Uses of Interface
com.compomics.util.experiment.io.biology.protein.SequenceProvider
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Uses of SequenceProvider in com.compomics.util.experiment.biology.genes
Methods in com.compomics.util.experiment.biology.genes with parameters of type SequenceProvider Modifier and Type Method Description GeneMaps
ProteinGeneDetailsProvider. getGeneMaps(GeneParameters genePreferences, FastaSummary fastaSummary, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, WaitingHandler waitingHandler)
Returns the gene maps for the given proteins. -
Uses of SequenceProvider in com.compomics.util.experiment.biology.ions
Methods in com.compomics.util.experiment.biology.ions with parameters of type SequenceProvider Modifier and Type Method Description HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>
IonFactory. getFragmentIons(Peptide peptide, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
This method returns the theoretic ions expected from a peptide.HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>
IonFactory. getFragmentIons(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
This method returns all the theoretic ions expected from a peptide. -
Uses of SequenceProvider in com.compomics.util.experiment.biology.proteins
Methods in com.compomics.util.experiment.biology.proteins with parameters of type SequenceProvider Modifier and Type Method Description void
Peptide. estimateTheoreticMass(ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Estimates the theoretic mass of the peptide.String[]
Peptide. getFixedModifications(ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the fixed modifications for this peptide based on the given modification parameters.double
Peptide. getMass(ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the mass, estimates it if not done before.String
Peptide. getTaggedModifiedSequence(ModificationParameters modificationProfile, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName, HashSet<String> displayedModifications)
Returns the modified sequence as an tagged string with potential modification sites color coded or with Modification tags, e.g, <mox>. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.features
Methods in com.compomics.util.experiment.identification.features with parameters of type SequenceProvider Modifier and Type Method Description static double
IdentificationFeaturesGenerator. estimateSpectrumCounting(Identification identification, SequenceProvider sequenceProvider, long proteinMatchKey, SpectrumCountingParameters spectrumCountingPreferences, int maxPepLength, IdentificationParameters identificationParameters)
Returns the spectrum counting index based on the project settings.Constructors in com.compomics.util.experiment.identification.features with parameters of type SequenceProvider Constructor Description IdentificationFeaturesGenerator(Identification identification, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, Metrics metrics, SpectrumCountingParameters spectrumCountingPreferences)
Constructor. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.filtering
Methods in com.compomics.util.experiment.identification.filtering with parameters of type SequenceProvider Modifier and Type Method Description boolean
AssumptionFilter. isValidated(long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)
Tests whether a match is validated by this filter.boolean
AssumptionFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean
AssumptionFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)
Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.boolean
MatchFilter. isValidated(long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
Tests whether a match is validated by this filter.abstract boolean
MatchFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.boolean
PeptideFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean
ProteinFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean
PsmFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean
PeptideAssumptionFilter. validateProteins(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceProvider sequenceProvider)
Validates a peptide depending on its protein inference status. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.modification
Methods in com.compomics.util.experiment.identification.modification with parameters of type SequenceProvider Modifier and Type Method Description static HashMap<PeptideFragmentIon,ArrayList<IonMatch>>
ModificationtableContent. getModificationPlotData(Peptide peptide, Modification modification, int nMod, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the modification plot series in the JFreechart format for one PSM.static ModificationtableContent
ModificationtableContent. getModificationTableContent(PeptideAssumption peptideAssumption, Modification modification, int nMod, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Get the table content. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.modification.mapping
Methods in com.compomics.util.experiment.identification.modification.mapping with parameters of type SequenceProvider Modifier and Type Method Description static HashMap<Integer,HashSet<String>>
