Package 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)

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	PEPTIDE_FEATURE_TYPE

Constructor Summary

Constructors

Constructor	Description
Digest()	Creates a new Digest Bean

Method Summary

Modifier and Type	Method	Description
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