Uses of Class
com.compomics.util.experiment.biology.proteins.Peptide

Packages that use Peptide

Package	Description
com.compomics.util.experiment.biology.ions	Experiment classes related to ions.
com.compomics.util.experiment.biology.proteins	Classes related to proteins.
com.compomics.util.experiment.identification.features	Classes for the generation of identification features.
com.compomics.util.experiment.identification.filtering	Classes for the filtering of identification objects.
com.compomics.util.experiment.identification.matches	Experiment classes related to matches.
com.compomics.util.experiment.identification.modification	Modification mapping and localization.
com.compomics.util.experiment.identification.modification.mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.modification.scores	PTM scores.
com.compomics.util.experiment.identification.modification.search_engine_mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation	This package contains the classes needed to generate ms2pip features.
com.compomics.util.experiment.identification.protein_inference	Classes related to protein inference.
com.compomics.util.experiment.identification.protein_sequences.digestion	This package contains classes used to digest protein sequences into peptides.
com.compomics.util.experiment.identification.psm_scoring	Main PSM scoring class.
com.compomics.util.experiment.identification.psm_scoring.psm_scores	Main PTM scoring classes.
com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators	This package contains implementations of the SimpleAnnotator allowing the annotation of specific sets of ions.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators	This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
com.compomics.util.experiment.identification.spectrum_assumptions	Implementations of the SpectrumIdentificationAssumption.
com.compomics.util.experiment.identification.utils	This package contains utilities classes to handle identification objects.
com.compomics.util.experiment.io.identification.writers	Writer for identification results.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.

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 peptide
boolean	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

Modifier	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, ModificationProvider modificationProvider)	Returns the PhosphoRS sequence probabilities for the modification possible locations.

Uses of Peptide in com.compomics.util.experiment.identification.modification.search_engine_mapping

Methods in com.compomics.util.experiment.identification.modification.search_engine_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 from a search engine modification indexed by site.
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, IdentificationParameters identificationParameters, IdfileReader idfileReader, ModificationProvider modificationProvider, SequenceProvider sequenceProvider)	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.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
final Peptide	ExtendedPeptide.peptide	The peptide.

Constructors in com.compomics.util.experiment.identification.protein_sequences.digestion with parameters of type Peptide

Modifier	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

Modifier	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

Modifier	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

Modifier	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 int[]	ModificationUtils.getPossibleModificationSites(Peptide peptide, Modification modification, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters, ModificationProvider modificationProvider, boolean avoidOverlap)	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

Modifier	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.