relative to the
monoisotopic peak (+1 for carbon 13).
- getImplementedPtmScores() - Static method in enum com.compomics.util.experiment.identification.ptm.PtmScore
-
Returns a list of the implemented scores.
- getImplementedSections() - Method in interface com.compomics.util.io.export.ExportFactory
-
Returns the implemented sections.
- getIndex() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Returns the index of a reporter ion.
- getIndex() - Method in enum com.compomics.util.experiment.identification.Advocate
-
Returns the index of the advocate.
- getIndex(String) - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Returns the index of the accession of interest.
- 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.TagAssumption
-
- getIndex(String) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Returns the index corresponding to the desired spectrum.
- getIndex(File) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Deserializes the index of an mgf file.
- getIndex() - Method in interface com.compomics.util.experiment.personalization.UrParameter
-
This method returns the index of the parameter.
- getIndex() - Method in class com.compomics.util.experiment.ProteomicAnalysis
-
get the index of the replicate
- getIndex() - Method in class com.compomics.util.experiment.refinementparameters.MascotScore
-
This method returns the index of the parameter.
- getIndex() - Method in class com.compomics.util.experiment.refinementparameters.PepnovoAssumptionDetails
-
- getIndexedFixedModifications() - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns an indexed map of all fixed modifications amino acid, (1 is the
first) -> list of modification names.
- getIndexes(String) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the indexes where the amino acid pattern was found in the input
using default single letter code of amino acids.
- getIndexes(AminoAcidPattern) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the indexes where the amino acid pattern was found in the input
using default single letter code of amino acids.
- getIndexes(String, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the indexes where the amino acid pattern was found in the input.
- getIndexes(AminoAcidPattern, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the indexes where the amino acid pattern was found in the input.
- getIndexes() - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Returns a map of all indexes of the FASTA file (accession -> index).
- 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.
- getIndexMap(File) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader
-
Returns the index of all spectra in the given mgf file.
- getIndexMap(File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader
-
Returns the index of all spectra in the given MGF file.
- getIndistinguishibleAminoAcids(Double) - Method in class com.compomics.util.experiment.biology.AminoAcid
-
Returns the amino acids which cannot be distinguished from this amino
acid given a mass tolerance.
- getInitialSize() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Retrieves the initial tag size from the db.
- getInput() - Method in class com.compomics.util.gui.searchsettings.algorithm_settings.OmssaSettingsDialog
-
Returns the user selection as OMSSA parameters object.
- getInput() - Method in class com.compomics.util.gui.searchsettings.algorithm_settings.XTandemSettingsDialog
-
Returns the user selection as X!tandem parameters object.
- getInstance() - Static method in class com.compomics.util.experiment.annotation.gene.GeneFactory
-
Static method returning the instance of the factory.
- getInstance() - Static method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Static method returning the instance of the factory.
- getInstance() - Static method in class com.compomics.util.experiment.biology.EnzymeFactory
-
Static method to get an instance of the factory.
- getInstance() - Static method in class com.compomics.util.experiment.biology.GlyconFactory
-
Static method to get the factory instance.
- getInstance() - Static method in class com.compomics.util.experiment.biology.IonFactory
-
Static method which returns the instance of the factory.
- getInstance() - Static method in class com.compomics.util.experiment.biology.PTMFactory
-
Static method to get the instance of the factory.
- getInstance() - Static method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Static method returning the instance of the factory.
- getInstance() - Static method in class com.compomics.util.experiment.identification.SequenceFactory
-
Static method returning the instance of the factory.
- getInstance(int) - Static method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the instance of the factory with the specified cache size.
- getInstance() - Static method in class com.compomics.util.experiment.io.identifications.IdfileReaderFactory
-
A static method to retrieve the instance of the factory.
- getInstance() - Static method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Static method returning the instance of the factory.
- getInstance(int) - Static method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Static method returning the instance of the factory with a new cache
size.
- 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.
- getInstruments() - Method in class com.compomics.util.pride.PrideObjectsFactory
-
Returns the instruments.
- getIntegerListFromString(String, String) - Static method in class com.compomics.software.CommandLineUtils
-
Parses a list of integers from a command line option.
- getIntensities(int, Integer, int) - Method in class com.compomics.util.experiment.identification.ptm.PtmtableContent
-
Get intensity.
- getIntensity() - Method in class com.compomics.util.experiment.massspectrometry.Peak
-
Returns the intensity.
- getIntensity() - Method in class com.compomics.util.experiment.massspectrometry.Precursor
-
Getter for the intensity.
- 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.
- getIntensityCutOffIncrement() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the intensity cut-off increment.
- getIntensityLimit(double) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the intensity limit.
- getIntensityPrideCvTerm() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the pride CV term for the ion match intensity.
- getIntensityValues() - Method in class com.compomics.util.io.PklFile
-
- getIntensityValuesAsArray() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the intensity values as an array.
- getIonAtRow(int) - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
-
Returns the ion type at the given row.
- getIonMassErrorPrideCvTerm() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Returns the pride CV term for the ion match error.
- getIons() - Static method in class com.compomics.util.experiment.identification.SearchParameters
-
Getter for the list of ion symbols used.
- getIonSearched1() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Getter for the first kind of ion searched.
- getIonSearched2() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Getter for the second kind of ion searched.
- getIonTypes() - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Returns the type of ions annotated.
- getIsotopeMass(int) - Method in class com.compomics.util.experiment.biology.Atom
-
Returns the mass corresponding to the given isotope number.
- getIsotopeNumber() - 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) - 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
- getIterativeReplaceEvalue() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the e-value threshold to use to replace a hit for the iterative
search.
- getIterativeSequenceEvalue() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the e-value threshold to use to consider a sequence for the
iterative search.
- getIterativeSpectrumEvalue() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the e-value threshold to use consider a spectrum for the
iterative search.
- 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.
- getJavaHomeAndOptions(String) - Method in class com.compomics.software.CompomicsWrapper
-
Returns an array list containing the Java home plus any parameters to the
JVM.
- getJFreePeakList() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Format the peaks so they can be plot in JFreeChart.
- getJOptionEditorPane(String) - Static method in class com.compomics.util.gui.JOptionEditorPane
-
Returns a JEditorPane with HTML support to be used in a JOptionsPane.
- getKey() - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the reference key of a peptide.
- getKey(String, ArrayList<ModificationMatch>) - Static method in class com.compomics.util.experiment.biology.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() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
- 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.
- getLastModified() - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Returns when the file was last modified.
- getLastModified() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Returns when the file was last modified.
- getLastSelectedFolder() - Method in class com.compomics.util.gui.protein.SequenceDbDetailsDialog
-
Returns the last selected folder.
- getLastSelectedFolder() - Method in interface com.compomics.util.gui.searchsettings.SearchSettingsDialogParent
-
Returns the last selected folder.
- getLastSelectedFolder() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
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.
- 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.Protein
-
Returns the number of amino acids in the sequence.
- 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.
- getLengthInAminoAcid() - Method in class com.compomics.util.experiment.identification.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.Atom
-
Returns the single letter code of the atom.
- getLevel() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns at which level the spectrum was recorded.
- getLine(int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getLines() - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getLink() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- getLinkHref() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- 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
-
- getLocalPrideFolder() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
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.
- getLongestAminoAcidSequence() - Method in class com.compomics.util.experiment.identification.tags.Tag
-
Returns the longest amino acid sequence contained in this tag.
- getLossesMass(ArrayList<NeutralLoss>) - Static method in class com.compomics.util.experiment.biology.IonFactory
-
Convenience summing the masses of various neutral losses.
- getLowIntensityCutOff() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the low intensity cut-off as percentage of the most intense ion
peak.
- getMainMatch() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Returns the main match accession after protein inference.
- getMainMatchKey() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
Returns the key of the main match.
- getMainTitle() - Method in class com.compomics.util.io.export.ExportScheme
-
Returns the main title of the report.
- getMap() - Method in class com.compomics.util.experiment.identification.ptm.PtmtableContent
-
Get the map.
- getMappedGeneNames() - Method in class com.compomics.util.experiment.annotation.gene.GeneFactory
-
Returns a list of the mapped genes indexed by their gene names.
- getMappedGenes() - Method in class com.compomics.util.experiment.annotation.gene.GeneFactory
-
Returns a list of the mapped genes indexed by their Ensembl Gene ID.
- getMapping() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.PeptideIterator
-
Returns the protein mapping of the current peptide.
- getMascotMaxEvalue() - Method in class com.compomics.util.preferences.IdFilter
-
Returns the maximal Mascot e-value allowed.
- getMass() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
- getMass() - Method in class com.compomics.util.experiment.biology.ElementaryElement
-
Returns the mass of the element.
- getMass(int) - Method in class com.compomics.util.experiment.biology.ions.Glycon
-
Get the glycon mass.
- getMass() - Method in class com.compomics.util.experiment.biology.Peptide
-
Getter for the mass.
- getMass() - Method in class com.compomics.util.experiment.biology.PTM
-
Getter for the mass difference induced by this modification.
- getMass() - Method in class com.compomics.util.experiment.identification.tags.Tag
-
Returns the mass of the tag.
- getMass(boolean, boolean) - Method in class com.compomics.util.experiment.identification.tags.Tag
-
Returns the theoretic mass of the tag, eventually without terminal gaps.
- getMass() - Method in interface com.compomics.util.experiment.identification.tags.TagComponent
-
Returns the mass of the tag component.
- getMass() - Method in class com.compomics.util.experiment.identification.tags.tagcomponents.MassGap
-
- 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.
- 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.
- getMassGap() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
-
Returns the mass gap comprised in this ion.
- getMassShift() - Method in class com.compomics.util.experiment.biology.Mutation
-
Returns the mass shift.
- getMassShift() - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Returns the m/z shift applied to the fragment ions.
- getMassShiftCTerm() - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Returns the C-terminal m/z shift applied to all reverse ions.
- getMassShiftNTerm() - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Returns the N-terminal m/z shift applied to all forward ions.
- getMatchedPeptideSequences(String, String, AminoAcidPattern.MatchingType, Double, boolean) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
-
Returns a list of peptides matched using the given peptide sequence in
the given protein according the provided matching settings.
- getMatchingAminoAcid(String, AminoAcidPattern.MatchingType, Double) - Static method in class com.compomics.util.experiment.biology.AminoAcid
-
Returns a matching amino acid using the given matching type and
massTolerance.
- getMatchingKey(AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns a unique key for the peptide when considering the given matching
type and mass tolerance.
- getMatchingSequence(String, AminoAcidPattern.MatchingType, Double) - Static method in class com.compomics.util.experiment.biology.AminoAcid
-
Returns the matching sequence of a given sequence.
- getMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification
-
Deprecated.
use the database match specific methods instead
- getMatchPArameter(String, UrParameter, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB
-
Deprecated.
use match specific mapping instead
- getMatchType(String) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the kind of match pointed by the given key in the identification
mappings.
- 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.io.massspectrometry.MgfIndex
-
Returns the maximal charge found in the mgf file.
- getMaxCharge(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the max precursor charge encountered for the given mgf file.
- getMaxCharge() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the max precursor charge encountered among all loaded mgf files.
- getMaxChargeSearched() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the maximal charge searched.
- getMaxEValue() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the maximal e-value searched for.
- getMaxEValue() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Returns the maximal e-value searched for.
- getMaxEValue() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- getMaxFragmentCharge() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the maximal fragment charge.
- getMaxFragmentPerSeries() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the maximal number of fragments to retain per series.
- getMaxHitsPerSpectrumPerCharge() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.MonitorableFileInputStream
-
This method reports on the maximum scale for the monitor.
- getMaximum() - Method in class com.compomics.util.io.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.experiment.identification.identification_parameters.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.
- getMaxIntensity() - Method in class com.compomics.util.experiment.identification.ptm.PtmtableContent
-
Returns the max intensity.
- getMaxIntensity() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Returns the maximum precursor intensity in this file.
- getMaxIntensity() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the max intensity value.
- getMaxIntensity(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the maximum precursor intensity for the desired file.
- getMaxIntensity() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the maximum precursor intensity for the whole project.
- getMaxMass() - Method in class com.compomics.util.gui.events.RescalingEvent
-
Returns the maximum mass.
- getMaxMz() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Returns the maximum m/z in this file.
- getMaxMz() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the max mz value.
- getMaxMz(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the maximum m/z for the desired file.
- getMaxMz() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the maximum m/z for the whole project.
- getMaxMzDeviation() - Method in class com.compomics.util.preferences.IdFilter
-
Returns the maximal m/z deviation allowed.
- getMaxMzLadders() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the maximal m/z ladder length.
- 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.massspectrometry.MgfIndex
-
Returns the maximum peak count in this file.
- getMaxPeakCount(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the max peak count encountered for the given mgf file.
- getMaxPeakCount() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the max peak count encountered among all loaded mgf files.
- getMaxPepLength() - Method in class com.compomics.util.preferences.IdFilter
-
Returns the maximal peptide length allowed.
- getMaxPeptideLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the maximal peptide length allowed.
- getMaxPeptideLength() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- 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 interface com.compomics.util.waiting.WaitingHandler
-
Returns the max primary progress counter.
- getMaxRT() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Returns the maximal RT in this file.
- getMaxRT(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the maximum RT for the desired file.
- getMaxRT() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the maximum RT for the whole project.
- 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 interface com.compomics.util.waiting.WaitingHandler
-
Returns the max secondary progress counter.
- 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.NonSymmetricalNormalDistribution
-
- getMaxValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- 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.
- getMDScore(SpectrumMatch, ArrayList<String>, AminoAcidPattern.MatchingType, Double) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.MDScore
-
Returns the MD score for the best peptide in a spectrum match (the best
peptide has to be set before).
- getMDScore(SpectrumMatch, Peptide, ArrayList<String>, AminoAcidPattern.MatchingType, Double) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.MDScore
-
Returns the MD score for the given peptide in a spectrum match.
- 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.
- getMemoryAllocation() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
-
Returns the memory allocation.
- getMemoryPreference() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the preferred upper memory limit in MB.
- getMemoryShare() - Method in class com.compomics.util.db.ObjectsCache
-
Returns the share of heap size which can be used before emptying the
cache.
- 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
-
- getMethodId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- 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.
- getMethodUsed() - Method in class com.compomics.util.experiment.identification.Identification
-
Getter for the identification method used.
- getMethodUsed() - Method in class com.compomics.util.experiment.quantification.Quantification
-
getter for the method used
- getMgfFileNames() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns a list of loaded mgf files.
- getMH() - Method in class com.compomics.util.experiment.refinementparameters.PepnovoAssumptionDetails
-
Returns the PepNovo mH.
- getMinAnnotatedPeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the minimal number of annotated peaks a peptide should have.
- getMinChargeSearched() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the minimal charge searched.
- getMinFragmentMz() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Returns the minimal fragment m/z.
- getMinimalChargeForMultipleChargedFragments() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the minimal precursor charge to account for multiply charged
fragments in OMSSA.
- getMinimalChargeForMultipleChargedFragments() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- getMinimumValue() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
-
Returns the current minimum value for the progressbar.
- getMinMass() - Method in class com.compomics.util.gui.events.RescalingEvent
-
Returns the minimum mass.
- getMinMz() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the min mz value.
- getMinPeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the minimal number of peaks a spectrum should contain.
- getMinPeaksPerSpectrum() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Returns the minimal number of peaks per spectrum.
- getMinPepLength() - Method in class com.compomics.util.preferences.IdFilter
-
Returns the maximal peptide length allowed.
- getMinPeptideLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the minimal peptide length allowed.
- getMinPeptideLength() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- getMinPrecPerSpectrum() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the minimal number of precursors per spectrum.
- getMinPrecursorMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Returns the minimal precursor mass.
- getMinRT() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Returns the minimum RT in this file.
- getMinRT(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the minimum RT for the desired file.
- getMinRT() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the minimum RT for the whole project.
- 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.NonSymmetricalNormalDistribution
-
- getMinValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- 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.
- getModel() - Method in class com.compomics.util.sun.TableMap
-
- getModification(int) - Method in class com.compomics.util.preferences.ModificationProfile
-
Returns the name of the modification indexed by the given OMSSA index.
- 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.
- getModificationCount(String, String) - Static method in class com.compomics.util.experiment.biology.Peptide
-
Returns how many of the given modification was found in the given
peptide.
