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.matches This package contains experiment classes releated to matches. e.g., pepties, proteins, modifications and spectra. 
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
 

Fields in com.compomics.util.experiment.identification with type parameters of type SpectrumMatch
protected  HashMap<String,SpectrumMatch> Identification.spectrumIdentification
          The identification results as a spectrum match map, indexed by spectrum id: FILE_TITLE
 

Methods in com.compomics.util.experiment.identification that return types with arguments of type SpectrumMatch
 HashMap<String,SpectrumMatch> Identification.getSpectrumIdentification()
          Returns the identification results in a spectrum identification map (spectrumMatch id -> spectrumMatch)
 

Methods in com.compomics.util.experiment.identification with parameters of type SpectrumMatch
 void Identification.addSpectrumMatch(SpectrumMatch newMatch)
          Add a spectrum match to the model.
 

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.matches
 

Methods in com.compomics.util.experiment.identification.matches that return SpectrumMatch
 SpectrumMatch PeptideMatch.getMainMatch()
          method returns the main match
 

Methods in com.compomics.util.experiment.identification.matches that return types with arguments of type SpectrumMatch
 HashMap<String,SpectrumMatch> PeptideMatch.getSpectrumMatches()
          returns all spectra matched
 

Methods in com.compomics.util.experiment.identification.matches with parameters of type SpectrumMatch
 void PeptideMatch.addSpectrumMatch(SpectrumMatch spectrumMatch)
          add a spectrum match
 void PeptideMatch.setMainMatch(SpectrumMatch spectrumMatch)
          methods sets the main match
 

Method parameters in com.compomics.util.experiment.identification.matches with type arguments of type SpectrumMatch
 void PeptideMatch.addSpectrumMatches(HashMap<String,SpectrumMatch> newMatches)
          add spectrum matches
 

Constructors in com.compomics.util.experiment.identification.matches with parameters of type SpectrumMatch
PeptideMatch(Peptide peptide, SpectrumMatch spectrumMatch)
          Constructor for the peptide 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()
          This methods retrieves all the identifications from an identification file as a list of spectrum matches
 

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> XTandemIdfileReader.getAllSpectrumMatches()
          method which returns all spectrum matches found in the file
 HashSet<SpectrumMatch> OMSSAIdfileReader.getAllSpectrumMatches()
          returns all spectrum matches found in the inspected file
 HashSet<SpectrumMatch> MascotIdfileReader.getAllSpectrumMatches()
          a method to get all the spectrum matches
 



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