Uses of Class
com.compomics.util.experiment.identification.matches.SpectrumMatch

Packages that use SpectrumMatch

Package	Description
com.compomics.util.experiment.identification	This package contains experiment classes related to identifications.
com.compomics.util.experiment.identification.matches	This package contains experiment classes releated to matches.
com.compomics.util.experiment.identification.ptm.ptmscores
com.compomics.util.experiment.io.identifications
com.compomics.util.experiment.io.identifications.idfilereaders	This package contains experiment classes related to reading search engine files.

Uses of SpectrumMatch in com.compomics.util.experiment.identification

Methods in com.compomics.util.experiment.identification that return SpectrumMatch

Modifier and Type	Method and Description
SpectrumMatch	Identification.getSpectrumMatch(java.lang.String spectrumKey) Returns a spectrum match.
SpectrumMatch	IdentificationDB.getSpectrumMatch(java.lang.String key, boolean useDB) Returns the desired spectrum match.
SpectrumMatch	Identification.getSpectrumMatch(java.lang.String spectrumKey, boolean useDB) Returns a spectrum match.

Methods in com.compomics.util.experiment.identification with parameters of type SpectrumMatch

Modifier and Type	Method and Description
void	IdentificationDB.addSpectrumMatch(SpectrumMatch spectrumMatch) Adds a spectrum match to the database.
void	Identification.addSpectrumMatch(SpectrumMatch newMatch, boolean ascendingScore) Adds a spectrum match to the identification.
void	IdentificationDB.updateSpectrumMatch(SpectrumMatch spectrumMatch) Updates a spectrum match.
void	Identification.updateSpectrumMatch(SpectrumMatch spectrumMatch) Updates a spectrum match in the database.

Method parameters in com.compomics.util.experiment.identification with type arguments of type SpectrumMatch

Modifier and Type	Method and Description
void	Identification.addSpectrumMatch(java.util.Set<SpectrumMatch> spectrumMatches, boolean ascendingScore) Add a set of spectrumMatches to the model.

Uses of SpectrumMatch in com.compomics.util.experiment.identification.matches

Methods in com.compomics.util.experiment.identification.matches that return SpectrumMatch

Modifier and Type

Method and Description

SpectrumMatch

SpectrumMatch.getPeptidesFromTags(ProteinTree proteinTree, AminoAcidPattern.MatchingType matchingType, java.lang.Double massTolerance, boolean scoreInAscendingOrder, java.util.ArrayList<java.lang.String> fixedModifications, java.util.ArrayList<java.lang.String> variableModifications, boolean ascendingScore) Creates a peptide based spectrum match where peptide assumptions are deduced from tag assumptions.

Uses of SpectrumMatch in com.compomics.util.experiment.identification.ptm.ptmscores

Methods in com.compomics.util.experiment.identification.ptm.ptmscores with parameters of type SpectrumMatch

Modifier and Type	Method and Description
static java.lang.Double	MDScore.getMDScore(SpectrumMatch spectrumMatch, java.util.ArrayList<java.lang.String> ptms, AminoAcidPattern.MatchingType matchingType, java.lang.Double massTolerance) Returns the MD score for the best peptide in a spectrum match (the best peptide has to be set before).
static java.lang.Double	MDScore.getMDScore(SpectrumMatch spectrumMatch, Peptide peptideCandidate, java.util.ArrayList<java.lang.String> ptms, AminoAcidPattern.MatchingType matchingType, java.lang.Double massTolerance) Returns the MD score for the given peptide in a spectrum match.

Uses of SpectrumMatch in com.compomics.util.experiment.io.identifications

Methods in com.compomics.util.experiment.io.identifications that return types with arguments of type SpectrumMatch

Modifier and Type	Method and Description
java.util.HashSet<SpectrumMatch>	IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler) This methods retrieves all the identifications from an identification file as a list of spectrum matches It is very important to close the file reader after creation.

Uses of SpectrumMatch in com.compomics.util.experiment.io.identifications.idfilereaders

Methods in com.compomics.util.experiment.io.identifications.idfilereaders that return types with arguments of type SpectrumMatch

Modifier and Type	Method and Description
java.util.HashSet<SpectrumMatch>	AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler)