org.expasy.mzjava.proteomics.mol.digest

Class LengthDigestionController

java.lang.Object

org.expasy.mzjava.proteomics.mol.digest.LengthDigestionController

All Implemented Interfaces:

DigestionController

public class LengthDigestionController
extends Object
implements DigestionController

DigestionController that excludes peptides that fall outside the length range.

Version:

sqrt -1

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
LengthDigestionController(int min, int max) Create a DigestionController that excludes peptides that have a length < min and > max

Method Summary

Methods

Modifier and Type	Method and Description
boolean	interruptDigestion(Protein protein, int proteinBoundsCount, 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

LengthDigestionController

public LengthDigestionController(int min,
                         int max)

Create a DigestionController that excludes peptides that have a length < min and > max

Parameters:

min - the minimum peptide length, peptides with a length smaller than this are excluded

max - the maximum peptide length, peptides with a length larger than this are excluded

Method Detail

interruptDigestion

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

Description copied from interface: DigestionController

Control digestion flow given the potential digest bounds

Specified by:

interruptDigestion in interface DigestionController

Parameters:

protein - the protein being digested

proteinBoundsCount - 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)

Description copied from interface: DigestionController

Make a peptide digest from the given protein.

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)

Description copied from interface: DigestionController

Process DigestedPeptide with/without missed cleavages

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)

Description copied from interface: DigestionController

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

Specified by:

retainSemiDigest in interface DigestionController

Parameters:

digest - the actual semi digest

Returns:

true if this semi digest is kept