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
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Constructor Summary
Constructors Constructor Description PeptideAndProteinBuilder()
Empty default constructorPeptideAndProteinBuilder(Identification identification)
Constructor. -
Method Summary
Modifier and Type Method Description void
buildPeptidesAndProteins(SpectrumMatch spectrumMatch, SequenceMatchingParameters sequenceMatchingPreferences, SequenceProvider sequenceProvider, boolean protein)
Creates the peptides and protein instances based on the given spectrum match.
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Constructor Details
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PeptideAndProteinBuilder
public PeptideAndProteinBuilder()Empty default constructor -
PeptideAndProteinBuilder
Constructor.- Parameters:
identification
- the identification object
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Method Details
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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 addsequenceMatchingPreferences
- the sequence matching preferencessequenceProvider
- a provider of protein sequencesprotein
- boolean indicating whether proteins should be built
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