Package com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation

Class FeaturesGenerator

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 Summary

Constructors

Constructor	Description
FeaturesGenerator()	Empty default constructor
FeaturesGenerator(FeaturesMap featuresMap)	Constructor.

Method Summary

Modifier and Type	Method	Description
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.
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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

FeaturesGenerator

public FeaturesGenerator()

Empty default constructor

FeaturesGenerator

public FeaturesGenerator(FeaturesMap featuresMap)

Constructor.

Parameters:

featuresMap - a map of the features to include.

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