org.biojava.bio.proteomics
Class Digest

java.lang.Object
  extended by 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)

Field Summary
static java.lang.String PEPTIDE_FEATURE_TYPE
           
 
Constructor Summary
Digest()
          Creates a new Digest Bean
 
Method Summary
 void addDigestFeatures()
          Adds peptides as features to the Sequence in this class.
 Sequence getSequence()
           
 void setMaxMissedCleavages(int maxMissedCleavages)
          Sets the maximum number of partial digest products to be annotated.
 void setProtease(Protease protease)
           
 void setSequence(Sequence sequence)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

PEPTIDE_FEATURE_TYPE

public static java.lang.String PEPTIDE_FEATURE_TYPE
Constructor Detail

Digest

public Digest()
Creates a new Digest Bean

Method Detail

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