ModificationNameMapper. getPossibleModificationNames(Peptide peptide, ModificationMatch modificationMatch, IdfileReader idfileReader, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)
Returns the possible modification names.static HashMap<Integer,HashSet<String>>
ModificationNameMapper. getPossibleModificationNamesAndromeda(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)
Returns the possible Andromeda modification names.static HashMap<Integer,HashSet<String>>
ModificationNameMapper. getPossibleModificationNamesByMass(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)
Returns the possible modifications names by mass.static HashMap<Integer,HashSet<String>>
ModificationNameMapper. getPossibleModificationNamesByName(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)
Returns the possible modifications by name.static HashMap<Integer,HashSet<String>>
ModificationNameMapper. getPossibleModificationNamesOmssa(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)
Returns the possible OMSSA modification names. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.modification.scores
Methods in com.compomics.util.experiment.identification.modification.scores with parameters of type SequenceProvider Modifier and Type Method Description static HashMap<Integer,Double>
PhosphoRS. getSequenceProbabilities(Peptide peptide, ArrayList<Modification> modifications, ModificationParameters modificationParameters, Spectrum spectrum, SequenceProvider sequenceProvider, AnnotationParameters annotationParameters, SpecificAnnotationParameters specificAnnotationSettings, boolean accountNeutralLosses, SequenceMatchingParameters sequenceMatchingParameters, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the modification possible locations. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation
Methods in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation with parameters of type SequenceProvider Modifier and Type Method Description int[]
FeaturesGenerator. getComplementaryIonsFeatures(Peptide peptide, int charge, int ionIndex, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingPreferences)
Returns the ms2pip features for the complementary ions of the given peptide at the given charge.int[]
FeaturesGenerator. getForwardIonsFeatures(Peptide peptide, int charge, int ionIndex, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingPreferences)
Returns the ms2pip features for the forward ions of the given peptide at the given charge. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.peptide_inference
Methods in com.compomics.util.experiment.identification.peptide_inference with parameters of type SequenceProvider Modifier and Type Method Description void
PeptideInference. peptideInference(Identification identification, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider, WaitingHandler waitingHandler)
Infers the PTM localization and its confidence for the best match of every spectrum. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.protein_inference
Methods in com.compomics.util.experiment.identification.protein_inference with parameters of type SequenceProvider Modifier and Type Method Description void
PeptideAndProteinBuilder. buildPeptidesAndProteins(SpectrumMatch spectrumMatch, SequenceMatchingParameters sequenceMatchingPreferences, SequenceProvider sequenceProvider, boolean protein)
Creates the peptides and protein instances based on the given spectrum match. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.protein_inference.fm_index
Classes in com.compomics.util.experiment.identification.protein_inference.fm_index that implement SequenceProvider Modifier and Type Class Description class
FMIndex
The FM index. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.protein_sequences
Classes in com.compomics.util.experiment.identification.protein_sequences that implement SequenceProvider Modifier and Type Class Description class
SingleProteinSequenceProvider
Sequence provider for a single protein. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.psm_scoring
Methods in com.compomics.util.experiment.identification.psm_scoring with parameters of type SequenceProvider Modifier and Type Method Description double
PsmScoresEstimator. getDecreasingScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)
Scores the match between the given peptide and spectrum using the given score.double
PsmScoresEstimator. getScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)
Scores the match between the given peptide and spectrum using the given score.double
PsmScoresEstimator. getScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, PsmScore psmScore)
Scores the match between the given peptide and spectrum using the given score. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.psm_scoring.psm_scores
Methods in com.compomics.util.experiment.identification.psm_scoring.psm_scores with parameters of type SequenceProvider Modifier and Type Method Description double
HyperScore. getScore(Peptide peptide, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the hyperscore.double
SnrScore. getScore(Peptide peptide, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the score. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.spectrum_annotation
Methods in com.compomics.util.experiment.identification.spectrum_annotation with parameters of type SequenceProvider Modifier and Type Method Description IonMatch[]
