All Implemented Interfaces:
Serializable

public class PeptideAssumption
extends SpectrumIdentificationAssumption
This object models the assumption made by an advocate.
Author:
Marc Vaudel, Harald Barsnes
See Also:
Serialized Form
  • Constructor Details

    • PeptideAssumption

      public PeptideAssumption()
      Default constructor for the purpose of instantiation.
    • PeptideAssumption

      public PeptideAssumption​(Peptide peptide, int rank, int advocate, int identificationCharge, double rawScore, double score, String identificationFile)
      Constructor for a peptide assumption.
      Parameters:
      peptide - the theoretic peptide
      rank - the identification rank
      advocate - the advocate used
      identificationCharge - the charge used by the search engine for identification
      rawScore - the raw score, i.e. the untransformed score given by the search engine
      score - the (potentially transformed) score, typically a search engine e-value (whether the score is ascending or descending can be known from the SearchEngine class)
      identificationFile - the identification file
    • PeptideAssumption

      public PeptideAssumption​(Peptide peptide, int rank, int advocate, int identificationCharge, double rawScore, double score)
      Constructor for a peptide assumption.
      Parameters:
      peptide - the theoretic peptide
      rank - the identification rank
      advocate - the advocate used
      identificationCharge - the charge used by the search engine for identification
      rawScore - the raw score, i.e. the untransformed score given by the search engine
      score - the (potentially transformed) score, typically a search engine e-value (whether the score is ascending or descending can be known from the SearchEngine class)
    • PeptideAssumption

      public PeptideAssumption​(Peptide peptide, int identificationCharge)
      Constructor for a simple peptide assumption containing only the information necessary for spectrum annotation.
      Parameters:
      peptide - the theoretic peptide
      identificationCharge - the charge used by the search engine for identification
  • Method Details