Uses of Class
com.compomics.util.experiment.identification.PeptideAssumption

Packages that use PeptideAssumption
com.compomics.util.experiment.identification.matches This package contains experiment classes releated to matches. e.g., pepties, proteins, modifications and spectra. 
 

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

Methods in com.compomics.util.experiment.identification.matches that return PeptideAssumption
 PeptideAssumption SpectrumMatch.getBestAssumption()
          Getter for the best assumption
 PeptideAssumption SpectrumMatch.getFirstHit(int advocateId)
          Returns the first hit obtained using the specified advocate
 

Methods in com.compomics.util.experiment.identification.matches that return types with arguments of type PeptideAssumption
 java.util.ArrayList<PeptideAssumption> SpectrumMatch.getAllAssumptions()
          Return all assumptions for all search engines as a list
 java.util.HashMap<java.lang.Double,java.util.ArrayList<PeptideAssumption>> SpectrumMatch.getAllAssumptions(int advocateId)
          Return all assumptions for the specified search engine indexed by their e-value
 

Methods in com.compomics.util.experiment.identification.matches with parameters of type PeptideAssumption
 void SpectrumMatch.addHit(int otherAdvocateId, PeptideAssumption otherAssumption)
          add a first hit
 void SpectrumMatch.setBestAssumption(PeptideAssumption bestAssumption)
          Setter for the best assumption
 void SpectrumMatch.setFirstHit(int advocateId, PeptideAssumption peptideAssumption)
          Sets the best peptideAssumption according to the search engine
 

Constructors in com.compomics.util.experiment.identification.matches with parameters of type PeptideAssumption
SpectrumMatch(java.lang.String spectrumKey, PeptideAssumption assumption)
          Constructor for the spectrum match
 



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