SpectrumAnnotator. getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the currently matched ions with the given settings using the intensity filter.abstract IonMatch[]
SpectrumAnnotator. getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
Returns the currently matched ions with the given settings.static NeutralLossesMap
SpectrumAnnotator. getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpectrumAnnotator spectrumAnnotator)
Returns the possible neutral losses expected by default for a given peptide.SpecificAnnotationParameters
AnnotationParameters. getSpecificAnnotationParameters(String spectrumFile, String spectrumTitle, SpectrumIdentificationAssumption spectrumIdentificationAssumption, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, SpectrumAnnotator spectrumAnnotator)
Returns the annotation preferences specific to a spectrum and an identification assumption. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators with parameters of type SequenceProvider Modifier and Type Method Description Map<Integer,ArrayList<IonMatch>>
PeptideSpectrumAnnotator. getCoveredAminoAcids(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
Returns the ion matches corresponding to fragment ions indexed by amino acid number in the sequence.IonMatch[]
PeptideSpectrumAnnotator. getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
IonMatch[]
TagSpectrumAnnotator. getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
static NeutralLossesMap
PeptideSpectrumAnnotator. getDefaultLosses(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the possible neutral losses expected by default for a given peptide.HashMap<Integer,ArrayList<Ion>>
PeptideSpectrumAnnotator. getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the expected ions in a map indexed by the possible charges.HashMap<Integer,ArrayList<Ion>>
PeptideSpectrumAnnotator. getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)
Returns the expected ions in a map indexed by the possible charges.IonMatch[]
PeptideSpectrumAnnotator. getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the spectrum annotations of a spectrum in a list of IonMatches using the intensity filter.IonMatch[]
PeptideSpectrumAnnotator. getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.IonMatch[]
PeptideSpectrumAnnotator. getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments, boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in an array of IonMatches.java.util.stream.Stream<IonMatch>
PeptideSpectrumAnnotator. getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the spectrum annotations of a spectrum in a list of IonMatches using the intensity filter.java.util.stream.Stream<IonMatch>
PeptideSpectrumAnnotator. getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.java.util.stream.Stream<IonMatch>
PeptideSpectrumAnnotator. getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments, boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a stream of IonMatches.ArrayList<IonMatch>
PeptideSpectrumAnnotator. matchPeak(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings, double peakMz, double peakIntensity)
This method matches the potential fragment ions of a given peptide with a given peak according to the annotation settings.void
PeptideSpectrumAnnotator. setPeptide(Peptide peptide, int precursorCharge, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings)
Sets a new peptide to annotate.void
PeptideSpectrumAnnotator. setPeptide(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons, int precursorCharge, SpecificAnnotationParameters specificAnnotationSettings)
Sets a new peptide to annotate. -
Uses of SequenceProvider in com.compomics.util.experiment.identification.utils
Methods in com.compomics.util.experiment.identification.utils with parameters of type SequenceProvider Modifier and Type Method Description static TreeMap<String,String[]>
PeptideUtils. getAaAfter(Peptide peptide, int nAa, SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string in a map based on the peptide protein mapping.static String
PeptideUtils. getAaAfter(Peptide peptide, String accession, int index, int nAa, SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string.static TreeMap<String,String[]>
PeptideUtils. getAaBefore(Peptide peptide, int nAa, SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string in a map based on the peptide protein mapping.static String
PeptideUtils. getAaBefore(Peptide peptide, String accession, int index, int nAa, SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string in a map based on the peptide protein mapping.static HashSet<String>
ModificationUtils. getAllModifications(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters)
Returns a set of the names of all modifications found on a peptide.static HashMap<Integer,HashSet<String>>
ModificationUtils. getExpectedModifications(double modMass, ModificationParameters modificationParameters, Peptide peptide, double massTolerance, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters, SearchParameters searchParameters)
Returns the expected modifications for a given modification mass indexed by site.static String
PeptideUtils. getFixedModificationsAsString(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the peptide modifications as a string.static int[]
