Class PeptideAndProteinBuilder

java.lang.Object
com.compomics.util.experiment.identification.protein_inference.PeptideAndProteinBuilder

public class PeptideAndProteinBuilder
extends Object
This class builds peptides and proteins based on PSMs. Note that the builder is buffered and needs to be closed.
Author:
Marc Vaudel
  • Constructor Details

  • Method Details

    • buildPeptidesAndProteins

      public void buildPeptidesAndProteins​(SpectrumMatch spectrumMatch, SequenceMatchingParameters sequenceMatchingPreferences, SequenceProvider sequenceProvider, boolean protein)
      Creates the peptides and protein instances based on the given spectrum match. Note that only the best peptide assumption is used, the method has no effect if it is null. This operation will be very slow if the cache is already full. Note: if proteins are not set for a peptide they will be assigned using the default protein tree and the given matching parameters.
      Parameters:
      spectrumMatch - the spectrum match to add
      sequenceMatchingPreferences - the sequence matching preferences
      sequenceProvider - a provider of protein sequences
      protein - boolean indicating whether proteins should be built