- getModificationFamily(String) - Static method in class com.compomics.util.experiment.biology.Peptide
-
Returns a list of names of the variable modifications found in the key of
a peptide.
- getModificationMatches() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Getter for the modifications carried by this sequence.
- getModificationMatches() - Method in class com.compomics.util.experiment.biology.Peptide
-
Getter for the modifications carried by this peptide.
- getModificationProfile() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the modification profile of the project.
- getModificationProfile() - Method in class com.compomics.util.gui.searchsettings.algorithm_settings.XTandemSettingsDialog
-
Returns the modification profile corresponding to the input by the user.
- getModifications() - Method in class com.compomics.util.protein.AASequenceImpl
-
Simple getter for the modifications.
- getModificationsAt(int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the modifications found at a given localization.
- getModificationsFile() - Method in class com.compomics.util.experiment.identification.search_parameters_cli.AbstractIdentificationParametersCli
-
Returns the modification file needed to initiate the factory.
- getModificationSite() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Getter for the modification site, 1 is the first amino acid.
- getModificationUse() - Method in interface com.compomics.util.gui.searchsettings.SearchSettingsDialogParent
-
Returns the list of modifications used.
- getModificationUseAsString(ArrayList<String>) - Static method in class com.compomics.util.gui.searchsettings.SearchSettingsDialog
-
Returns a line with the most used modifications.
- getModifiedIndexes() - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the indexes of the residues in the peptide that contain at least
one variable modification.
- getModifiedIndexes(boolean) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the indexes of the residues in the peptide that contain at least
one modification.
- getModifiedSequence() - Method in class com.compomics.util.protein.AASequenceImpl
-
This method will return the sequence with annotated modifications.
- getMolecularFormula() - Method in class com.compomics.util.protein.AASequenceImpl
-
This method calculates the molecular formula based on the sequence
- getMonoisotopicMass() - Method in class com.compomics.util.experiment.biology.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.
- getMutation(Mutation) - Static method in class com.compomics.util.experiment.biology.MutationFactory
-
Returns the requested mutation by lookup in the mutation map.
- getMutationsAsString() - Static method in class com.compomics.util.experiment.biology.MutationFactory
-
Returns the mutation as a string.
- getMz() - Method in class com.compomics.util.experiment.massspectrometry.Peak
-
Returns the mz.
- getMz() - Method in class com.compomics.util.experiment.massspectrometry.Precursor
-
Getter for the m/z.
- 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.
- getMzAndIntensityAsArray() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the m/z and intensity values as an array in increasing order
sorted on m/z value.
- getMzMLFileNames() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns a list of loaded mzML files.
- 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
-
- getMzValuesAsArray() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the mz values as an array.
- getName() - Method in class com.compomics.util.db.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.Atom
-
Returns the name of the atom.
- getName() - Method in class com.compomics.util.experiment.biology.ElementaryElement
-
Returns the name of the element.
- getName() - Method in class com.compomics.util.experiment.biology.Enzyme
-
Get the enzyme name.
- getName() - Method in class com.compomics.util.experiment.biology.Ion
-
Returns the name of the ion.
- getName() - Method in class com.compomics.util.experiment.biology.ions.ElementaryIon
-
- getName() - Method in class com.compomics.util.experiment.biology.ions.Glycon
-
- getName() - Method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
- getName() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
-
- getName() - Method in class com.compomics.util.experiment.biology.ions.PrecursorIon
-
- getName() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
-
This method returns the name of the reporter ion.
- getName() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
-
- getName() - Method in class com.compomics.util.experiment.biology.PTM
-
Getter for the modification name.
- getName() - Method in enum com.compomics.util.experiment.identification.Advocate
-
Returns the name of the advocate.
- getName() - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Returns the name of the database.
- getName() - Method in enum com.compomics.util.experiment.identification.ptm.PtmScore
-
Returns the name of the score.
- 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.pride.CvTerm
-
- 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.
- getNameWithGapAndNumber() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
-
Returns the name with number and mass gap.
- getNameWithNumber() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
-
Returns the name with number.
- getNameWithNumber() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
-
Returns the name with number.
- getnAnnotatedMostIntensePeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the minimal number of annotated most intense peaks.
- getnCache() - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the size of the cache.
- getNCleavageSites(Enzyme) - Method in class com.compomics.util.experiment.biology.Protein
-
Returns the number of cleavage sites.
- getNColumns() - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getNestedException() - Method in exception com.compomics.util.db.GeneratorException
-
This method returns the nested exception for this exception, or
'null' if none is present.
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.Ion
-
Returns the possible neutral losses of this ion type.
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.ElementaryIon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.Glycon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.PrecursorIon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
-
- getNeutralLosses() - Method in class com.compomics.util.experiment.biology.PTM
-
Returns the neutral losses possibly encountered with this modification.
- getNeutralLosses() - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Returns the considered neutral losses.
- getNeutralLossesAsString() - Method in class com.compomics.util.experiment.biology.Ion
-
Returns the neutral loss (if any), the empty string if no loss.
- getNeutralLossesAsString(ArrayList<NeutralLoss>) - Static method in class com.compomics.util.experiment.biology.Ion
-
Returns the neutral loss (if any), the empty string if no loss.
- getNeutronThreshold() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the mass after which exact neutron mass should be considered in
the calculation.
- getNExcludedAA(int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the number of excluded amino acids at the given index.
- getNext() - Method in class com.compomics.util.experiment.identification.SequenceFactory.HeaderIterator
-
Returns the next header in the FASTA file.
- getNextFeature() - Method in class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerResultReader
-
Get the next feature in the xml string.
- getNextProtein() - Method in class com.compomics.util.experiment.identification.SequenceFactory.ProteinIterator
-
Returns the next protein.
- getNLines() - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getNmissedCleavages(String) - Method in class com.compomics.util.experiment.biology.Enzyme
-
Returns the number of missed cleavages in an amino acid sequence.
- getNMissedCleavages(Enzyme) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the number of missed cleavages using the specified enzyme.
- getNMissedCleavages(String, Enzyme) - Static method in class com.compomics.util.experiment.biology.Peptide
-
Returns the number of missed cleavages using the specified enzyme for the
given sequence.
- getnMissedCleavages() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the allowed number of missed cleavages.
- getNModificationLocalized(String, String) - Static method in class com.compomics.util.experiment.biology.Peptide
-
Returns the list of modifications confidently localized or inferred for
the peptide indexed by the given key.
- getNode(String) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Retrieves the node of the given tag.
- getNodesInCache() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
-
Returns the number of nodes currently loaded in cache.
- getNodesInCache() - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the number of nodes currently loaded in cache.
- getNoModPeptide(Peptide, ArrayList<PTM>) - Static method in class com.compomics.util.experiment.biology.Peptide
-
Returns a version of the peptide which does not contain the inspected
PTMs.
- getNonDiagonalScore() - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
Returns a score based on the non-diagonal values.
- getNoProlineRuleSeries() - Method in class com.compomics.util.experiment.identification.identification_parameters.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 interface com.compomics.util.gui.export.graphics.ExportGraphicsDialogParent
-
Returns the normal icon.
- getNormalIcon() - Method in class com.compomics.util.gui.VennDiagramDialog
-
- getNormalIcon() - Method in class com.compomics.util.gui.XYPlottingDialog
-
- getNormalisationFactor(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
Returns the normalisation factor for the given sample.
- getNote() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- 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.
- getnPeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Returns the number of most intense peaks to consider.
- getnPeaksInDoubleChargeWindow() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the number of peaks in doubly charged windows.
- getnPeaksInSingleChargeWindow() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the number of peaks in singly charged windows.
- getNProteins(String) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Returns the number of proteins for the match corresponding to the given.
- getNProteins() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Returns the number of proteins for this match.
- getNProteinsForTerm(String) - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Returns the total number of protein accessions mapping to a given GO
term.
- getNSequences() - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Returns the number of sequences in the database.
- getNSequences() - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the number of sequences in the fasta file.
- getNSpectra() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Returns the number of imported spectra.
- getNSpectra(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the number of spectra in the desired file.
- getNSpectra() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the total number of spectra in all files.
- getNTarget() - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Returns the number of target sequences in the database.
- getNTargetedAA(int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the number of targeted amino acids at the given index.
- getNTargetSequences() - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the number of target sequences in the database.
- getNTerminal() - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the N-terminal of the peptide as a String.
- getNTerminal(boolean) - Method in class com.compomics.util.experiment.identification.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.tags.Tag
-
Returns the N-terminal gap of the tag.
- getNTermsForProtein(String) - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Returns the total number of GO terms mapping to a given protein.
- 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.
- getNumber() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
-
Returns the number of the fragment in the sequence.
- getNumber() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
-
Returns the number of the fragment in the tag.
- 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.
- getNumberOfItotopicPeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the number of isotopic peaks to consider.
- getNumberOfLines(File) - Static method in class com.compomics.util.Util
-
Returns the number of lines in the given file.
- getNumberOfProteins() - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Returns the total number of proteins in this mapping.
- getNumberOfTerms() - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Returns the total number of GO terms in this mapping.
- getNVariableModifications(double) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the number of variable modifications found with the given mass.
- getObject(String, String, String) - Method in class com.compomics.util.db.ObjectsCache
-
Returns the objects if present in the cache.
- getObjectsCache() - Method in class com.compomics.util.db.ObjectsDB
-
Returns the cache used by this database.
- getObservableLength(Enzyme, int) - Method in class com.compomics.util.experiment.biology.Protein
-
Returns the number of observable amino acids in the sequence.
- getOccurrence() - Method in class com.compomics.util.general.IsotopicElement
-
Getter for the occurrence of this element
- 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.ptm.ModificationsDialog
-
Returns the protein accession number as a web link to the given PSI-MOD
at http://www.ebi.ac.uk/ontology-lookup.
- getOmssaIndex(String) - Method in class com.compomics.util.preferences.ModificationProfile
-
Returns the OMSSA index of a given modification, null if not found.
- getOMSSAIndexes(File) - Static method in class com.compomics.util.experiment.biology.PTMFactory
-
Imports the OMSSA indexes from an XML file.
- getOmssaIndexes() - Method in class com.compomics.util.preferences.ModificationProfile
-
Returns the OMSSA indexes as a map.
- getOmssaMaxEvalue() - Method in class com.compomics.util.preferences.IdFilter
-
Returns the OMSSA maximal e-value allowed.
- getOmssaOutputTypes() - Static method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the output types available.
- getOmssaUserModBloc(String, int) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns an MSModSpec bloc as present in the OMSSA user modification files
for a given PTM.
- getOntology() - Method in class com.compomics.util.pride.CvTerm
-
- getOperatingSystem() - Static method in class com.compomics.util.io.FileSystemAccessor
-
Get the operating system.
- 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() - Method in class com.compomics.util.experiment.identification.search_parameters_cli.AbstractIdentificationParametersCli
-
Returns the options left to the user as a string.
- getOrderedMzValues() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns a list of the m/z values sorted in ascending order.
- getOrderedSpectrumFileNames() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the ordered list of spectrum file names.
- getOrientation() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- getOrigin() - Method in class com.compomics.util.experiment.biology.Mutation
-
Returns the origin amino acid.
- getOriginalKey(String, String) - Method in class com.compomics.util.db.ObjectsDB
-
Returns the original key of the corrected long key.
- getOtherProteins(String, String) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Returns the proteins in a group (group1) which are not in another group
(group2).
- getPackageName() - Method in enum com.compomics.util.enumeration.CompomicsTools
-
Return the package name of the tool.
- getParameterKey(UrParameter) - Static method in class com.compomics.util.experiment.personalization.ExperimentObject
-
Returns the key of a personalization parameter.
- 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.
- getParametersFile() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the parameters file loaded.
- getParameterTable(UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB
-
Deprecated.
use match specific mapping instead
- getParentProteins(boolean, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the parent proteins and eventually remaps the peptide to the
protein using the default protein tree.
- getParentProteins(AminoAcidPattern.MatchingType, Double, ProteinTree) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the parent proteins and remaps the peptide to the protein if no
protein mapping was set.
- getParentProteins(AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the parent proteins and remaps the peptide to the protein if no
protein mapping was set using the default protein tree of the sequence
factory.
- getParentProteins(boolean, AminoAcidPattern.MatchingType, Double, ProteinTree) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the parent proteins and eventually remaps the peptide to the
protein.
- getParentProteinsNoRemapping() - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the parent proteins without remapping them.
- getPathOfClass(String) - Static method in class com.compomics.util.io.FileSystemAccessor
-
Returns the absolute path of the underlying file system of the given
class.
- getPatientInformation(PatientInformation) - Method in class com.compomics.util.experiment.patient.Patient
-
Returns patient information,
- getPattern() - Method in class com.compomics.util.experiment.biology.PTM
-
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
-
- getPdbAccession() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
-
- getPdbaccession() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
- getPdbEnd() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
-
- getPdbGroup() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
-
- 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
-
- 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, Charge) - 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, Charge) - 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.
- getPeakList() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the peak list.
- getPeakMap() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns a peak map where peaks are indexed by their m/z.
- 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(double) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns an array containing the intensity of all peak above the provided
threshold.
- 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.experiment.identification.identification_parameters.PepnovoParameters
-
Returns the PepNovo to utilities PTM map.
- getPepNovoPtmMap() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- getPeptide() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
-
Get the theoretic peptide.
- getPeptideCount() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Returns the number of peptides found.
- getPeptideFDR() - Method in class com.compomics.util.preferences.ProcessingPreferences
-
Returns the initial peptide FDR.
- getPeptideIdentification() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a list of the keys of all encountered peptides.
- getPeptideIterator() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
-
Returns a PeptideIterator which iterates alphabetically all peptides
corresponding to the end of a branch in the tree.
- getPeptideMatch(String) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a peptide match.
- getPeptideMatch(String, boolean) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a peptide match.
- getPeptideMatch(String, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB
-
Returns the desired peptide match.
- getPeptideMatches() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Getter for the peptide keys.
- getPeptideMatches(String, int, int, AminoAcidPattern.MatchingType, Double, ArrayList<String>, ArrayList<String>) - Method in class com.compomics.util.experiment.identification.tags.Tag
-
Returns the start and end indexes of the tag in the given sequence.
- getPeptideMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the desired peptide match parameter.
- getPeptideMatchParameter(String, UrParameter, boolean) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the desired peptide match parameter.
- getPeptideMatchParameter(String, UrParameter, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB
-
Returns the desired peptide match parameter.
- getPeptideParameterTable(UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB
-
Returns the table name associated with the given peptide parameter.
- getPeptideScoreToPositionMap(HashMap<Integer, HashMap<Integer, Double>>) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.AScore
-
Estimates the peptide score for every modification localization and
returns a map score -> localization.
- getPeptideSelected() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the color for a selected peptide.
- getPeptideSequences() - Method in class com.compomics.util.gui.spectrum.IsotopicDistributionPanel
-
Get the set of peptide sequences.
- getPeptidesFromTags(ProteinTree, AminoAcidPattern.MatchingType, Double, boolean, ArrayList<String>, ArrayList<String>, boolean) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Creates a peptide based spectrum match where peptide assumptions are
deduced from tag assumptions.
- getPeptideShakerPath() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the path to the PeptideShaker installation.
- getPeptideStart(String, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Protein
-
Returns the list of indexes where a peptide can be found in the protein
sequence.
- 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
-
- 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.pride.prideobjects.Reference
-
Returns the PubMed ID of the reference.
- getPosition() - Method in class com.compomics.util.protein.Enzyme
-
Simple getter for the cleavage position of the Enzyme.
- getPositionToScoreMap(Peptide, Peptide, ArrayList<Integer>, MSnSpectrum, HashMap<Integer, MSnSpectrum>, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, double, PeptideSpectrumAnnotator, PTM) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.AScore
-
Returns a map PTM localization -> score.
- getPossibilities() - Static method in enum com.compomics.util.experiment.identification.Advocate
-
Returns the implemented advocates.
- getPossibleCharges() - Method in class com.compomics.util.experiment.massspectrometry.Precursor
-
Getter for the possible charges.
- getPossibleChargesAsString() - Method in class com.compomics.util.experiment.massspectrometry.Precursor
-
Returns the possible charges as a string.
- getPossibleSubtypes(Ion.IonType) - Static method in class com.compomics.util.experiment.biology.Ion
-
Returns an arraylist of possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.ElementaryIon
-
Returns an arraylist of possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.Glycon
-
Returns an arraylist of possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
Returns an arraylist of possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
-
Returns an arraylist of possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.PrecursorIon
-
Returns an arraylist of possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Returns an arraylist of possible subtypes.
- getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
-
Returns an arraylist of possible subtypes.
- getPotentialModificationSites(Double, AminoAcidPattern.MatchingType, Double, ModificationProfile) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the potential modification sites as an ordered list of string.
- getPotentialModificationSites(PTM, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the potential modification sites as an ordered list of string.
- getPotentialModificationSites(String, PTM) - Static method in class com.compomics.util.experiment.biology.Peptide
-
Deprecated.
use getPotentialModificationSites(PTM ptm,
AminoAcidPattern.MatchingType matchingType, Double massTolerance)
- getPotentialModificationSites(PTM, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.identification.tags.Tag
-
Returns the potential modification sites as an ordered list of string.
- 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.
- getPrecurorCharge() - Method in class com.compomics.util.io.PklFile
-
- getPrecursor(BufferedRandomAccessFile, Long, String) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader
-
Returns the next precursor starting from the given index.
- getPrecursor() - Method in class com.compomics.util.experiment.massspectrometry.MSnSpectrum
-
Returns the precursor.
- getPrecursor(String, String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the precursor of the desired spectrum.
- getPrecursor(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the precursor of the desired spectrum.
- getPrecursor(String, boolean) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the precursor of the desired spectrum.
- getPrecursorAccuracy() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the precursor tolerance.
- getPrecursorAccuracyDalton() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the precursor tolerance in Dalton (for de novo searches).
- getPrecursorAccuracyType() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the precursor accuracy type.
- getPrecursorIntensity() - Method in class com.compomics.util.io.PklFile
-
- getPrecursorMatch(Peak) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the ion match.
- 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
-
- getPreferredAccessionColumnWidth(JTable, int, int) - Method in class com.compomics.util.gui.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.Ion
-
Returns the pride cv term adapted to the fragment ion.
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.ElementaryIon
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.Glycon
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.PrecursorIon
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
-
- getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
-
- 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 interface com.compomics.util.waiting.WaitingHandler
-
Returns the primary progress counter.
- getProbabilisticScoreThreshold() - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
Returns the probabilistic score threshold.
- 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.NonSymmetricalNormalDistribution
-
- getProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- 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.
- 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.
- getPrositeFormat() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the pattern in the prosite format.
- getProtein(String) - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the desired protein.
- getProteinConfidenceMwPlots() - Method in class com.compomics.util.preferences.ProcessingPreferences
-
Returns the minimum confidence required for a protein to be included in
the average molecular weight analysis in the Fractions tab.
- getProteinEvidencAsString(Integer) - Static method in class com.compomics.util.preferences.GenePreferences
-
Return the protein evidence type as text.
- getProteinEvidence() - Method in class com.compomics.util.protein.Header
-
- getProteinFDR() - Method in class com.compomics.util.preferences.ProcessingPreferences
-
Returns the initial protein FDR.
- getProteinGoAccessions(String) - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Returns a list of non redundant GO accession numbers corresponding to a
protein match.
- getProteinGoDescriptions(String) - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Returns a list of non redundant GO term descriptions corresponding to a
protein match.
- getProteinIdentification() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a list of the keys of all encountered proteins.
- getProteinIterator(boolean) - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns an iterator of all the proteins in the FASTA file.
- getProteinKey() - Method in class com.compomics.util.experiment.biology.Protein
-
Returns the key for protein indexing.
- getProteinLength(String) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Retrieves the length of a protein.
- 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.
- getProteinMapped() - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Returns a non redundant list of all the proteins mapped.
- getProteinMapping(AminoAcidPattern, String, AminoAcidPattern.MatchingType, Double, boolean) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node
-
Returns the protein mappings for the given peptide sequence.
- getProteinMapping(String) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
-
Returns the protein mapping in the sequence factory for the given peptide
sequence based on string matching only.
- getProteinMapping(String, AminoAcidPattern.MatchingType, Double, boolean) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
-
Returns the protein mapping in the sequence factory for the given peptide
sequence.
- getProteinMapping(Tag, AminoAcidPattern.MatchingType, Double, ArrayList<String>, ArrayList<String>, boolean) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
-
Returns the protein mappings for the given peptide sequence.
- getProteinMatch(String) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a protein match.
- getProteinMatch(String, boolean) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a protein match.
- getProteinMatch(String, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB
-
Returns the desired protein match.
- getProteinMatches(Peptide) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the keys of the protein matches where a peptide can be found.
- getProteinMatchKey(Peptide) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Convenience method which returns the protein key of a peptide.
- getProteinMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the desired protein match parameter.
- getProteinMatchParameter(String, UrParameter, boolean) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the desired protein match parameter.
- getProteinMatchParameter(String, UrParameter, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB
-
Returns the desired protein match parameter.
- getProteinParameterTable(UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB
-
Returns the table name associated with the given protein parameter.
- getProteinTreeFolder() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the protein tree folder.
- getProteinTreeImportTime() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the protein tree import times in a map: file size -> list of
import sizes.
- getProteomicAnalysis(int) - Method in class com.compomics.util.experiment.SampleAnalysisSet
-
Returns the analysis corresponding to the selected replicate
- getProtocols() - Method in class com.compomics.util.pride.PrideObjectsFactory
-
Returns the protocols.
- getPsmFDR() - Method in class com.compomics.util.preferences.ProcessingPreferences
-
Returns the initial PSM FDR.
- getPTM(ModificationProfile, int) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Get a PTM according to its OMSSA index.
- getPTM(String) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns the PTM indexed by its name.
- getPTM(double, String, String) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Deprecated.
This method can generate inconsistent results in case a
measurement matches to various PTMs.
- getPtm(String) - Method in class com.compomics.util.preferences.ModificationProfile
-
Returns the back-ed up PTM with the given name.
- getPtmName() - Method in class com.compomics.util.gui.protein.ModificationProfile
-
Returns the PTM name.
- getPTMPlotData(Peptide, PTM, int, MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, double, double) - Static method in class com.compomics.util.experiment.identification.ptm.PtmtableContent
-
Returns the PTM plot series in the JFreechart format for one PSM.
- getPTMs() - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns the names of all imported PTMs.
- getPTMTableContent(Peptide, PTM, int, MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, double, double) - Static method in class com.compomics.util.experiment.identification.ptm.PtmtableContent
-
Get the PTM table content.
- getPtmToPrideMap() - Method in class com.compomics.util.pride.PrideObjectsFactory
-
Returns the utilities PTM to pride map.
- getQuantification(Quantification.QuantificationMethod) - Method in class com.compomics.util.experiment.ProteomicAnalysis
-
returns quantification results obtain with a quantification method
- getQuantile(int, Integer, int, double) - Method in class com.compomics.util.experiment.identification.ptm.PtmtableContent
-
Get the quantile.
- getQuoteType() - Static method in class com.compomics.software.CommandLineUtils
-
Returns the quote type to use.
- getRank() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
-
- getRank() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Get the identification rank.
- getRankScore() - Method in class com.compomics.util.experiment.refinementparameters.PepnovoAssumptionDetails
-
Returns the PepNovo rank score.
- getReadTweets() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
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.
- getRecalibratedPeakList(HashMap<Double, Double>) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns a recalibrated peak list.
- getRecalibratedPrecursor(double, double) - Method in class com.compomics.util.experiment.massspectrometry.Precursor
-
Returns a recalibrated precursor.
- getReducedSpectra(MSnSpectrum, double) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.AScore
-
Generates a map containing the spectra filtered on intensity with a basis
of 20*m/z tolerance indexed by the depth used.
- getReducedSpectra(MSnSpectrum, double, int) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.AScore
-
Generates a map containing the spectra filtered on intensity with a basis
of 20*m/z tolerance indexed by the depth used.
- getReducedSpectra(MSnSpectrum, double) - Static method in class com.compomics.util.experiment.identification.scoring.PsmScores
-
Generates a map containing the spectra filtered on intensity with a basis
of 20*mz tolerance indexed by the depth used.
- getReducedSpectra(MSnSpectrum, double, int) - Static method in class com.compomics.util.experiment.identification.scoring.PsmScores
-
Generates a map containing the spectra filtered on intensity with a basis
of 20*mz tolerance indexed by the depth used.
- 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.experiment.biology.Sample
-
Getter for the sample reference
- getReference() - Method in class com.compomics.util.experiment.MsExperiment
-
Returns the reference of the experiment.
- 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.
- getReferences() - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
-
Returns the references.
- getRefinementFixedModifications() - Method in class com.compomics.util.preferences.ModificationProfile
-
Return the refinement fixed modifications used for the second pass
search.
- getRefinementVariableModifications() - Method in class com.compomics.util.preferences.ModificationProfile
-
Return the refinement variable modifications used for the second pass
search.
- getRelativeError(boolean) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Get the relative m/z matching error in ppm.
- getRelativeError() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
-
Get the relative m/z matching error in ppm without isotope removal.
- getRelimsPath() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the path to the Relims installation.
- getReplicateNumberList() - Method in class com.compomics.util.experiment.SampleAnalysisSet
-
Returns a list containing replicate numbers
- getReport(File) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Returns the report.
- getReporterIndex(Sample) - 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.ReporterIon
-
Returns the reporter ion indexed by the given index.
- getReporterIon(String) - Static method in class com.compomics.util.experiment.biology.ions.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() - Method in class com.compomics.util.experiment.biology.PTM
-
Returns the reporter ions possibly encountered with this modification.
- getReporterMethod() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
returns the reporter method used.
- getReporterPath() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the path to the Reporter installation.
- getResidue(int) - Static method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
Returns the amino acid of the immonium ion based on the subtype index.
- getResidues() - Method in class com.compomics.util.experiment.biology.PTM
-
Deprecated.
use amino acid pattern instead
- 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
-
- getResolution() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
- getResponseString() - Method in class com.compomics.util.io.FTP
-
Returns all server response strings.
- getResponseStringNoReset() - Method in class com.compomics.util.io.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.protein.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.Enzyme
-
Getter for the amino acids restricting when following the cleavage.
- getRestrictionBefore() - Method in class com.compomics.util.experiment.biology.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() - Static method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns the list of rewind ions.
- getRobustCorrelation(ArrayList<Double>, ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
-
Returns the population Pearson correlation r between series1 and series2.
- 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.
- 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
- getRoundedMassShift() - Method in class com.compomics.util.experiment.biology.Mutation
-
Get rounded mass shift.
- 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.sun.TableMap
-
- getRowNumber(int) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
-
Returns the row number of the given view index.
- getRt() - Method in class com.compomics.util.experiment.massspectrometry.Precursor
-
Getter for the retention time.
- getRtWindow() - Method in class com.compomics.util.experiment.massspectrometry.Precursor
-
Returns an array containing the min and max of the RT window.
- getSample(int) - Method in class com.compomics.util.experiment.MsExperiment
-
Returns a single sample accessed by its index.
- getSample(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
-
This method returns the sample associated to the given ion.
- 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.experiment.MsExperiment
-
Returns the implemented samples.
- getSamples() - Method in class com.compomics.util.pride.PrideObjectsFactory
-
Returns the samples.
- getScanNumber() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Getter for the scan number.
- getScanStartTime() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the scan start time.
- getScore() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
-
- getScore(int) - Static method in enum com.compomics.util.experiment.identification.ptm.PtmScore
-
Returns the PTM score indexed by the given id.
- getScore(String) - Static method in enum com.compomics.util.experiment.identification.ptm.PtmScore
-
Returns the PTM score of the given name.
- 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.refinementparameters.MascotScore
-
Getter for Mascot score.
- getScore() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- getScore() - Method in class com.compomics.util.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
- getScoreNames() - Static method in enum com.compomics.util.experiment.identification.ptm.PtmScore
-
Returns a list containing the names of the implemented scores.
- getSearchedPTM(PTM) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns the standard search compatible PTM corresponding to this pattern.
- getSearchedPTM(String) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns the standard search compatible PTM corresponding to this pattern,
i.e., a pattern targeting a single amino acid and not a complex pattern.
- getSearchEngine(File) - Method in class com.compomics.util.experiment.io.identifications.IdfileReaderFactory
-
This method return the identification software corresponding to the given
file.
- getSearchGuiPath() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the path to the SearchGUI installation.
- getSearchParameters() - Method in class com.compomics.util.experiment.identification.search_parameters_cli.IdentificationParametersInputBean
-
Returns the search parameters.
- getSearchParameters(Properties, File) - Static method in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
-
Deprecated.
Conversion methods which converts an old school set of identification
properties into a SearchParameters instance.
- getSearchParameters() - Method in class com.compomics.util.gui.searchsettings.SearchSettingsDialog
-
Returns a SearchParameters instance based on the user input in the GUI.
- getSearchParameters() - Method in interface com.compomics.util.gui.searchsettings.SearchSettingsDialogParent
-
Returns the search parameters.
- 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 interface com.compomics.util.waiting.WaitingHandler
-
Returns the secondary progress counter.
- getSections() - Method in class com.compomics.util.io.export.ExportScheme
-
returns the list of sections to be included in the scheme.
- 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.
- getSelectedFile() - Method in class com.compomics.util.gui.filehandling.FileSelectionDialog
-
Returns the file selected by the user.
- getSelectedFiles() - Method in class com.compomics.util.gui.filehandling.FileDisplayDialog
-
Returns the list of selected files.
- getSelectedOutput() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the selected output type, omx or csv.
- getSelectedPositions() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- getSelectedProbabilisticScore() - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
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.
- getSelection() - Method in class com.compomics.util.gui.ptm.PtmChooser
-
Returns a list of PTMs selected by the user.
- getSelection() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- 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.Peptide
-
Getter for the sequence.
- getSequence(String) - Static method in class com.compomics.util.experiment.biology.Peptide
-
Returns the sequence of the peptide indexed by the given key.
- getSequence() - Method in class com.compomics.util.experiment.biology.Protein
-
Getter for the protein sequence.
- 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.
- getSequenceAsPattern() - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the sequence of this peptide as AminoAcidPattern.
- getSequenceAsPattern(String) - Static method in class com.compomics.util.experiment.biology.Peptide
-
Returns the given sequence as AminoAcidPattern.
- getSequenceProbabilities(Peptide, ArrayList<PTM>, MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, double, boolean, AminoAcidPattern.MatchingType) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.PhosphoRS
-
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
- getSerializationDirectory() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the serialization directory.
- getShortName() - Method in class com.compomics.util.experiment.biology.PTM
-
Getter for the short modification name.
- getShortName(String) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns the user favorite short name, a default short name otherwise.
- getSimilarNotFixedModifications(Double) - Method in class com.compomics.util.preferences.ModificationProfile
-
Returns a list containing all not fixed modifications with the same mass.
- getSimpleProteinDescription() - Method in class com.compomics.util.protein.Header
-
Returns a simplified protein description for a UniProt header.
- getSingleChargeWindow() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Returns the window size for singly charged ions.
- getSize() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node
-
Returns the size of the node in accession*tag.
- getSkylinePath() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Returns the skyline path.
- getSoftwareVersion() - Method in interface com.compomics.util.experiment.io.identifications.IdfileReader
-
Returns the name and version of the software used to generate the
identification file, e.g., Mascot 2.3.0 or X! Tandem Sledgehammer
(2013.09.01.1).
- getSoftwareVersion() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader
-
- 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
-
This method reports on the sourcefile currently used in transfer.
- getSpAccession() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
-
- getSpAccession() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
-
- getSparklineColor() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Getter for the sparkline color.
- getSparklineColorNonValidated() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Getter for the non-validated sparkline color.
- getSparklineColorNotFound() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the color for a not found sparkline bar chart plots.
- getSparklineColorPossible() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the color for a possible sparkline bar chart plots.
- getSpecies() - Method in class com.compomics.util.preferences.GenePreferences
-
Deprecated.
use getAllSpecies instead
- getSpeciesMap() - Method in class com.compomics.util.preferences.GenePreferences
-
Deprecated.
use getAllSpeciesMap instead
- getSpectra(File) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfReader
-
Reads an MGF file and retrieves a list of spectra.
- getSpectrum(BufferedRandomAccessFile, long, String) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader
-
Returns the next spectrum starting from the given index.
- getSpectrum(String, String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the desired spectrum.