ModificationUtils. getPossibleModificationSites(Peptide peptide, Modification modification, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters)
Returns an array of the possible modification sites for the given modification on the given peptide.static boolean
PeptideUtils. isCterm(Peptide peptide, SequenceProvider sequenceProvider)
Indicates whether a peptide is at the C-terminus of a protein.static boolean
PeptideUtils. isCterm(Peptide peptide, String proteinAccession, SequenceProvider sequenceProvider)
Indicates whether a peptide is at the C-terminus of a given protein.static boolean
PeptideUtils. isDecoy(Peptide peptide, SequenceProvider sequenceProvider)
Returns a boolean indicating whether the peptide matches a decoy sequence.static boolean
ProteinUtils. isDecoy(String accession, SequenceProvider sequenceProvider)
Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given sequence provider.static boolean
PeptideUtils. isEnzymatic(Peptide peptide, SequenceProvider sequenceProvider, ArrayList<Enzyme> enzymes)
Returns a boolean indicating whether the peptide is enzymatic in at least one protein using one of the given enzymes.static boolean
PeptideUtils. isNterm(Peptide peptide, SequenceProvider sequenceProvider)
Indicates whether a peptide is at the N-terminus of a protein.static boolean
PeptideUtils. isNterm(Peptide peptide, String proteinAccession, SequenceProvider sequenceProvider)
Indicates whether a peptide is at the N-terminus of a given protein. -
Uses of SequenceProvider in com.compomics.util.experiment.io.identification.writers
Constructors in com.compomics.util.experiment.io.identification.writers with parameters of type SequenceProvider Constructor Description SimpleMzIdentMLExporter(String softwareName, String softwareVersion, String softwareUrl, File tempFolder, File destinationFile, ArrayList<File> spectrumFiles, File searchEngineFile, HashMap<String,ArrayList<String>> searchEngines, File fastaFile, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider, ModificationProvider modificationProvider, FastaSummary fastaSummary, String contactFirstName, String contactLastName, String contactAddress, String contactEmail, String contactOrganizationName, String contactOrganizationAddress, String contactOrganizationEmail, boolean peptideInference)
Constructor. -
Uses of SequenceProvider in com.compomics.util.experiment.quantification.spectrumcounting
Methods in com.compomics.util.experiment.quantification.spectrumcounting with parameters of type SequenceProvider Modifier and Type Method Description void
ScalingFactorsEstimators. estimateScalingFactors(Identification identification, Metrics metrics, SequenceProvider sequenceProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, ProcessingParameters processingParameters)
Estimates the scaling factors and stores them in the given metrics. -
Uses of SequenceProvider in com.compomics.util.gui.modification
Constructors in com.compomics.util.gui.modification with parameters of type SequenceProvider Constructor Description ModificationTable(Identification identification, AnnotationParameters annotationParameters, PeptideMatch peptideMatch, Modification modification, boolean areaChart, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Constructor. -
Uses of SequenceProvider in com.compomics.util.gui.spectrum
Methods in com.compomics.util.gui.spectrum with parameters of type SequenceProvider Modifier and Type Method Description void
SpectrumPanel. addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Add reference areas annotating the de novo tags, using default percent height of 0.9 for the forward ions and 1.0 for the reverse ions default alpha levels of 0.2.void
SpectrumPanel. addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Add reference areas annotating the de novo tags, using default alpha levels of 0.2.void
SpectrumPanel. addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Add reference areas annotating the de novo tags, using default alpha levels of 0.2.void
SpectrumPanel. addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, float forwardIonAlphaLevel, float rewindIonAlphaLevel, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Add reference areas annotating the de novo tags.void
SpectrumPanel. addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Add reference areas annotating the de novo tags.Constructors in com.compomics.util.gui.spectrum with parameters of type SequenceProvider Constructor Description FragmentIonTable(Peptide currentPeptide, ArrayList<IonMatch[]> allAnnotations, ArrayList<Spectrum> allSpectra, HashSet<Integer> currentFragmentIonTypes, NeutralLossesMap neutralLosses, boolean singleCharge, boolean twoCharges, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Creates a novel fragment ion table displaying bar charts with the intensity of each fragment ion type.FragmentIonTable(Peptide currentPeptide, ArrayList<IonMatch[]> allAnnotations, HashSet<Integer> currentFragmentIonTypes, NeutralLossesMap neutralLosses, boolean singleCharge, boolean twoCharges, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Creates a traditional fragment ion table with the theoretical mz values and the detected fragment ions highlighted.