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. 
com.compomics.util.preferences   
 

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
 ArrayList<PeptideAssumption> SpectrumMatch.getAllAssumptions()
          Return all assumptions for all search engines as a list.
 HashMap<Double,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.removeAssumption(PeptideAssumption peptideAssumption)
          Removes an assumption from the mapping
 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(String spectrumKey, PeptideAssumption assumption)
          Constructor for the spectrum match.
 

Uses of PeptideAssumption in com.compomics.util.preferences
 

Methods in com.compomics.util.preferences with parameters of type PeptideAssumption
 boolean IdFilter.validatePeptideAssumption(PeptideAssumption assumption)
          Validates the peptide assumption based on the peptide length and maximal e-values allowed.
 boolean IdFilter.validatePrecursor(PeptideAssumption assumption, String spectrumKey, SpectrumFactory spectrumFactory)
          Validates the mass deviation of a peptide assumption.
 



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