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

Packages that use SpectrumMatch
com.compomics.util.experiment.identification This package contains experiment classes related to identifications. 
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
 SpectrumMatch Identification.getSpectrumMatch(String spectrumKey)
          Returns a spectrum match.
 SpectrumMatch IdentificationDB.getSpectrumMatch(String key, boolean useDB)
          Returns the desired spectrum match.
 SpectrumMatch Identification.getSpectrumMatch(String spectrumKey, boolean useDB)
          Returns a spectrum match.
 

Methods in com.compomics.util.experiment.identification with parameters of type SpectrumMatch
 void IdentificationDB.addSpectrumMatch(SpectrumMatch spectrumMatch)
          Adds a spectrum match to the database.
 void Identification.addSpectrumMatch(SpectrumMatch newMatch)
          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
 void Identification.addSpectrumMatch(Set<SpectrumMatch> spectrumMatches)
          Add a set of spectrumMatches to the model.
 

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
static Double MDScore.getMDScore(SpectrumMatch spectrumMatch, ArrayList<String> ptms)
          Returns the MD score for the best peptide in a spectrum match (the best peptide has to be set before).
static Double MDScore.getMDScore(SpectrumMatch spectrumMatch, Peptide peptideCandidate, ArrayList<String> ptms)
          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
 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
 HashSet<SpectrumMatch> AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler)
           
 



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