Uses of Class
com.compomics.util.experiment.biology.proteins.Peptide
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Uses of Peptide in com.compomics.util.experiment.biology.ions
Methods in com.compomics.util.experiment.biology.ions with parameters of type Peptide 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 Peptide in com.compomics.util.experiment.biology.proteins
Methods in com.compomics.util.experiment.biology.proteins that return Peptide Modifier and Type Method Description Peptide
Peptide. getNoModPeptide(HashSet<String> forbiddenModifications)
Returns a version of the peptide which does not contain the given list of modifications.Methods in com.compomics.util.experiment.biology.proteins with parameters of type Peptide Modifier and Type Method Description boolean
Peptide. isSameModificationStatus(Peptide anotherPeptide)
Indicates whether another peptide has the same variable modifications as this peptide.boolean
Peptide. isSameSequence(Peptide anotherPeptide, SequenceMatchingParameters sequenceMatchingPreferences)
Returns a boolean indicating whether another peptide has the same sequence as the given peptideboolean
Peptide. isSameSequenceAndModificationStatus(Peptide anotherPeptide, SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether another peptide has the same sequence and modification status without accounting for modification localization.boolean
Peptide. sameModificationsAs(Peptide anotherPeptide)
Indicates whether another peptide has the same modifications at the same localization as this peptide.boolean
Peptide. sameModificationsAs(Peptide anotherPeptide, ArrayList<String> modifications)
Indicates whether another peptide has the same variable modifications at the same localization as this peptide. -
Uses of Peptide in com.compomics.util.experiment.identification.features
Methods in com.compomics.util.experiment.identification.features with parameters of type Peptide Modifier and Type Method Description int
IdentificationFeaturesGenerator. getNEnzymaticTermini(Peptide peptide, String accession)
Returns the maximal number of termini for the given peptide on the given protein. -
Uses of Peptide in com.compomics.util.experiment.identification.filtering
Methods in com.compomics.util.experiment.identification.filtering with parameters of type Peptide Modifier and Type Method Description boolean
PeptideAssumptionFilter. validateModifications(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceMatchingParameters modificationSequenceMatchingPreferences, ModificationParameters modificationProfile)
Verifies that the definition of every modification name is available.boolean
PeptideAssumptionFilter. validatePeptide(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, DigestionParameters digestionPreferences)
Validates the peptide based on the peptide length, the share of X's in the sequence and the allowed number of missed cleavages.boolean
PeptideAssumptionFilter. validateProteins(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceProvider sequenceProvider)
Validates a peptide depending on its protein inference status. -
Uses of Peptide in com.compomics.util.experiment.identification.matches
Methods in com.compomics.util.experiment.identification.matches that return Peptide Modifier and Type Method Description Peptide
PeptideMatch. getPeptide()
Getter for the peptide.Methods in com.compomics.util.experiment.identification.matches with parameters of type Peptide Modifier and Type Method Description static long
ProteinMatch. getProteinMatchKey(Peptide peptide)
Convenience method which returns the protein key from a peptide.void
PeptideMatch. setPeptide(Peptide peptide)
Setter for the peptide.Constructors in com.compomics.util.experiment.identification.matches with parameters of type Peptide Constructor Description PeptideMatch(Peptide peptide, long matchKey, long spectrumMatchKey)
Constructor for the peptide match.ProteinMatch(Peptide peptide, long peptideMatchKey)
Constructor for the protein match. -
Uses of Peptide in com.compomics.util.experiment.identification.modification
Methods in com.compomics.util.experiment.identification.modification with parameters of type Peptide 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. -
Uses of Peptide in com.compomics.util.experiment.identification.modification.mapping
Methods in com.compomics.util.experiment.identification.modification.mapping with parameters of type Peptide 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.static void
ModificationLocalizationMapper. modificationLocalization(Peptide peptide, HashMap<Integer,ArrayList<String>> expectedNames, HashMap<ModificationMatch,ArrayList<String>> modNames, IdentificationParameters identificationParameters, IdfileReader idfileReader, ModificationProvider modificationProvider)
Makes an initial modification mapping based on the search engine results and the compatibility to the searched modifications. -
Uses of Peptide in com.compomics.util.experiment.identification.modification.scores
Methods in com.compomics.util.experiment.identification.modification.scores with parameters of type Peptide Modifier and Type Method Description static Double
MDScore. getMDScore(ArrayList<SpectrumIdentificationAssumption> mascotAssumptions, Peptide peptideCandidate, ArrayList<String> ptms, SequenceMatchingParameters sequenceMatchingPreferences, Integer rounding)
Returns the MD score for the given peptide in a spectrum match.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 Peptide 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 Peptide 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 Peptide in com.compomics.util.experiment.identification.protein_inference
Methods in com.compomics.util.experiment.identification.protein_inference that return types with arguments of type Peptide Modifier and Type Method Description static Collection<Peptide>
PeptideProteinMapping. getPeptides(ArrayList<PeptideProteinMapping> peptideProteinMappings, SequenceMatchingParameters sequenceMatchingPreferences)
Aggregates the given mapping into a list of peptides. -
Uses of Peptide in com.compomics.util.experiment.identification.protein_sequences.digestion
Fields in com.compomics.util.experiment.identification.protein_sequences.digestion declared as Peptide Modifier and Type Field Description Peptide
