org.biojava.bio.proteomics
Class Digest
java.lang.Object
org.biojava.bio.proteomics.Digest
- public class Digest
- extends java.lang.Object
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)
Constructor Summary |
Digest()
Creates a new Digest Bean |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
PEPTIDE_FEATURE_TYPE
public static java.lang.String PEPTIDE_FEATURE_TYPE
Digest
public Digest()
- Creates a new Digest Bean
setProtease
public void setProtease(Protease protease)
setSequence
public void setSequence(Sequence sequence)
getSequence
public Sequence getSequence()
setMaxMissedCleavages
public void setMaxMissedCleavages(int maxMissedCleavages)
- Sets the maximum number of partial digest products to be annotated.
- Parameters:
maxMissedCleavages
- the max number of partial digest products
addDigestFeatures
public void addDigestFeatures()
throws BioException,
ChangeVetoException
- 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