- getSpectrum(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the desired spectrum.
- getSpectrumAnnotatedPeakColor() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the color to use for the annotated peaks.
- getSpectrumAnnotatedPeakWidth() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the width of the annotated peaks.
- getSpectrumAnnotation(HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, MSnSpectrum, Peptide, double, double, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotators.PeptideSpectrumAnnotator
-
Returns the spectrum annotations of a spectrum in a list of IonMatches.
- getSpectrumAnnotation(HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, MSnSpectrum, Tag, double, double, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotators.TagSpectrumAnnotator
-
Returns the spectrum annotations of a spectrum in a list of IonMatches.
- getSpectrumAnnotation(ArrayList<IonMatch>) - Static method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Translates the list of ion matches into a vector of annotations which can
be read by the SpectrumPanel.
- getSpectrumBackgroundPeakColor() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the color to use for the background peaks.
- getSpectrumBackgroundPeakWidth() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Returns the width of the background peaks.
- getSpectrumCount() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
Returns the number of spectra matched.
- getSpectrumFile(String) - Static method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Convenience method to retrieve the name of a file from the spectrum key.
- getSpectrumFileFromIdName(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns the spectrum file corresponding to the name of the file used for
identification
- getSpectrumFileId() - Method in class com.compomics.util.io.PklFile
-
- getSpectrumFiles() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the names of the mgf files used in the spectrum identification
map as a list.
- getSpectrumIdentification() - Method in class com.compomics.util.experiment.identification.Identification
-
Deprecated.
use file specific names instead
- getSpectrumIdentification(String) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the keys of the spectrum identifications for a given spectrum
file name.
- getSpectrumIdentificationMap() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the keys of all identified spectra indexed by the spectrum file.
- getSpectrumIdentificationSize() - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the number of spectrum identifications.
- getSpectrumKey(String, String) - Static method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Convenience method returning the key for a spectrum.
- getSpectrumKey() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the key of the spectrum.
- getSpectrumMatch(String) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a spectrum match.
- getSpectrumMatch(String, boolean) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns a spectrum match.
- getSpectrumMatch(String, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB
-
Returns the desired spectrum match.
- getSpectrumMatches() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
Returns all spectra matched.
- getSpectrumMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the desired spectrum match parameter.
- getSpectrumMatchParameter(String, UrParameter, boolean) - Method in class com.compomics.util.experiment.identification.Identification
-
Returns the desired spectrum match parameter.
- getSpectrumMatchParameter(String, UrParameter, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB
-
Returns the desired spectrum match parameter.
- getSpectrumMatchTable(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB
-
Returns the table name associated with the given spectrum key.
- getSpectrumNumber() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Returns the spectrum number in the spectrum file.
- getSpectrumParameterTable(String, UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB
-
Returns the table name associated with the given spectrum parameter.
- getSpectrumTitle(String) - Static method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Convenience method to retrieve the name of a spectrum from the spectrum
key.
- getSpectrumTitle() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the spectrum title.
- getSpectrumTitles() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Returns an ordered list of all spectrum titles.
- getSpectrumTitles(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns a list of titles from indexed spectra in the given file.
- getSpEnd() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
-
- getSpStart() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
-
- getStandardSearchPattern() - Method in class com.compomics.util.experiment.biology.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.
- 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
-
- getStart_block() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- getStart_protein() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- getStartLocation() - Method in class com.compomics.util.protein.Header
-
This method reports on the start index of the header.
- getStartPosition() - Method in class com.compomics.util.pdbfinder.das.readers.StartEndPosition
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.AminoAcid
-
In case of a combination of amino acids, returns the comprised amino
acids or amino acid groups represented by their single letter code.
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Alanine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Arginine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Asparagine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.AsparticAcid
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.B
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Cysteine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.GlutamicAcid
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Glutamine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Glycine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Histidine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Isoleucine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.J
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Leucine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Lysine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Methionine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Phenylalanine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Proline
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Pyrrolysine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Selenocysteine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Serine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Threonine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Tryptophan
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Tyrosine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Valine
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.X
-
- getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.Z
-
- getSubMatrix(int, int, int, int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- getSubNode(String) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node
-
Returns the subnode associated to an amino acid sequence.
- getSubNumber() - Method in class com.compomics.util.experiment.biology.ions.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.AminoAcidPattern
-
Returns a sub pattern of the pattern.
- getSubPattern(int, boolean) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns a sub pattern of the pattern.
- getSubSpectrum(double, double) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Returns the part of the spectrum contained between mzMin (inclusive) and
mzMax (exclusive) as a peak list
- getSubtree() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node
-
Returns the subtree.
- getSubType() - Method in class com.compomics.util.experiment.biology.Ion
-
Returns the ion subtype.
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.ElementaryIon
-
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.Glycon
-
- getSubtype(char) - Static method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
Returns the subtype identifier based on the amino acid one letter symbol.
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
-
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.PrecursorIon
-
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
-
- getSubType() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
-
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.Ion
-
Returns the subtype as string.
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.ElementaryIon
-
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.Glycon
-
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
-
- getSubTypeAsString(int) - Static method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
-
Returns the type of fragment ion as a letter.
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.PrecursorIon
-
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
-
- getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
-
- getSubTypeAsString(int) - Static method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
-
Returns the type of fragment ion as a letter.
- getSurroundingAA(String, int, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Protein
-
Returns the amino acids surrounding a peptide in the sequence of the
given protein in a map: peptide start index -> (amino acids before, amino
acids after).
- 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
-
Sets up the cell renderer for the given component.
- 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
-
Sets up the cell renderer for the given component.
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer
-
Sets up the cell renderer for the given cell.
- 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.
- getTag() - Method in class com.compomics.util.experiment.identification.spectrum_annotators.TagSpectrumAnnotator
-
Returns the tag to annotate.
- getTag() - Method in class com.compomics.util.experiment.identification.TagAssumption
-
Returns the tag of this assumption.
- getTaggedModifiedSequence(ModificationProfile, boolean, boolean, boolean) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
- getTaggedModifiedSequence(ModificationProfile, AminoAcidPattern, HashMap<Integer, ArrayList<String>>, HashMap<Integer, ArrayList<String>>, HashMap<Integer, ArrayList<String>>, boolean, boolean) - Static method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
- getTaggedModifiedSequence(ModificationProfile, boolean, boolean, boolean, boolean) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
- getTaggedModifiedSequence(ModificationProfile, boolean, boolean, boolean) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
- getTaggedModifiedSequence(ModificationProfile, Peptide, HashMap<Integer, ArrayList<String>>, HashMap<Integer, ArrayList<String>>, HashMap<Integer, ArrayList<String>>, boolean, boolean, boolean) - Static method in class com.compomics.util.experiment.biology.Peptide
-
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
- getTaggedModifiedSequence(ModificationProfile, boolean, boolean, boolean, boolean, boolean) - Method in class com.compomics.util.experiment.identification.tags.Tag
-
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
- getTaggedModifiedSequence(ModificationProfile, boolean, boolean, boolean, boolean) - Method in class com.compomics.util.experiment.identification.tags.Tag
-
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
- getTaggedModifiedSequence(ModificationProfile, Tag, boolean, boolean, boolean, boolean, boolean) - Static method in class com.compomics.util.experiment.identification.tags.Tag
-
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
- getTarget() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the index of the amino acid of interest in the pattern.
- getTarget() - Method in class com.compomics.util.experiment.biology.Mutation
-
Returns the target amino acid.
- getTargetDecoyFileNameTag() - Static method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns the target-decoy file name tag.
- getTargetedAA(int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Returns the targeted amino acids at a given index in the pattern.
- getTaxonomy() - Method in class com.compomics.util.protein.Header
-
- getTermAccession(String) - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Returns the accession number of a GO term.
- getTermDescription(String) - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Returns the description of a GO term.
- getTermini() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node
-
Returns the terminal mappings (they are not in the subtree).
- getTermNamesMapped() - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Returns a non redundant list of all the GO term descriptions mapped.
- getTermsMapped() - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Returns a non redundant list of all the GO accession numbers mapped.
- 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(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.
- getTheoreticMass() - Method in class com.compomics.util.experiment.biology.Ion
-
Returns the theoretic mass.
- getTheoreticMass() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
-
- getTheoreticMass() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
-
- getTheoreticMass() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the theoretic mass of the given assumption.
- getTheoreticMass() - Method in class com.compomics.util.experiment.identification.TagAssumption
-
- getTheoreticMass(boolean, boolean) - Method in class com.compomics.util.experiment.identification.TagAssumption
-
Returns the theoretic mass of the tag, eventually without terminal gaps.
- getTheoreticMz(int) - Method in class com.compomics.util.experiment.biology.Ion
-
Returns the theoretic m/z of an ion at a given charge state.
- getTheoreticMz() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
Returns the theoretic m/z.
- getTheoreticMz(boolean, boolean) - Method in class com.compomics.util.experiment.identification.TagAssumption
-
Returns the theoretic mass of the tag, eventually without terminal gaps.
- getTheoreticPeptide() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
Getter for the theoretic peptide.
- getTheoreticProteinsAccessions() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Returns the accessions of the possible theoretic proteins.
- getTheoreticPtm() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Getter for the theoretic PTM name.
- 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 class com.compomics.util.messages.FeedBack
-
Returns the title.
- getTitle() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
-
- getTitle() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
- 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.
- getTitles() - Method in interface com.compomics.util.io.export.ExportFeature
-
Returns the column titles of the feature.
- getTotalIntensity() - Method in class com.compomics.util.experiment.massspectrometry.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.
- getTrace() - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- 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.AminoAcidPattern
-
Returns the trypsin example as amino acid pattern.
- getType() - Method in class com.compomics.util.experiment.biology.Ion
-
Returns the ion type.
- getType() - Method in class com.compomics.util.experiment.biology.PTM
-
Getter for the modification type.
- 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.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.pdbfinder.das.readers.DasFeature
-
- getTypeAsString() - Method in class com.compomics.util.experiment.biology.Ion
-
Returns the type of ion as string.
- getTypeAsString(Ion.IonType) - Static method in class com.compomics.util.experiment.biology.Ion
-
Returns the type of ion as string.
- getTypeCategory() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- getTypeId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- getTypeReference() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- getTypeSubparts() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- getTypeSuperparts() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- 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.
- getUrlOfZippedVersion(URL, String, boolean) - Static method in class com.compomics.software.autoupdater.WebDAO
-
Gets the first zip file from an 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
-
Method which returns the refinement parameter.
- getUserModifications() - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns the names of the user defined modifications.
- getUserModificationsFile() - Method in class com.compomics.util.experiment.identification.search_parameters_cli.AbstractIdentificationParametersCli
-
Returns the user modification file needed to initiate the factory.
- getUserModificationsFile() - Method in interface com.compomics.util.gui.searchsettings.SearchSettingsDialogParent
-
Returns the user modifications file.
- getUserModificationsOrdered() - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Returns the alphabetically ordered names of the user defined
modifications.
- getUserSelectedFile(Component, String, String, String, String, boolean) - Static method in class com.compomics.util.Util
-
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.Util
-
Returns the folder selected by the user, or null if no folder was
selected.
- getUtilitiesEnzyme(String) - Method in class com.compomics.util.experiment.biology.EnzymeFactory
-
Tries to map the enzyme name given in the PRIDE file a utilities/OMSSA
enzyme.
- getUtilitiesUserPreferences() - Method in interface com.compomics.software.dialogs.JavaOptionsDialogParent
-
Returns the utilities user preferences.
- getValidatedCharges() - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Returns the fragment ion charges considered for the desired precursor
charge.
- 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
-
- 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.math.matrix.DoubleMatrix
-
Returns the value of the matrix at given indexes.
- getValueAt(double) - Method in class com.compomics.util.math.statistics.ROC
-
Returns the sensitivity at a given 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.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.NonSymmetricalNormalDistribution
-
- getValueAtDescendingCumulativeProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
-
- getVariableModifications() - Method in class com.compomics.util.preferences.ModificationProfile
-
Returns the expected variable modification names included in this
profile.
- getVennDiagramPanel() - Method in class com.compomics.util.gui.VennDiagramDialog
-
Returns the Venn diagram panel.
- getVersion() - Method in class com.compomics.util.examples.UtilitiesDemo
-
Retrieves the version number set in the pom file.
- getVersion() - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Returns the database version.
- getVersion() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Returns the version.
- 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 interface com.compomics.util.gui.export.graphics.ExportGraphicsDialogParent
-
Returns the waiting icon.
- 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.
- getWindow() - Method in class com.compomics.util.gui.ptm.PtmDialog
-
- getX() - Method in class com.compomics.util.XYZDataPoint
-
- 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.experiment.biology.Enzyme
-
Get the X!Tandem enzyme format.
- getXtandemMaxEvalue() - Method in class com.compomics.util.preferences.IdFilter
-
Returns the maximal X!Tandem e-value allowed.
- getY() - Method in class com.compomics.util.XYZDataPoint
-
- getYAxisData() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Returns the y-axis data.
- getYStart(NeutralLoss) - Method in class com.compomics.util.experiment.identification.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).
- getZ() - Method in class com.compomics.util.XYZDataPoint
-
- gif - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
-
- GIF - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
-
- GLUTAMIC_ACID - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
Subtype int for a glutamic acid immonium ion.
- GlutamicAcid - Class in com.compomics.util.experiment.biology.aminoacids
-
Glutamic Acid.
- GlutamicAcid() - Constructor for class com.compomics.util.experiment.biology.aminoacids.GlutamicAcid
-
Constructor.
- Glutamine - Class in com.compomics.util.experiment.biology.aminoacids
-
Glutamine.
- Glutamine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Glutamine
-
Constructor.
- GLUTAMINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
Subtype int for a glutamine immonium ion.
- Glycine - Class in com.compomics.util.experiment.biology.aminoacids
-
Glycine.
- Glycine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Glycine
-
Constructor.
- GLYCINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
Subtype int for a glycine immonium ion.
- Glycon - Class in com.compomics.util.experiment.biology.ions
-
This class will models a glycon fragment.
- Glycon(String, String) - Constructor for class com.compomics.util.experiment.biology.ions.Glycon
-
Constructor for a glycon.
- GlyconFactory - Class in com.compomics.util.experiment.biology
-
This factory will provide theoretic glycons.
- GO_MAPPING_FILE_SUFFIX - Static variable in class com.compomics.util.preferences.GenePreferences
-
The suffix to use for files containing GO mappings.
- GOFactory - Class in com.compomics.util.experiment.annotation.go
-
The GOFactory annotates identification results based on Ensembl Gene Ontology
terms.
- GraphicsPanel - 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, or a chromatogram.
- GraphicsPanel() - Constructor for class com.compomics.util.gui.spectrum.GraphicsPanel
-
- 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(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.
- 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
-
- I - Static variable in class com.compomics.util.experiment.biology.AminoAcid
-
- iAnnotations - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The Vector that holds a set of Annotation instances.
- iAnnotationYAxisThreshold - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The procentual 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.
- iClickedIndex - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Int that indicates which point was clicked.
- 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.
- 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.util.experiment.identification.search_parameters_cli.IdentificationParametersCLIParams
-
Short Id for the CLI parameter.
- 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 contains identification results.
- Identification() - Constructor for class com.compomics.util.experiment.identification.Identification
-
- IdentificationAlgorithmParameter - Interface in com.compomics.util.experiment.identification
-
Interface for the algorithm specific parameters.
- identificationCharge - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
The charge used for identification.
- IdentificationDB - Class in com.compomics.util.experiment.identification
-
This class uses a database to manage identification matches.
- IdentificationDB(String, String, boolean, ObjectsCache) - Constructor for class com.compomics.util.experiment.identification.IdentificationDB
-
Constructor creating the database and the protein and protein parameters
tables.
- identificationFile - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
-
The identification file.
- 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
-
- 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(int) - Constructor for class com.compomics.util.experiment.identification.IdentificationMethod
-
Constructor for the identification method
- IdentificationParametersCLIParams - Enum in com.compomics.util.experiment.identification.search_parameters_cli
-
Enum class specifying the SearchParameter command line option parameters to
create a SearchParameters object
- IdentificationParametersInputBean - Class in com.compomics.util.experiment.identification.search_parameters_cli
-
This class contains the parses parameters from a command line and stores them
in a SearchParameters object.
