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
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Constructor Summary
Constructors Constructor Description FeaturesGenerator()
Empty default constructorFeaturesGenerator(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.
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Constructor Details
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FeaturesGenerator
public FeaturesGenerator()Empty default constructor -
FeaturesGenerator
Constructor.- Parameters:
featuresMap
- a map of the features to include.
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Method Details
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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 peptidecharge
- the chargeionIndex
- the ion indexmodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingPreferences
- the sequence matching preferences for modification to peptide mapping- Returns:
- the ms2pip features for the b ions
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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 peptidecharge
- the chargeionIndex
- the ion indexmodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingPreferences
- the sequence matching preferences for modification to peptide mapping- Returns:
- the ms2pip features for the b ions
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