ExtendedPeptide. peptide
The peptide.Constructors in com.compomics.util.experiment.identification.protein_sequences.digestion with parameters of type Peptide Constructor Description ExtendedPeptide(Peptide peptide, int position, String[] fixedModifications)
Constructor. -
Uses of Peptide in com.compomics.util.experiment.identification.psm_scoring
Methods in com.compomics.util.experiment.identification.psm_scoring with parameters of type Peptide 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 Peptide 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 Peptide Modifier and Type Method Description double
HyperScore. getScore(Peptide peptide, int charge, Spectrum spectrum, ArrayList<IonMatch> ionMatches)
Returns the hyperscore.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
PrecursorAccuracy. getScore(Peptide peptide, int identificationCharge, Precursor precursor, boolean ppm, int minIsotope, int maxIsotope)
Scores the match between the given peptide and spectrum using the precursor m/z accuracy.double
SnrScore. getScore(Peptide peptide, Spectrum spectrum, ArrayList<IonMatch> ionMatchesList)
Returns the score.double
SnrScore. getScore(Peptide peptide, Spectrum spectrum, HashMap<Double,ArrayList<IonMatch>> ionMatches)
Returns the score.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 Peptide in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators
Constructors in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators with parameters of type Peptide Constructor Description FragmentAnnotator(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries)
Constructor.FragmentAnnotator(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, boolean forward, boolean complementary)
Constructor.FragmentAnnotatorNL(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, boolean sequenceDependent)
Constructor.FragmentAnnotatorNL(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, boolean sequenceDependent, boolean forward, boolean complementary)
Constructor.PrecursorAnnotator(Peptide peptide, String[] fixedModifications)
Constructor. -
Uses of Peptide in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators that return Peptide Modifier and Type Method Description Peptide
PeptideSpectrumAnnotator. getCurrentlyLoadedPeptide()
Returns the currently inspected peptide.Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators with parameters of type Peptide 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.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.Constructors in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators with parameters of type Peptide Constructor Description SimplePeptideAnnotator(Peptide peptide, String[] fixedModifications, int charge, boolean a, boolean b, boolean c, boolean x, boolean y, boolean z, boolean precursor, boolean immonium, boolean related, boolean reporter, boolean neutralLosses, boolean neutralLossesSequenceDependent, ReporterIon[] reporterIons)
Constructor.SimplePeptideAnnotator(Peptide peptide, String[] fixedModifications, int charge, AnnotationParameters annotationSettings)
Constructor. -
Uses of Peptide in com.compomics.util.experiment.identification.spectrum_assumptions
Methods in com.compomics.util.experiment.identification.spectrum_assumptions that return Peptide Modifier and Type Method Description Peptide
PeptideAssumption. getPeptide()
Get the theoretic peptide.Methods in com.compomics.util.experiment.identification.spectrum_assumptions with parameters of type Peptide Modifier and Type Method Description void
PeptideAssumption. setPeptide(Peptide peptide)
Returns the peptides.Constructors in com.compomics.util.experiment.identification.spectrum_assumptions with parameters of type Peptide Constructor Description PeptideAssumption(Peptide peptide, int identificationCharge)
Constructor for a simple peptide assumption containing only the information necessary for spectrum annotation.PeptideAssumption(Peptide peptide, int rank, int advocate, int identificationCharge, double rawScore, double score)
Constructor for a peptide assumption.PeptideAssumption(Peptide peptide, int rank, int advocate, int identificationCharge, double rawScore, double score, String identificationFile)
Constructor for a peptide assumption. -
Uses of Peptide in com.compomics.util.experiment.identification.utils
Methods in com.compomics.util.experiment.identification.utils with parameters of type Peptide 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 String
PeptideUtils. getTaggedModifiedSequence(Peptide peptide, ModificationParameters modificationParameters, String[] allFixedModifications, String[] allVariableModifications, String[] confidentModificationSites, String[] representativeAmbiguousModificationSites, String[] secondaryAmbiguousModificationSites, String[] fixedModificationSites, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName)
Returns the modified sequence as an tagged string with potential modification sites color coded or with Modification tags, e.g, <mox>.static String
PeptideUtils. getVariableModificationsAsString(Peptide peptide)
Returns the peptide modifications as a string.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
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. isEnzymatic(Peptide peptide, String proteinAccession, String proteinSequence, ArrayList<Enzyme> enzymes)
Returns a boolean indicating whether the peptide is enzymatic 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.static boolean
PeptideUtils. isVariant(Peptide peptide, String accession)
Returns a boolean indicating whether the peptide needs variants to be mapped to the given protein. -
Uses of Peptide in com.compomics.util.experiment.io.identification.writers
Methods in com.compomics.util.experiment.io.identification.writers with parameters of type Peptide Modifier and Type Method Description String
SimpleMzIdentMLExporter. getModificationName(double modMass, Peptide peptide, int modSite)
Returns the name of the modification corresponding to he given modification mass at the given site on the given peptide. -
Uses of Peptide in com.compomics.util.gui.spectrum
Methods in com.compomics.util.gui.spectrum with parameters of type Peptide 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 Peptide 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.