- IdentificationParametersInputBean(CommandLine) - Constructor for class com.compomics.util.experiment.identification.search_parameters_cli.IdentificationParametersInputBean
-
Takes all the arguments from a command line.
- IdentificationParametersReader - Class in com.compomics.util.experiment.io.identifications
-
Deprecated.
use the SearchParameters class instead
- IdentificationParametersReader() - Constructor for class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
-
Deprecated.
- IdfileReader - Interface in com.compomics.util.experiment.io.identifications
-
This interface will retrieve spectrum matches from any identification file.
- IdfileReaderFactory - Class in com.compomics.util.experiment.io.identifications
-
This factory will provide the appropriate identification file reader for each
type of file.
- IdFilter - Class in com.compomics.util.preferences
-
This class achieves a pre-filtering of the identifications for PeptideShaker.
- IdFilter() - Constructor for class com.compomics.util.preferences.IdFilter
-
Constructor with default settings.
- IdFilter(int, int, double, double, double, double, boolean, boolean) - Constructor for class com.compomics.util.preferences.IdFilter
-
Constructor for an Identification filter.
- 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.
- 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.
- iHighLightIndex - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Index of the point that needs to be highlighted.
- 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
-
Represents an immonium ion.
- ImmoniumIon(char) - Constructor for class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
Constructor for an immonium ion.
- ImmoniumIon(int) - Constructor for class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
Constructor for an immonium ion.
- importComplete() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Returns a boolean indicating whether the import was complete.
- importEnzymes(File) - Method in class com.compomics.util.experiment.biology.EnzymeFactory
-
Import enzymes.
- importGlycons(File) - Method in class com.compomics.util.experiment.biology.GlyconFactory
-
Import glycons from an xml file.
- importMethods(File) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
-
Imports the methods from an XML file.
- importModifications(File, boolean) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Import modifications from a modification file.
- importModifications(File, boolean, boolean) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Import modifications from a modification file.
- ImportSettingsDialog - Class in com.compomics.util.preferences.gui
-
The PeptideShaker import settings dialog.
- ImportSettingsDialog(JFrame, IdFilter, boolean) - Constructor for class com.compomics.util.preferences.gui.ImportSettingsDialog
-
Creates a new ImportSettingsDialog.
- ImportSettingsDialog(JDialog, IdFilter, boolean) - Constructor for class com.compomics.util.preferences.gui.ImportSettingsDialog
-
Creates a new ImportSettingsDialog.
- iMSLevel - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The ms level of the current spectrum.
- inCache(String, String, String) - Method in class com.compomics.util.db.ObjectsCache
-
Indicates whether an object is loaded in the cache
- include(RowFilter.Entry<? extends DefaultTableModel, ? extends Integer>) - Method in class com.compomics.util.gui.XYPlottingDialog.SelectedValuesTableFilter
-
- 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
-
Increase the progress bar value by one "counter".
- increasePrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Increase the progress bar value by the given amount.
- 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 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
-
Increases the progress bar.
- increaseSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
Increases the value of the progress bar.
- 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
-
Increase the secondary progress bar value by the given amount.
- 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 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 amount.
- inDB(String, String, boolean) - Method in class com.compomics.util.db.ObjectsDB
-
Indicates whether an object is loaded in the given table.
- initialize(File, WaitingHandler) - Method in class com.compomics.util.experiment.annotation.gene.GeneFactory
-
Initializes the factory on the given file.
- initialize(File, WaitingHandler) - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Initializes the factory on the given file
- initiate() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Initiates the connection to the database and indicates whether the
corresponding folder is already created.
- initiate(String[]) - Method in class com.compomics.util.experiment.identification.search_parameters_cli.AbstractIdentificationParametersCli
-
Initiates the IdentificationParametersCli.
- initiateSorter() - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
-
Initiates the sorter to the current order of the table.
- initiateTree(int, int, int, WaitingHandler, boolean, boolean) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
-
Initiates the tree.
- initiateTree(int, int, int, Enzyme, WaitingHandler, boolean, boolean) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
-
Initiates the tree.
- insertObject(String, String, Object, boolean) - Method in class com.compomics.util.db.ObjectsDB
-
Stores an object in the desired table.
- insertObjects(String, HashMap<String, Object>, WaitingHandler) - Method in class com.compomics.util.db.ObjectsDB
-
Inserts a set of objects in the given table.
- insertObjects(String, HashMap<String, Object>, WaitingHandler, boolean) - Method in class com.compomics.util.db.ObjectsDB
-
Inserts a set of objects in the given table.
- insertOLSResult(String, String, String, String, String, int, String, Map<String, String>) - Method in class com.compomics.util.gui.ptm.PtmDialog
-
- InstanceVariables - Class in com.compomics.util.db.components
-
This class represents the instance variables for a generated DBAccessor.
- 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(String, CvTerm, CvTerm, ArrayList<CvTerm>) - Constructor for class com.compomics.util.pride.prideobjects.Instrument
-
Create a new Instrument object.
- intensity - Variable in class com.compomics.util.experiment.massspectrometry.Peak
-
The intensity of the peak.
- IntensityHistogram - Class in com.compomics.util.gui.spectrum
-
Creates an IntensityHistogram plot.
- IntensityHistogram(ArrayList<IonMatch>, MSnSpectrum, double) - Constructor for class com.compomics.util.gui.spectrum.IntensityHistogram
-
Creates an IntensityHistogram plot
- intensityLimit - Variable in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
The intensity limit to use.
- 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.)
- interrupt() - Method in class com.compomics.util.sun.SwingWorker
-
A new method that interrupts the worker thread.
- Ion - Class in com.compomics.util.experiment.biology
-
This class models an ion.
- Ion() - Constructor for class com.compomics.util.experiment.biology.Ion
-
- ion - Variable in class com.compomics.util.experiment.identification.matches.IonMatch
-
The matching ion.
- Ion.IonType - Enum in com.compomics.util.experiment.biology
-
An enumerator of the supported ion types.
- IonFactory - Class in com.compomics.util.experiment.biology
-
This factory generates the expected ions from a peptide.
- IonLabelColorTableModel - Class in com.compomics.util.gui.spectrum
-
A table model to use for the ion label annotation colors.
- IonLabelColorTableModel(HashMap<Ion.IonType, ArrayList<Integer>>, ArrayList<NeutralLoss>) - 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 will model the assignment of a peak to a theoretical ion.
- IonMatch(Peak, Ion, Charge) - Constructor for class com.compomics.util.experiment.identification.matches.IonMatch
-
Constructor for an ion peak.
- 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.
- is64BitJava() - Static method in class com.compomics.software.CompomicsWrapper
-
Returns if the Java version used is 64 bit.
- isAccounted(NeutralLossesMap, NeutralLoss, Ion) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Returns a boolean indicating whether the neutral loss should be accounted
for.
- 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.
- isAScoreCalculated() - Method in class com.compomics.util.preferences.ProcessingPreferences
-
Deprecated.
use the PTM scoring preferences instead
- isaScoreNeutralLosses() - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
Deprecated.
use isProbabilisticScoreNeutralLosses instead
- isAutomatedMemoryManagement() - Method in class com.compomics.util.db.ObjectsCache
-
Returns whether the cache is in automated memory management mode.
- isCanceled() - Method in class com.compomics.util.gui.AminoAcidPatternDialog
-
indicates whether the changes have been canceled
- isCanceled() - Method in class com.compomics.util.gui.filehandling.FileSelectionDialog
-
Indicates whether the user pushed on cancel.
- isCanceled() - Method in class com.compomics.util.gui.ptm.PtmChooser
-
Boolean indicating whether the cancel button was pressed by the user.
- isCancelled() - Method in class com.compomics.util.gui.searchsettings.algorithm_settings.OmssaSettingsDialog
-
Indicates whether the user canceled the process.
- isCancelled() - Method in class com.compomics.util.gui.searchsettings.algorithm_settings.XTandemSettingsDialog
-
Indicates whether the user canceled the process.
- isCellEditable(int, int) - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
-
- 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.
- isCleavageSite(String, String) - Method in class com.compomics.util.experiment.biology.Enzyme
-
Deprecated.
use the isCleavageSite method using chars as input instead
- isCleavageSite(char, char) - Method in class com.compomics.util.experiment.biology.Enzyme
-
Returns a boolean indicating whether the given amino acids represent a
cleavage site.
- isCleaveNterMethionine() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Indicates whether N-terminal methionines should be cleaved.
- isClosed() - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Indicates whether the connection to the random access file has been
closed.
- isConcatenatedTargetDecoy() - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Indicates whether the database is a concatenated target/decoy database.
- isConfident() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Returns a boolean indicating whether the modification is confidently
localized on the sequence.
- isCorrectPrecursorMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters
-
Returns a boolean indicating whether the precursor mass shall be
corrected (TagDB setting).
- isCorrectPrecursorMass() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- isCorrupted() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Returns a boolean indicating whether the database is corrupted.
- isCterm(AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns a list of proteins where this peptide can be found in the
C-terminus.
- isCTerm(String, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Protein
-
Returns a boolean indicating whether the protein ends with the given
peptide.
- isCTerm() - Method in class com.compomics.util.experiment.biology.PTM
-
Returns true if the PTM is a c-term PTM.
- isDB() - Method in class com.compomics.util.experiment.identification.Identification
-
Indicates whether the identification matches should be stored in a
database (true, default value) or serialized files (false, deprecated
default).
- isDecoy() - Method in class com.compomics.util.experiment.biology.Peptide
-
Indicates whether a peptide can be derived from a decoy protein.
- isDecoy() - Method in class com.compomics.util.experiment.biology.Protein
-
Indicates if the protein is factice (from a decoy database for instance).
- isDecoy(String) - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Returns true if the given accession number is a decoy.
- isDecoy() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Method indicates if the protein match is a decoy one.
- isDecoy(String) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Convenience method indicating whether a match is decoy based on the match
key.
- isDecoy(String, String) - Static method in class com.compomics.util.experiment.identification.SequenceFactory
-
Returns a boolean indicating whether a protein is decoy or not based on
the protein accession and a given decoy flag.
- isDecoy(String) - Static method in class com.compomics.util.experiment.identification.SequenceFactory
-
Deprecated.
deprecated, use the isDecoy(proteinAccession, flag) with file
dependent flag or isDecoyAccession(String proteinAccession) instead.
- isDecoyAccession(String) - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Indicates whether a protein is a decoy in the selected loaded FASTA file.
- isDefaultReversed() - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Indicates whether the decoy sequences are reversed versions of the target
and the decoy accessions built based on the sequence factory methods.
- isDefaultReversed() - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Indicates whether the decoy sequences are reversed versions of the target
and the decoy accessions built based on the sequence factory methods.
- isDeleted() - Method in interface com.compomics.util.db.interfaces.DBElement
-
This method signals whether the DBElement has been deleted in the persistent
store.
- isDetermineChargePlusOneAlgorithmically() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.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.
- 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
- isEmpty() - Method in class com.compomics.util.db.ObjectsCache
-
Indicates whether the cache is empty.
- isEmpty() - Method in class com.compomics.util.experiment.identification.NeutralLossesMap
-
Returns a boolean indicating if the mapping is empty.
- isEmpty() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node
-
Indicates whether the node is empty.
- isEnding(String) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Indicates whether the given amino acid sequence ends with the pattern
using default single letter code of amino acids.
- isEnding(AminoAcidPattern) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Indicates whether the given amino acid sequence ends with the pattern
using default single letter code of amino acids.
- isEnding(AminoAcidPattern, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Indicates whether the given amino acid sequence ends with the pattern.
- isEnding(String, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Indicates whether the given amino acid sequence ends with the pattern.
- isEnzymaticPeptide(String, Enzyme, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Protein
-
Returns true of the peptide is non-enzymatic, i.e., has one or more end
points that cannot be caused by the enzyme alone.
- 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
-
- isEstimateCharge() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Indicates whether the precursor charge shall be estimated for OMSSA.
- isEstimateCharge() - Method in class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters
-
Indicates whether the precursor charge shall be estimated for OMSSA.
- isEstimateCharge() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- isEstimateFlr() - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
Indicates whether the threshold is FLR based.
- isExcluded(char, int, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Indicates whether the given amino acid at the given index of the pattern
shall be excluded.
- isFixed() - Method in class com.compomics.util.experiment.biology.NeutralLoss
-
Returns a boolean indicating whether the neutral loss is fixed or not.
- isHeader() - Method in class com.compomics.util.io.export.ExportScheme
-
Indicates whether column header shall be used.
- isIncludeSectionTitles() - Method in class com.compomics.util.io.export.ExportScheme
-
Indicates whether section titles shall be used.
- 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.
- isInferred() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Returns a boolean indicating whether the modification is inferred from
another peptide.
- isIsPpm() - Method in class com.compomics.util.preferences.IdFilter
-
Indicates whether the mass tolerance is in ppm (true) or Dalton (false).
- isListMods() - Method in class com.compomics.util.experiment.identification.search_parameters_cli.IdentificationParametersInputBean
-
Indicates whether the modifications should be printed on the screen.
- isMappingFileOpen() - Method in class com.compomics.util.experiment.annotation.gene.GeneFactory
-
Returns true of the mapping file is currently open.
- isMappingFileOpen() - Method in class com.compomics.util.experiment.annotation.go.GOFactory
-
Returns true of the mapping file is currently open.
- isMemoryMappedSequenceLibraries() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
- isModifiable(PTM, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Peptide
-
Indicates whether the given modification can be found on the peptide.
- isModified(String) - Static method in class com.compomics.util.experiment.biology.Peptide
-
Returns a boolean indicating whether the peptide has variable
modifications based on its key.
- isModified(String, String) - Static method in class com.compomics.util.experiment.biology.Peptide
-
Returns a boolean indicating whether the peptide has the given variable
modification based on its key.
- isNterm(AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns a list of proteins where this peptide can be found in the
N-terminus.
- isNTerm(String, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Protein
-
Returns a boolean indicating whether the protein starts with the given
peptide.
- isNTerm() - Method in class com.compomics.util.experiment.biology.PTM
-
Returns true if the PTM is an n-term PTM.
- Isoleucine - Class in com.compomics.util.experiment.biology.aminoacids
-
Isoleucine.
- Isoleucine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Isoleucine
-
Constructor.
- ISOLEUCINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
Subtype int for an isoleucine immonium ion.
- 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.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(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.experiment.identification.identification_parameters.XtandemParameters
-
Indicates whether histograms should be written in the result file.
- isOutputProteins() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Indicates whether the protein bloc should be included in the export.
- isOutputSequences() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Returns whether the protein sequences should be included in the protein
block of the export.
- isOutputSpectra() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Indicate whether the spectra should be exported in the result file.
- isPeakPicked() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Returns true of the indexed file seems to contain only peak picked
spectra.
- iSpecPanelListeners - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
The list of SpectrumPanelListeners.
- isPotentialModificationsForFullRefinment() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Indicates whether the refinement modifications should be used for the
full refinement.
- isPpm - Variable in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Boolean indicating whether the tolerance is in ppm (true) or in Dalton
(false).
- isPrecursorAccuracyTypePpm() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Returns true if the current precursor accuracy type is ppm.
- isProbabilisticScoreNeutralLosses() - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
Indicates whether the neutral losses shall be taken into account for
spectrum annotation when calculating the probabilistic score.
- isProbabilitsticScoreCalculation() - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
Indicates whether a probabilistic PTM score is required.
- 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.experiment.identification.identification_parameters.XtandemParameters
-
Indicates whether the protein quick acetylation option should be
triggered.
- isQuickPyrolidone() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Returns whether the quick pyrolidone option should be triggered.
- isRefine() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Returns whether the second pass search should be triggered.
- isRefinePointMutations() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Indicates whether point mutations should be looked for during the
refinement process.
- isRefineSemi() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Indicates whether the semi enzymatic option of the second pass search
should be triggered.
- isRefineSnaps() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether snAPs should be used during the refinement process.
- isRefineSpectrumSynthesis() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Indicates whether the spectrum synthesis option should be used during the
refinement process.
- isRefineUnanticipatedCleavages() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Returns whether the unanticipated cleavages option should be used during
the refinement process.
- isRemovePrecursor() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Indicates whether the precursor shall be removed for OMSSA.
- isRemovePrecursor() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- 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 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
-
Returns true if the run is canceled.
- isRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- 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 interface com.compomics.util.waiting.WaitingHandler
-
Returns true if the process is finished.
