org.expasy.mzjava.proteomics.mol.digest

Class AcceptAllDigestionController

java.lang.Object

org.expasy.mzjava.proteomics.mol.digest.AcceptAllDigestionController

All Implemented Interfaces:

DigestionController

public class AcceptAllDigestionController
extends Object
implements DigestionController

DigestionController that accepts all peptides and does not interrupt the digestion.

Author:

fnikitin, Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
AcceptAllDigestionController()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	interruptDigestion(Protein protein, int proteinCleavageSiteCount, int inclusiveLowerBoundIndex, int inclusiveUpperBoundIndex) Control digestion flow given the potential digest bounds
boolean	makeDigest(Protein protein, int inclusiveProteinLowerIndex, int exclusiveProteinUpperIndex, int missedCleavagesCount) Make a peptide digest from the given protein.
boolean	retainDigest(Protein protein, Peptide digest, int digestIndex) Process DigestedPeptide with/without missed cleavages
boolean	retainSemiDigest(Peptide digest) Process Semi digested products.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AcceptAllDigestionController

public AcceptAllDigestionController()

Method Detail

interruptDigestion

public boolean interruptDigestion(Protein protein,
                         int proteinCleavageSiteCount,
                         int inclusiveLowerBoundIndex,
                         int inclusiveUpperBoundIndex)

Control digestion flow given the potential digest bounds

Digestion never interrupted.

Specified by:

interruptDigestion in interface DigestionController

Parameters:

protein - the protein being digested

proteinCleavageSiteCount - the number of cleavage bounds found in the protein (+ 2 terminal bounds)

inclusiveLowerBoundIndex - lower bound index (from 0 to proteinBoundsCount-2)

inclusiveUpperBoundIndex - upper bound index (from 1 to proteinBoundsCount-1)

Returns:

true if the digestion must be interrupted

makeDigest

public boolean makeDigest(Protein protein,
                 int inclusiveProteinLowerIndex,
                 int exclusiveProteinUpperIndex,
                 int missedCleavagesCount)

Make a peptide digest from the given protein.

Make all digest peptides.

Specified by:

makeDigest in interface DigestionController

Parameters:

protein - the protein to get peptide from.

inclusiveProteinLowerIndex - the lower protein index

exclusiveProteinUpperIndex - the upper protein index

missedCleavagesCount - the number of missed cleavages

Returns:

true if a peptide digest has to be created

retainDigest

public boolean retainDigest(Protein protein,
                   Peptide digest,
                   int digestIndex)

Process DigestedPeptide with/without missed cleavages

Retain all digests.

Specified by:

retainDigest in interface DigestionController

Parameters:

protein - the protein being digested

digest - the actual digest

digestIndex - the digest starting index in the protein

Returns:

true if this digest is kept

retainSemiDigest

public boolean retainSemiDigest(Peptide digest)

Process Semi digested products. If enabled, the semi-digest are produced from all digests

Retain all semi digests.

Specified by:

retainSemiDigest in interface DigestionController

Parameters:

digest - the actual semi digest

Returns:

true if this semi digest is kept