Package org.biojava.bio.proteomics
Class Digest
java.lang.Object
org.biojava.bio.proteomics.Digest
This class contains methods for calculating the results of proteolytic digestion
of a protein sequence
this class is not designed to be thread safe
- Author:
- Michael Jones, Mark Schreiber (refactoring, some documentation)
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Adds peptides as features to the Sequence in this class.void
setMaxMissedCleavages
(int maxMissedCleavages) Sets the maximum number of partial digest products to be annotated.void
setProtease
(Protease protease) void
setSequence
(Sequence sequence)
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Field Details
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PEPTIDE_FEATURE_TYPE
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Constructor Details
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Digest
public Digest()Creates a new Digest Bean
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Method Details
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setProtease
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setSequence
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getSequence
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setMaxMissedCleavages
Sets the maximum number of partial digest products to be annotated.- Parameters:
maxMissedCleavages
- the max number of partial digest products
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addDigestFeatures
Adds peptides as features to the Sequence in this class. The feature will contain a small annotation specifying the protease with the key "protease". For Example:Sequence sequence = ... Digest bioJavaDigest = new Digest(); bioJavaDigest.setMaxMissedCleavages(2); bioJavaDigest.setProtease(ProteaseManager.getProteaseByName(Protease.ASP_N)); bioJavaDigest.setSequence(sequence); bioJavaDigest.addDigestFeatures();
- Throws:
BioException
- if the Protease or Sequence are null.ChangeVetoException
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