- isRunning() - Method in class com.compomics.util.io.FolderMonitor
-
This method can be consulted to find out whether the monitor is running.
- isSameAs(AminoAcidPattern) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Indicates whether another AminoAcidPattern targets the same pattern.
- isSameAs(TagComponent) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.Ion
-
Returns a boolean indicating whether the ion is the same as another ion.
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.ElementaryIon
-
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.Glycon
-
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
-
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.PrecursorIon
-
- isSameAs(ReporterIon) - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Compares the current reporter ion with another one based on their masses.
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
-
- isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
-
- isSameAs(NeutralLoss) - Method in class com.compomics.util.experiment.biology.NeutralLoss
-
Method indicating whether another neutral loss is the same as the one
considered.
- isSameAs(Protein) - Method in class com.compomics.util.experiment.biology.Protein
-
A method to compare proteins.
- isSameAs(PTM) - Method in class com.compomics.util.experiment.biology.PTM
-
Compares two PTMs.
- isSameAs(Sample) - Method in class com.compomics.util.experiment.biology.Sample
-
Comparator for samples.
- isSameAs(ModificationMatch) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Indicates whether this modification match is the same of another one.
- isSameAs(Tag) - Method in class com.compomics.util.experiment.identification.tags.Tag
-
Indicates whether this tag is the same as another tag.
- isSameAs(TagComponent) - Method in interface com.compomics.util.experiment.identification.tags.TagComponent
-
Indicates whether another component is the same as the component of
interest
- isSameAs(TagComponent) - Method in class com.compomics.util.experiment.identification.tags.tagcomponents.MassGap
-
- isSameAs(Peak) - Method in class com.compomics.util.experiment.massspectrometry.Peak
-
Returns true if the peak has the same mz and intensity.
- isSameModificationStatus(Peptide) - Method in class com.compomics.util.experiment.biology.Peptide
-
Indicates whether another peptide has the same variable modifications as
this peptide.
- isSameSequence(Peptide, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Peptide
-
Returns a boolean indicating whether another peptide has the same
sequence as the given peptide
- isSameSequenceAndModificationStatus(Peptide, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.Peptide
-
Indicates whether another peptide has the same sequence and modification
status without accounting for modification localization.
- isScalePrecursor() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Indicates whether the precursor shall be scaled for OMSSA.
- isScalePrecursor() - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- isSearchForwardFragmentFirst() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Indicates whether forward ions (b1) should be searched first.
- isSearchPositiveIons() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Indicates whether positive ions are searched.
- isSearchRewindFragments() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
- isSemiSpecific() - Method in class com.compomics.util.experiment.biology.Enzyme
-
Returns true if the enzyme is semi-specific.
- 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.PTM
-
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) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Indicates whether the given amino acid sequence starts with the pattern
using default single letter code of amino acids.
- isStarting(AminoAcidPattern) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Indicates whether the given amino acid sequence starts with the pattern
using default single letter code of amino acids.
- isStarting(String, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Indicates whether the given amino acid sequence starts with the pattern.
- isStarting(AminoAcidPattern, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Indicates whether the given amino acid sequence starts with the pattern.
- isStpBias() - Method in class com.compomics.util.experiment.identification.identification_parameters.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
-
This method allows the caller to issue a command to the server.
- issueCommandCheck(String) - Method in class com.compomics.util.io.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.
- isTargeted(char, int, AminoAcidPattern.MatchingType, Double) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Indicates whether the given amino acid at the given index of the pattern
is targeted.
- 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.
- isTruncated() - Method in class com.compomics.util.protein.Protein
-
This method reports on the 'truncatedness' of the protein.
- isUnique(Peptide) - Method in class com.compomics.util.experiment.identification.Identification
-
Indicates whether a peptide is found in a single protein match.
- isUseCorrelationCorrectionScore() - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Indicates whether the correlation correction score should be used.
- isUseNoiseSuppression() - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Indicates whether noise suppression should be used when importing
spectra.
- isUserDefined(String) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Convenience method returning a boolean indicating whether a PTM is user
defined or default.
- isValid() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
-
- isValidModifications(CommandLine) - Static method in class com.compomics.util.experiment.identification.search_parameters_cli.IdentificationParametersInputBean
-
Verifies that modifications are correctly recognized.
- isValidStartup(CommandLine) - Static method in class com.compomics.util.experiment.identification.search_parameters_cli.IdentificationParametersInputBean
-
Verifies the command line start parameters.
- isVariable() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Returns a boolean indicating if the modification is variable.
- iTemplate - Variable in class com.compomics.util.protein.ModificationImplementation
-
The ModificationTemplate which holds all the shared information for a modification.
- 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).
- iTRAQ113 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Standard reporter ion iTRAQ 113.
- iTRAQ114 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Standard reporter ion iTRAQ 114.
- iTRAQ115 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Standard reporter ion iTRAQ 115.
- iTRAQ116 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Standard reporter ion iTRAQ 116.
- iTRAQ117 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Standard reporter ion iTRAQ 117.
- iTRAQ118 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Standard reporter ion iTRAQ 118.
- iTRAQ119 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Standard reporter ion iTRAQ 119.
- iTRAQ121 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Standard reporter ion iTRAQ 121.
- iTRAQ_145 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Standard reporter ion iTRAQ (reporter + balancer).
- iTRAQ_305 - Static variable in class com.compomics.util.experiment.biology.ions.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.AminoAcid
-
- S - Static variable in class com.compomics.util.experiment.biology.Atom
-
A 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.Peptide
-
Indicates whether another peptide has the same modifications at the same
localization as this peptide.
- sameModificationsAs(Peptide) - Method in class com.compomics.util.experiment.biology.Peptide
-
Indicates whether another peptide has the same modifications at the same
localization as this peptide.
- Sample - Class in com.compomics.util.experiment.biology
-
This class models a proteomic sample.
- Sample(String) - Constructor for class com.compomics.util.experiment.biology.Sample
-
Constructor for a sample
- Sample - Class in com.compomics.util.pride.prideobjects
-
An object for storing Sample details.
- Sample(String, ArrayList<CvTerm>) - Constructor for class com.compomics.util.pride.prideobjects.Sample
-
Create a new Sample object.
- SampleAnalysisSet - Class in com.compomics.util.experiment
-
A sample measurement set is a set of replicates from a common sample.
- SampleAnalysisSet(Sample, ProteomicAnalysis) - Constructor for class com.compomics.util.experiment.SampleAnalysisSet
-
Contructor for an analysis of a sample without replicates
- SampleAnalysisSet(Sample, ArrayList<ProteomicAnalysis>) - Constructor for class com.compomics.util.experiment.SampleAnalysisSet
-
Contructor for a set of analysis of a 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.
- save(File, MsExperiment) - Static method in class com.compomics.util.experiment.io.ExperimentIO
-
Method which saves an experiment.
- saveAsPressed() - Method in class com.compomics.util.gui.searchsettings.SearchSettingsDialog
-
This method is called when the user clicks the 'Save As' button.
- saveCache(WaitingHandler, boolean) - Method in class com.compomics.util.db.ObjectsCache
-
Saves the cache content in the database.
- saveFactory() - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Saves the factory in the user folder.
- saveFile(File) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
-
Save to file.
- saveIdentificationParameters(SearchParameters, File) - Static method in class com.compomics.util.experiment.identification.SearchParameters
-
Saves the identification parameters to a serialized file.
- saveIdentificationParametersAsTextFile(File) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Saves the identification parameters as a human readable text file.
- saveIndex() - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Saves the index.
- saveInitialSize(int) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Saves the initial tag size in the parameters table of the DB.
- saveNode(String, Node) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Adds a node to the database.
- saveNodes(HashMap<String, Object>) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Adds nodes to the database.
- saveObject(String) - Method in class com.compomics.util.db.ObjectsCache
-
Saves an entry in the database if modified and clears it from the cache.
- saveObject(String, boolean) - Method in class com.compomics.util.db.ObjectsCache
-
Saves an entry in the database if modified.
- saveObjects(ArrayList<String>) - Method in class com.compomics.util.db.ObjectsCache
-
Saves an entry in the database if modified and clears it from the cache.
- saveObjects(ArrayList<String>, WaitingHandler) - Method in class com.compomics.util.db.ObjectsCache
-
Saves an entry in the database if modified and clears it from the cache.
- saveObjects(ArrayList<String>, WaitingHandler, boolean) - Method in class com.compomics.util.db.ObjectsCache
-
Saves an entry in the database if modified.
- savePressed() - Method in class com.compomics.util.gui.searchsettings.SearchSettingsDialog
-
This method is called when the user clicks the 'Save' button.
- saveProteinLengths(HashMap<String, Object>) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Adds a protein length to the database.
- saveProteinLengths(HashMap<String, Object>, WaitingHandler) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Adds a protein length to the database.
- saveUserPreferences(UtilitiesUserPreferences) - Static method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Convenience method saving the user preferences.
- scanNumber - Variable in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Scan number or range.
- scanStartTime - Variable in class com.compomics.util.experiment.massspectrometry.Spectrum
-
The time point when the spectrum was recorded (scan start time in mzML
files).
- 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.
- sdf - Static variable in interface com.compomics.util.waiting.WaitingHandler
-
Convenience date format.
- SEARCH_SUFFIX - Static variable in class com.compomics.util.experiment.biology.PTMFactory
-
Suffix for the modifications searched but not in the factory.
- searchGuiParametersFileOption - Static variable in class com.compomics.software.ToolFactory
-
The command line argument for a parameters file 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.
- searchGuiSpectrumFileOption - Static variable in class com.compomics.software.ToolFactory
-
The command line argument for mgf files for SearchGUI.
- SearchParameters - Class in com.compomics.util.experiment.identification
-
This class groups the parameters used for identification.
- SearchParameters() - Constructor for class com.compomics.util.experiment.identification.SearchParameters
-
Constructor.
- SearchParameters.MassAccuracyType - Enum in com.compomics.util.experiment.identification
-
Possible mass accuracy types.
- SearchParameters.PrecursorAccuracyType - Enum in com.compomics.util.experiment.identification
-
Deprecated.
use MassAccuracyType
- SearchSettingsDialog - Class in com.compomics.util.gui.searchsettings
-
The search settings dialog.
- SearchSettingsDialog(JFrame, SearchSettingsDialogParent, SearchParameters, Image, Image, boolean, boolean) - Constructor for class com.compomics.util.gui.searchsettings.SearchSettingsDialog
-
Creates a new SearchSettingsDialog.
- SearchSettingsDialogParent - Interface in com.compomics.util.gui.searchsettings
-
Interface for parents of the SearchSettingsDialog.
- SELECT_SPECIES_TAG - Static variable in class com.compomics.util.gui.gene_mapping.SpeciesDialog
-
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.protein.SequenceDbDetailsDialog
-
Allows the user to select a db and loads its information.
- Selenocysteine - Class in com.compomics.util.experiment.biology.aminoacids
-
SeC (U) (Mascot)-
- Selenocysteine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Selenocysteine
-
Constructor.
- SELENOCYSTEINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
Subtype int for a 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.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.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.FTPClient
-
This method sends a group of files to the default FTP location on the server.
- 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
-
Sends command cmd to the server.
- sendTextFile(String) - Method in class com.compomics.util.io.FTPClient
-
This method sends a text file to the default FTP location on the server.
- SEPARATOR - Static variable in class com.compomics.software.CommandLineUtils
-
The command line argument separator.
- separator - Static variable in class com.compomics.util.experiment.annotation.gene.GeneFactory
-
The separator used to separate line contents.
- separator - Static variable in class com.compomics.util.experiment.annotation.go.GOFactory
-
The separator used to separate line contents.
- separator - Static variable in class com.compomics.util.Util
-
Separator which can be used to separate things.
- Sequence - Interface in com.compomics.util.interfaces
-
This interface defines the default behaviour of any kind of
sequence with a certain mass - be it DNA, portein or something
else.
- SequenceDbDetailsDialog - Class in com.compomics.util.gui.protein
-
This dialog displays information about a sequence database.
- SequenceDbDetailsDialog(Frame, String, boolean, Image, Image) - Constructor for class com.compomics.util.gui.protein.SequenceDbDetailsDialog
-
Creates a new SequenceDbDetailsDialog.
- SequenceFactory - Class in com.compomics.util.experiment.identification
-
Factory retrieving the information of the loaded FASTA file.
- SequenceFactory.HeaderIterator - Class in com.compomics.util.experiment.identification
-
Convenience iterator iterating the headers of a FASTA file without using
the cache.
- SequenceFactory.HeaderIterator(File, boolean) - Constructor for class com.compomics.util.experiment.identification.SequenceFactory.HeaderIterator
-
Constructor.
- SequenceFactory.ProteinIterator - Class in com.compomics.util.experiment.identification
-
Convenience iterator iterating all proteins in a FASTA file without using
index or cache.
- SequenceFactory.ProteinIterator(File, boolean) - Constructor for class com.compomics.util.experiment.identification.SequenceFactory.ProteinIterator
-
Constructor.
- 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(String, ArrayList<IonMatch>, boolean, boolean, ModificationProfile) - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
-
Deprecated.
use the panel with ion selection instead
- SequenceFragmentationPanel(String, ArrayList<IonMatch>, boolean, boolean, ModificationProfile, int, int) - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
-
Creates a new SequenceFragmentationPanel working with B and Y ions.
- SequenceFragmentationPanel(String, ArrayList<IonMatch>, boolean, ModificationProfile, int, int) - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
-
Creates a new SequenceFragmentationPanel working with B and Y ions.
- SequenceModificationPanel - Class in com.compomics.util.gui.protein
-
A panel for displaying modification profiles.
- SequenceModificationPanel(String, ArrayList<ModificationProfile>, boolean, String, String) - Constructor for class com.compomics.util.gui.protein.SequenceModificationPanel
-
Creates a new SequenceFragmentationPanel.
- SequestParamsFileFilter - Class in com.compomics.util.io.filefilters
-
File filter for sequest.params files.
- SequestParamsFileFilter() - Constructor for class com.compomics.util.io.filefilters.SequestParamsFileFilter
-
- serializationDirectory - Variable in class com.compomics.util.experiment.identification.Identification
-
The directory where matches will be serialized/the database stored.
- SerializationUtils - Class in com.compomics.util.io
-
This class implements convenience methods for serialization and
deserialization.
- SerializationUtils() - Constructor for class com.compomics.util.io.SerializationUtils
-
- serialVersionUID - Static variable in interface com.compomics.util.experiment.personalization.UrParameter
-
The version UID for Serialization/Deserialization compatibility
- 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
-
Serine.
- Serine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Serine
-
Constructor.
- SERINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon
-
Subtype int for a serine immonium ion.
- serverInput - Variable in class com.compomics.util.io.FTP
-
Buffered stream for reading replies from server.
- serverIsOpen() - Method in class com.compomics.util.io.FTP
-
Return server connection status
- serverOutput - Variable in class com.compomics.util.io.FTP
-
Stream for printing to the server.
- serverResponse - Variable in class com.compomics.util.io.FTP
-
Array of strings (usually 1 entry) for the last reply from the server.
- setAccession(String) - Method in class com.compomics.util.pride.CvTerm
-
- setAccession(String) - Method in class com.compomics.util.protein.Header
-
- 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
- setAnnotationLevel(double) - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Sets the annotation level.
- setAnnotations(Vector) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This method sets all the annotations on this instance.
- setAnnotationYAxisThreshold(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This method allows the caller to set the procentual minimal,
non-inclusive y-axis value threshold (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 chromatograms and profile
spectra for the dataset with the given dataset index.
- setaScoreCalculation(boolean) - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
Deprecated.
use setProbabilitsticScoreCalculation instead
- setaScoreNeutralLosses(boolean) - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
Deprecated.
use setProbabilisticScoreNeutralLosses instead
- setAutomatedMemoryManagement(boolean) - Method in class com.compomics.util.db.ObjectsCache
-
Sets whether the cache is in automated memory management mode.
- setBackgroundPeakWidth(float) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set the backgroundPeakWidth peak width.
- setBatchSize(int) - Method in class com.compomics.util.db.ObjectsCache
-
Sets the batch size in number of objects.
- setBestPeptideAssumption(PeptideAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Setter for the best peptide assumption.
- setBlock(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- setBlocks(PdbBlock[]) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
- 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.
