java.lang.Object
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation.FeaturesGenerator

public class FeaturesGenerator
extends Object
This class computes the ms2PIP features from a peptide. It is a java implementation of https://github.com/mvaudel/ms2pip_c/blob/master/ms2pipfeatures_c.c with the permission of Sven Degroeve. No license found, no copyright infringement intended.
Author:
Marc Vaudel
  • Constructor Details

  • Method Details

    • getForwardIonsFeatures

      public int[] getForwardIonsFeatures​(Peptide peptide, int charge, int ionIndex, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingPreferences)
      Returns the ms2pip features for the forward ions of the given peptide at the given charge.
      Parameters:
      peptide - the peptide
      charge - the charge
      ionIndex - the ion index
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingPreferences - the sequence matching preferences for modification to peptide mapping
      Returns:
      the ms2pip features for the b ions
    • getComplementaryIonsFeatures

      public int[] getComplementaryIonsFeatures​(Peptide peptide, int charge, int ionIndex, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingPreferences)
      Returns the ms2pip features for the complementary ions of the given peptide at the given charge.
      Parameters:
      peptide - the peptide
      charge - the charge
      ionIndex - the ion index
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingPreferences - the sequence matching preferences for modification to peptide mapping
      Returns:
      the ms2pip features for the b ions