- setCacheSize(int) - Method in class com.compomics.util.db.ObjectsCache
-
Sets the cache size in number of objects.
- setCacheSize(int) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
-
Sets the size of the cache used for peptide mappings (note that there are
two of them).
- setCacheSize(int) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Sets the spectrum cache size.
- 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.
- 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
-
- setCleaveNterMethionine(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets whether N-terminal methionines should be cleaved.
- 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, Color) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
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, Color) - Method in class com.compomics.util.preferences.ModificationProfile
-
Sets a new color for the given expected modification.
- setColumn(int, ArrayList<Double>) - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- setConcatenatedTargetDecoy(boolean) - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Sets whether the database is a concatenated target/decoy database.
- 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.experiment.identification.identification_parameters.OmssaParameters
-
Set the consecutive ion probability.
- setContacts(ArrayList<Contact>) - Method in class com.compomics.util.pride.prideobjects.ContactGroup
-
Set the contacts.
- 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 labelled as control.
- setCorrectPrecursorMass(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters
-
Sets whether the precursor mass shall be corrected (TagDB setting).
- setCorrupted(boolean) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Sets whether the database is corrupted.
- setCurrentSettings(SpectrumIdentificationAssumption, boolean, AminoAcidPattern.MatchingType, double) - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Sets the annotation settings for the current peptide and precursor
charge.
- setCurrentSpecies(String) - Method in class com.compomics.util.preferences.GenePreferences
-
Set the current species.
- setCurrentSpeciesType(String) - Method in class com.compomics.util.preferences.GenePreferences
-
Set the current species type.
- 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(Header.DatabaseType) - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Sets the database type.
- setDatabaseType(Header.DatabaseType) - Method in class com.compomics.util.protein.Header
-
- 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.preferences.UtilitiesUserPreferences
-
Sets the last used database folder.
- setDecoyTag(String) - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Sets the decoy tag.
- setDefaultNeutralLosses() - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Sets the default neutral losses of PTMs when not implemented.
- setDefaultReporterIons() - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Sets the default reporter ions of PTMs when not implemented.
- 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.
- setDeNovoCharge(int) - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Set the charge to use for the fragment ions in the de novo sequencing
- setDescription(String) - Method in class com.compomics.util.experiment.patient.PatientInformation
-
Sets the description of the information.
- setDescription(String) - Method in class com.compomics.util.protein.Header
-
- setDescriptionProteinName(String) - Method in class com.compomics.util.protein.Header
-
- setDescriptionShort(String) - Method in class com.compomics.util.protein.Header
-
- setDestinationFile(String) - Method in class com.compomics.util.io.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.experiment.identification.identification_parameters.OmssaParameters
-
Sets whether charge plus one should be determined algorithmically.
- setDirectory(String, boolean) - Method in class com.compomics.util.experiment.identification.Identification
-
Deprecated.
use establishConnection(String dbFolder) instead
- setDiscardLowQualitySpectra(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters
-
Sets whether low quality spectra shall be discarded.
- setDiscardLowQualitySpectra(Boolean) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- setDisplayedTips(ArrayList<String>) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Set the list of displayed tips.
- setDoi(String) - Method in class com.compomics.util.pride.prideobjects.Reference
-
Set the Digital Object Identifier (DOI) of the reference.
- setDoubleChargeWindow(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
- setDynamicRange(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
- setEnd(double) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set the end value.
- setEnd_block(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- setEnd_protein(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- setEnzyme(Enzyme) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Sets the enzyme used for digestion.
- setEstimateCharge(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets whether the precursor charge shall be estimated for OMSSA.
- setEstimateCharge(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters
-
Sets whether the precursor charge shall be estimated for OMSSA.
- setEstimateCharge(Boolean) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- setEstimateFlr(boolean) - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
Sets whether the threshold is FLR based.
- 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..
- setExcluded(int, ArrayList<AminoAcid>) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Sets the amino acids excluded at a given index.
- setExperiment_type(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
- setExportFeatures(String, ArrayList<ExportFeature>) - Method in class com.compomics.util.io.export.ExportScheme
-
Sets the export features of a given section.
- setFastaFile(File) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Sets the sequence database file used for identification.
- SetFileMode(int) - Method in class com.compomics.util.io.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
-
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.
- setFirstHit(int, SpectrumIdentificationAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Sets the best assumption according to the search engine.
- setFixed(boolean) - Method in class com.compomics.util.experiment.biology.NeutralLoss
-
Sets whether the loss is fixed or not.
- setFlrThreshold(double) - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
Sets the FLR threshold.
- 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.protein.Header
-
- setForeignDescription(String) - Method in class com.compomics.util.protein.Header
-
- setForeignID(String) - Method in class com.compomics.util.protein.Header
-
- setFractionMolecularWeightRanges(HashMap<String, XYDataPoint>) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Set the user provided molecular weight ranges for the fractions.
- setFractionMolecularWeights(HashMap<String, Double>) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use setFractionMolecularWeightRanges instead
- setFractionOfPeaksForChargeEstimation(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the fraction of peaks to be retained for charge >1 estimation.
- setFragmentAccuracyType(SearchParameters.MassAccuracyType) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Sets the fragment accuracy type.
- setFragmentationModel(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters
-
Sets the name of the fragmentation model.
- setFragmentationModel(String) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- setFragmentIonAccuracy(Double) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Sets the fragment ion m/z tolerance.
- setFragmentIonAccuracy(double) - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Sets the fragment ion accuracy.
- setGeneName(String) - Method in class com.compomics.util.protein.Header
-
- setGenerateQuery(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters
-
Sets a boolean indicating whether a blast query shall be generated.
- setGenerateQuery(Boolean) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- 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.
- setHighIntensityCutOff(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the high intensity cut-off as percentage of the most intense ion
peak.
- setHitListLength(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the length of the hit list for OMSSA.
- setHitListLength(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters
-
Sets the length of the hit list.
- setHitListLength(Integer) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- setHitListLengthDeNovo(Integer) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- setID(String) - Method in class com.compomics.util.protein.Header
-
- setIdentificationAlgorithmParameter(int, IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Adds identification algorithm specific paramters
- setIdentifier(String) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Sets the references identifier.
- setIgnoreExceptions(boolean) - Method in class com.compomics.util.general.ExceptionHandler
-
Sets whether exceptions should be ignored.
- setImportComplete(boolean) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Sets whether the import was completed.
- setIndeterminate() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
-
This method makes the progressbar indeterminate.
- setInferred(boolean) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Sets whether the modification is inferred from another peptide.
- setInstitution(String) - Method in class com.compomics.util.pride.prideobjects.Contact
-
Set the instituttion.
- setIntensity(double) - Method in class com.compomics.util.experiment.massspectrometry.Peak
-
Set the intensity.
- 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.experiment.identification.identification_parameters.OmssaParameters
-
Sets the intensity cut-off increment.
- setIntensityIonTable(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Set if the intensity or m/z ion table should be shown.
- setIntensityValues(double[]) - Method in class com.compomics.util.io.PklFile
-
- setIonColor(Ion, Color) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel
-
Sets an annotation color for the given ion.
- setIonMatches(ArrayList) - Method in class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
-
Set the ArrayList with FragmentIon matches.
- setIonSearched1(String) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Setter for the first kind of ion searched, indexed by its single letter
code, for example "a".
- setIonSearched2(String) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Setter for the second kind of ion searched, indexed by its single letter
code, for example "a".
- setIsDB(Boolean) - Method in class com.compomics.util.experiment.identification.Identification
-
Sets whether the identification matches should be stored in a database or
serialized files.
- setIsPpm(boolean) - Method in class com.compomics.util.preferences.IdFilter
-
Sets whether the mass tolerance is in ppm (true) or Dalton (false).
- setIterativeReplaceEvalue(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the e-value threshold to use to replace a hit for the iterative
search.
- setIterativeSequenceEvalue(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the e-value threshold to use to consider a sequence for the
iterative search.
- setIterativeSpectrumEvalue(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the e-value threshold to use consider a spectrum for the iterative
search.
- setKey(String) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Replaces the new key.
- 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 interface com.compomics.util.gui.searchsettings.SearchSettingsDialogParent
-
Set the last selected folder.
- setLastSelectedFolder(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Sets the last selected folder.
- 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.
- setLine(int, ArrayList<Double>) - Method in class com.compomics.util.math.matrix.DoubleMatrix
-
- setLocalPrideFolder(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Set the local PRIDE folder.
- setLocation(int) - Method in interface com.compomics.util.interfaces.Modification
-
This method allows the setting of the location for this modification.
- setLocation(int, int) - Method in class com.compomics.util.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 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.
- setLowIntensityCutOff(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the low intensity cut-off as percentage of the most intense ion
peak.
- setMainMatch(String) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
Sets the main match.
- setMainMatch(String) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
-
Sets the main protein accession after protein inference.
- setMascotMaxEvalue(double) - Method in class com.compomics.util.preferences.IdFilter
-
Sets the maximal Mascot e-value allowed.
- setMass(double) - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Method to set the mass of the reporter ion.
- setMassShift(double) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Sets an m/z shift on all ions.
- setMassShifts(double, double, double) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Sets the m/z shifts.
- setMassTolerance(double, boolean) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Sets a new m/z tolerance for peak matching.
- setMaxCharge(Integer) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Sets the maximum charge in this file.
- setMaxChargeSearched(Charge) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Sets the maximal charge searched.
- setMaxEValue(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the maximal e-value searched for.
- setMaxEValue(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets the maximal e-value searched for.
- setMaxEValue(Double) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- setMaxFragmentCharge(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the maximal fragment charge.
- setMaxFragmentPerSeries(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the maximal number of fragments to retain per series.
- setMaxHitsPerSpectrumPerCharge(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Set the maximal number of hits searched per spectrum and per charge.
- setMaximumExpectationValueRefinement(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets the maximum expectation value to use for refinement.
- setMaxIntensity(Double) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Sets the maximum precursor intensity in this file.
- setMaxMz(Double) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Sets the maximum m/z in this file.
- setMaxMzDeviation(double) - Method in class com.compomics.util.preferences.IdFilter
-
Sets the maximal m/z deviation allowed.
- setMaxMzLadders(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the maximal m/z ladder length.
- 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.massspectrometry.MgfIndex
-
Sets the maximum peak count in this file.
- setMaxPepLength(int) - Method in class com.compomics.util.preferences.IdFilter
-
Sets the maximal peptide length allowed.
- setMaxPeptideLength(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the maximal peptide length allowed.
- setMaxPeptideLength(Integer) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- setMaxPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- setMaxPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Set the maximum value of the progress bar.
- setMaxPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setMaxPrimaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
-
Set the maximum value for the primary progress counter.
- setMaxRT(Double) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Sets the maximal RT in this file.
- setMaxSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
Sets the maximal value of the progress bar.
- setMaxSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Set the maximum value of the secondary progress bar.
- setMaxSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setMaxSecondaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
-
Set the maximum value for the secondary progress counter.
- setMemoryAllocation(int) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
-
Sets the memory allocation.
- setMemoryMappedSequenceLibraries(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets whether sequence libraries should be mapped in memory.
- setMemoryPreference(int) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Sets the preferred upper memory limit.
- setMemoryShare(double) - Method in class com.compomics.util.db.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
- setMH(double) - Method in class com.compomics.util.experiment.refinementparameters.PepnovoAssumptionDetails
-
Sets the PepNovo provided mH.
- setMinAnnotatedPeaks(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the minimal number of annotated peaks a peptide should have.
- setMinChargeSearched(Charge) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Sets the minimal charge searched.
- setMinFragmentMz(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.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(Charge) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the minimal precursor charge to account for multiply charged
fragments in OMSSA.
- setMinimalChargeForMultipleChargedFragments(Charge) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- setMinPeaks(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the minimal number of peaks a spectrum should contain.
- setMinPeaksPerSpectrum(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets the minimal number of peaks per spectrum.
- setMinPepLength(int) - Method in class com.compomics.util.preferences.IdFilter
-
Sets the maximal peptide length allowed.
- setMinPeptideLength(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the minimal peptide length allowed.
- setMinPeptideLength(Integer) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- setMinPrecPerSpectrum(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the minimal number of precursors per spectrum.
- setMinPrecursorMass(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets the minimal precursor mass.
- setMinRT(Double) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Sets the minimum RT in this file.
- 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.
- 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
-
- setModificationProfile(ModificationProfile) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Sets the modification profile of the project.
- setModifications(Vector) - Method in class com.compomics.util.protein.AASequenceImpl
-
Simple setter for the modifications.
- setModificationSite(int) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Setter for the modification site, 1 is the first amino acid.
- setMz(double) - Method in class com.compomics.util.experiment.massspectrometry.Peak
-
Set the mz.
- setMzValues(double[]) - Method in class com.compomics.util.io.PklFile
-
- setName(String) - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
-
Setter for the ion name.
- setName(String) - Method in class com.compomics.util.experiment.biology.PTM
-
Sets the PTM name.
- setName(String) - Method in class com.compomics.util.experiment.identification.FastaIndex
-
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.pride.CvTerm
-
- 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(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the minimal number of annotated most intense peaks.
- setnCache(int) - Method in class com.compomics.util.experiment.identification.SequenceFactory
-
Sets the size of the cache.
- setNeutralLosses(ArrayList<NeutralLoss>) - Method in class com.compomics.util.experiment.biology.PTM
-
Sets the neutral losses possibly encountered with this modification.
- setNeutralLossesSequenceDependant(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Set whether neutral losses are considered only for amino acids of
interest or not.
- setNeutronThreshold(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.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(Integer) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Sets the allowed number of missed cleavages.
- setNoProlineRuleSeries(ArrayList<Integer>) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the id numbers of ion series to apply no product ions at proline
rule at.
- setnPeaks(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets the number of most intense peaks to consider.
- setnPeaksInDoubleChargeWindow(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the number of peaks in doubly charged windows.
- setnPeaksInSingleChargeWindow(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the number of peaks in singly charged windows.
- setNumberOfItotopicPeaks(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the number of isotopic peaks to consider.
- setObjectCache(ObjectsCache) - Method in class com.compomics.util.db.ObjectsDB
-
Sets the object cache to be used by this database.
- setOmssaIndex(String, int) - Method in class com.compomics.util.preferences.ModificationProfile
-
Sets the OMSSA index for a given modification.
- setOmssaMaxEvalue(double) - Method in class com.compomics.util.preferences.IdFilter
-
Sets the OMSSA maximal e-value allowed.
- setOntology(String) - Method in class com.compomics.util.pride.CvTerm
-
- setOrderedListOfSpectrumFileNames(ArrayList<String>) - Method in class com.compomics.util.experiment.identification.Identification
-
Set the ordered list of spectrum file names.
- setOutputHistograms(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether histograms should be written in the result file
- setOutputProteins(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether the protein bloc should be included in the export.
- setOutputSequences(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether the protein sequences should be included in the protein
block of the export.
- setOutputSpectra(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether the spectra should be exported in the result file.
- setParametersFile(File) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Sets the parameter file loaded.
- setParentProteins(ArrayList<String>) - Method in class com.compomics.util.experiment.biology.Peptide
-
Sets the parent proteins.
- setPassive(boolean) - Method in class com.compomics.util.io.FTP
-
Set Passive mode Trasfers.
- setPattern(AminoAcidPattern) - Method in class com.compomics.util.experiment.biology.PTM
-
Sets the amino acid pattern targeted by this modification.
- setPdbaccession(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
- setPeakList(HashMap<Double, Peak>) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Sets the peak list.
- setPeakPicked(Boolean) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
-
Set if the indexed file seems to contain only peak picked spectra or not.
- setPeaks(ArrayList<Peak>) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Set the peaks.
- 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.experiment.identification.identification_parameters.PepnovoParameters
-
Set the PepNovo to utilities PTM map.
- setPepNovoPtmMap(Map<String, String>) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- setPeptide(Peptide, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotators.PeptideSpectrumAnnotator
-
Sets a new peptide to match.
- setPeptideFDR(double) - Method in class com.compomics.util.preferences.ProcessingPreferences
-
Sets the initial peptide FDR.
- setPeptideShakerPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Set the path to the PeptideShaker installation.
- setPercentLength(double) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set the length of the reference area in percent.
- 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.
- setPointSize(Integer) - Method in class com.compomics.util.gui.spectrum.ChromatogramPanel
-
This method allows the caller to set the point size for the
chromatogram.
- 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.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether the refinement modifications should be used for the full
refinement
- setPrecurorCharge(int) - Method in class com.compomics.util.io.PklFile
-
- setPrecursor(Precursor) - Method in class com.compomics.util.experiment.massspectrometry.MSnSpectrum
-
Set the precursor.
- setPrecursorAccuracy(Double) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Sets the precursor tolerance.
- setPrecursorAccuracyDalton(Double) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Sets the precursor tolerance in Dalton (for de novo searches).
- setPrecursorAccuracyType(SearchParameters.MassAccuracyType) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Sets the precursor accuracy type.
- setPrecursorIntensity(double) - Method in class com.compomics.util.io.PklFile
-
- 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
-
- setPreferencesFromSearchParamaers(SearchParameters) - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Updates the annotation parameters based on the search parameters
- setPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
Sets the value of the progress bar.
- setPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Sets the primary progress bar to the given value.
- setPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- 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 interface com.compomics.util.waiting.WaitingHandler
-
Sets whether the primary progress counter is indeterminate or not.
- setProbabilisticScoreNeutralLosses(boolean) - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
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.preferences.PTMScoringPreferences
-
Sets the probabilistic score threshold.
- setProbabilitsticScoreCalculation(boolean) - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
Sets whether a probabilistic PTM score is required.
- setProfile(double[][]) - Method in class com.compomics.util.gui.protein.ModificationProfile
-
Sets the profile.
- 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.
- setProteinConfidenceMwPlots(Double) - Method in class com.compomics.util.preferences.ProcessingPreferences
-
Sets the minimum confidence required for a protein to be included in the
average molecular weight analysis in the Fractions tab.
- setProteinEvidence(String) - Method in class com.compomics.util.protein.Header
-
- setProteinFDR(double) - Method in class com.compomics.util.preferences.ProcessingPreferences
-
Sets the initial protein FDR.
- setProteinQuickAcetyl(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether the protein quick acetylation option should be triggered.
- setProteinTreeFolder(File) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Sets the protein tree folder.
- setPsmFDR(double) - Method in class com.compomics.util.preferences.ProcessingPreferences
-
Sets the initial PSM FDR.
- 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.
- setQuickPyrolidone(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.refinementparameters.PepnovoAssumptionDetails
-
Sets the PepNovo rank score.
- setReadTweets(ArrayList<String>) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
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.experiment.biology.Sample
-
setter for the reference of a sample
- setReference(String) - Method in class com.compomics.util.experiment.MsExperiment
-
Sets the reference of the experiment.
- setReference(String) - Method in class com.compomics.util.pride.prideobjects.Reference
-
Set the reference.
- setReferences(ArrayList<Reference>) - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
-
Set the reference.
- setRefine(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether the second pass search should be triggered.
- setRefinePointMutations(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether point mutations should be looked for during the refinement
process.
- setRefineSemi(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether the semi enzymatic option of the second pass search should
be triggered.
- setRefineSnaps(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether snAPs should be used during the refinement process.
- setRefineSpectrumSynthesis(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether the spectrum synthesis option should be used during the
refinement process.
- setRefineUnanticipatedCleavages(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether the unanticipated cleavages option should be used during the
refinement process.
- setRelimsPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Set the path to the Relims installation.
- setRemovePrecursor(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets whether the precursor shall be removed for OMSSA.
- setRemovePrecursor(Boolean) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- setRemoveUnknownPTMs(boolean) - Method in class com.compomics.util.preferences.IdFilter
-
Set whether unknown PTMs shall be removed.
- 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.PTM
-
Sets the reporter ions possibly encountered with this modification.
- setReporterPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Set the path to the PeptideShaker installation.
- setResolution(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
- setRest(String) - Method in class com.compomics.util.protein.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.
- setRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
- setRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Set the process as canceled.
- setRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- 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
-
Set the process as finished.
- setRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- setRunFinished() - Method in interface com.compomics.util.waiting.WaitingHandler
-
Set the process as finished.
- setRunNotFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Set the run to not finished.
- setSample(int, Sample) - Method in class com.compomics.util.experiment.MsExperiment
-
Set a new sample.
- setScalePrecursor(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets whether the precursor shall be scaled for OMSSA.
- setScalePrecursor(Boolean) - Method in class com.compomics.util.experiment.identification.SearchParameters
-
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
- setScanNumber(String) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Setter for the scan number or range.
- setScanStartTime(double) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Sets the scan start time.
- 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.
- setSearchedOMSSAIndexes(ModificationProfile) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Set the OMSSA indexes used for this search.
- setSearchForwardFragmentFirst(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets whether forward ions (b1) should be searched first.
- setSearchGuiPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Set the path to the SearchGUI installation.
- setSearchParameters(SearchParameters) - Method in interface com.compomics.util.gui.searchsettings.SearchSettingsDialogParent
-
Set the search parameters.
- setSearchPositiveIons(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets whether positive ions are searched.
- setSearchRewindFragments(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets whether C-terminal fragments should be searched.
- setSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
-
Sets the value of the progress bar.
- setSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Sets the secondary progress bar to the given value.
- setSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- 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
-
Makes the dialog indeterminate or not indeterminate.
- setSecondaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
-
Sets the secondary progress bar to indeterminate or not.
- setSecondaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
-
- 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 interface com.compomics.util.waiting.WaitingHandler
-
Set the secondary progress counter text.
- setSelectedExportFolder(String) - Method in interface com.compomics.util.gui.export.graphics.ExportGraphicsDialogParent
-
Set the default folder to use for exporting the graphics.
- setSelectedExportFolder(String) - Method in class com.compomics.util.gui.VennDiagramDialog
-
- setSelectedExportFolder(String) - Method in class com.compomics.util.gui.XYPlottingDialog
-
- setSelectedOutput(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the output type, omx or csv.
- setSelectedPositions(Integer[]) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- setSelectedProbabilisticScore(PtmScore) - Method in class com.compomics.util.preferences.PTMScoringPreferences
-
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.
- setSemiSpecific(boolean) - Method in class com.compomics.util.experiment.biology.Enzyme
-
Set if the enzyme is semi-specific.
- 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.
- setShortName(String) - Method in class com.compomics.util.experiment.biology.PTM
-
Sets the short PTM name.
- setShortName(String, String) - Method in class com.compomics.util.experiment.biology.PTMFactory
-
Sets the short name for a modification.
- setShowAllPeaks(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Set if all peaks or just the annotated ones are to be shown.
- setShowBars(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Set if the bars in the bubble plot are to be shown or not.
- setShowForwardIonDeNovoTags(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
-
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.preferences.AnnotationPreferences
-
Set if the automatic rewind ion de novo tags are to be shown.
- setSingleChargeWindow(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets the window size for singly charged ions.
- setSkylinePath(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets the skyline path.
- 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
-
This method allows to set the source for the file that is to be
transferred.
- setSparklineColor(Color) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Setter for the sparkline color.
- setSparklineColorNonValidated(Color) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Setter for the non-validated sparkline color.
- setSparklineColorPossible(Color) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Setter for the possible sparkline color.
- setSpectrum(MSnSpectrum, double) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Sets a new spectrum to annotate.
- setSpectrumAnnotatedPeakColor(Color) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Set the color to use for the annotated peaks.
- setSpectrumAnnotatedPeakWidth(float) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Set the width of the annotated peaks.
- setSpectrumBackgroundPeakColor(Color) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Set the color to use for the background peaks.
- setSpectrumBackgroundPeakWidth(float) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
-
Set the width of the background peaks.
- 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
-
- setSpectrumNumber(Integer) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Sets the spectrum number in the spectrum file
- 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.massspectrometry.Spectrum
-
Set the spectrum title.
- setStart(double) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
-
Set the start value.
- setStart_block(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- setStart_protein(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
-
- setStpBias(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
- 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, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotators.TagSpectrumAnnotator
-
Sets a new peptide to match.
- setTarget(Integer) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Sets the index of the amino acid of interest in the pattern.
- setTargetDecoyFileNameTag(String) - Static method in class com.compomics.util.experiment.identification.SequenceFactory
-
Set the target-decoy file name tag.
- setTargeted(int, ArrayList<AminoAcid>) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
-
Sets the amino acids targeted at a given index.
- setTaxonomy(String) - Method in class com.compomics.util.protein.Header
-
- setTerminalMassShifts(double, double) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Sets the terminal m/z shifts.
- setTheoreticMass(double) - Method in class com.compomics.util.experiment.biology.Ion
-
Sets a new theoretic mass.
- setTheoreticPeptide(Peptide) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
-
Setter for the theoretic peptide.
- setTheoreticPtm(String) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
-
Sets the theoretic PTM.
- setTitle(String) - Method in class com.compomics.util.messages.FeedBack
-
Sets the title.
- setTitle(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
-
- 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.
- 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.
- 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..
- 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.
- setUseCorrelationCorrectionScore(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters
-
Sets whether the correlation correction score 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.
- setUseNoiseSuppression(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters
-
Sets whether noise suppression should be used when importing spectra.
- 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
-
- 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
-
- setVersion(String) - Method in class com.compomics.util.experiment.identification.FastaIndex
-
Sets the database version.
- setVersion(String) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
-
Sets the version.
- 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 interface com.compomics.util.waiting.WaitingHandler
-
Sets the text describing what is currently being waited for.
- setX(double) - Method in class com.compomics.util.XYZDataPoint
-
- setXAxisStartAtZero(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
This method sets the start value of the x-axis to zero.
- setXtandemMaxEvalue(double) - Method in class com.compomics.util.preferences.IdFilter
-
Sets the OMSSA maximal e-value allowed.
- setY(double) - Method in class com.compomics.util.XYZDataPoint
-
- setYAxisZoomExcludesBackgroundPeaks(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
-
Set if the automatic y-axis zoom only considers the anotated peaks.
- setYAxisZoomExcludesBackgroundPeaks(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
-
Set if the automatic y-axis zoom only considers the anotated 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
-
- showAllPeaks - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
-
If false, only the annotated peaks will be shown.
- showAllPeaks() - Method in class com.compomics.util.preferences.AnnotationPreferences
-
If true, all peaks are shown, false displays the annotated peaks, and the
non-annotated in the background.
- showAnnotatedPeaksOnly(boolean) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
-
If true only the annotated peaks will be drawn.
- showBars() - Method in class com.compomics.util.preferences.AnnotationPreferences
-
If true, bars are shown in the bubble plot highlighting the ions.
- 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.preferences.AnnotationPreferences
-
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.preferences.AnnotationPreferences
-
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
-
- sign - Variable in class com.compomics.util.experiment.massspectrometry.Charge
-
Sign of the charge according to the static fields.
- signalStop() - Method in class com.compomics.util.io.FolderMonitor
-
This method can be used to signal the monitor to halt its monitoring.
- singleLetterCode - Variable in class com.compomics.util.experiment.biology.AminoAcid
-
Single letter code of the amino acid.
- site(String) - Method in class com.compomics.util.io.FTP
-
Site Command
- skip(long) - Method in class com.compomics.util.io.MonitorableFileInputStream
-
Skips over and discards n
bytes of data from the
input stream.
- skip(long) - Method in class com.compomics.util.io.MonitorableInputStream
-
Skips over and discards n
bytes of data from the
input stream.
- 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
-
- SpeciesDialog - Class in com.compomics.util.gui.gene_mapping
-
A dialog for choosing the species.
- SpeciesDialog(JFrame, GenePreferences, boolean, Image, Image) - Constructor for class com.compomics.util.gui.gene_mapping.SpeciesDialog
-
Creates a new SpeciesDialog.
- SpeciesDialog(JDialog, JFrame, GenePreferences, boolean, Image, Image) - Constructor for class com.compomics.util.gui.gene_mapping.SpeciesDialog
-
Creates a new SpeciesDialog.
- speciesOption - Static variable in class com.compomics.software.ToolFactory
-
The command line argument for the species.
- speciesTypeOption - Static variable in class com.compomics.software.ToolFactory
-
The command line argument for the species type.
- Spectrum - Class in com.compomics.util.experiment.massspectrometry
-
This class models a spectrum.
- Spectrum() - Constructor for class com.compomics.util.experiment.massspectrometry.Spectrum
-
- SPECTRUM_KEY_SPLITTER - Static variable in class com.compomics.util.experiment.massspectrometry.Spectrum
-
The splitter in the key between spectrumFile and spectrumTitle.
- spectrumAnnotation - Variable in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
The spectrum annotation as a map: theoretic fragment key -> ionmatch.
- 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
-
The spectrum annotator annotates peaks in a spectrum.
- SpectrumAnnotator() - Constructor for class com.compomics.util.experiment.identification.SpectrumAnnotator
-
- SpectrumCounting - Class in com.compomics.util.experiment.quantification.spectrumcounting
-
This class evaluates the spectrum counting indices for a protein.
- SpectrumCounting() - Constructor for class com.compomics.util.experiment.quantification.spectrumcounting.SpectrumCounting
-
- SpectrumCounting.SpectrumCountingMethod - Enum in com.compomics.util.experiment.quantification.spectrumcounting
-
The implemented reporter ion quantification methods.
- SpectrumFactory - Class in com.compomics.util.experiment.massspectrometry
-
This factory will provide the spectra when needed.
- 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.Identification
-
Deprecated.
use file specific mapping instead
- 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
-
- spectrumIdentificationMap - Variable in class com.compomics.util.experiment.identification.Identification
-
List of all imported PSMs indexed by mgf file name.
- spectrumLoaded(String, String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
Returns a boolean indicating whether the spectrum is contained in the
given spectrum file.
- spectrumLoaded(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
-
A boolean indicating whether the spectrum is loaded in the factory.
- 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, SpectrumIdentificationAssumption) - Constructor for class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Constructor for the spectrum match.
- SpectrumMatch(String) - Constructor for class com.compomics.util.experiment.identification.matches.SpectrumMatch
-
Constructor for the spectrum match.
- spectrumMatchLoaded(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB
-
Indicates whether a spectrum match is loaded.
- 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(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.
- spectrumTitle - Variable in class com.compomics.util.experiment.massspectrometry.Spectrum
-
Spectrum title.
- 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) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfReader
-
Splits an mgf file into smaller ones and returns the indexes of the
generated files.
- splitInput(String) - Static method in class com.compomics.software.CommandLineUtils
-
Splits the input of comma separated command line input and returns the
results as an arraylist.
- splitNode(int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node
-
Splits the node into subnode if its size is larger than the maxNodeSize
and does the same for every sub node.
- spo - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
-
- SPO - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
-
- 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.
- 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
-
Created by IntelliJ IDEA.
- StartEndPosition(int, int) - Constructor for class com.compomics.util.pdbfinder.das.readers.StartEndPosition
-
- 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.
- 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.
- startRelims(JFrame) - Static method in class com.compomics.software.ToolFactory
-
Deprecated.
use PeptideShaker's own Reshake option instead.
- startReporter(JFrame) - Static method in class com.compomics.software.ToolFactory
-
Starts Reporter from the location of utilities preferences.
- startSearchGUI(JFrame) - Static method in class com.compomics.software.ToolFactory
-
Starts SearchGUI from the location of utilities preferences.
- startSearchGUI(JFrame, ArrayList<File>, File, File, 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(InputStream) - Constructor for class com.compomics.util.io.StreamGobbler
-
Constructor.
- strFileNameAndPath - Variable in class com.compomics.util.io.FTP
-
String to hold the file we are up/downloading
- subtractIsotope - Static variable in class com.compomics.util.experiment.identification.SpectrumAnnotator
-
Boolean indicating whether the isotopic number shall be removed from the
theoretic mass when matching an ion.
- Sulfur - Class in com.compomics.util.experiment.biology.atoms
-
A sulfur atom.
- Sulfur() - Constructor for class com.compomics.util.experiment.biology.atoms.Sulfur
-
Constructor.
- svg - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
-
- SVG - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
-
- SvgFileFilter - Class in com.compomics.util.io.filefilters
-
File filter for *.svg files.
- SvgFileFilter() - Constructor for class com.compomics.util.io.filefilters.SvgFileFilter
-
- swap(int, int) - Method in class com.compomics.util.sun.TableSorter
-
- swapRows(int, int) - Method in class com.compomics.util.experiment.biology.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
-
- 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.
- syst() - Method in class com.compomics.util.io.FTP
-
Retrieve the system type from the remote server.