org.expasy.mzjava.proteomics.mol.digest

Interface DigestionController

All Known Implementing Classes:

AcceptAllDigestionController, LengthDigestionController

public interface DigestionController

This interface delegates to callbacks to control the digestion handled by ProteinDigester. In the following we give some explanations about when those methods are called back.

Potential digest bounds

A bound in a digested protein is defined by the protease potential cleavage sites and the protein N/C terminal end points. A protein with n potential cleavage sites will have n+2 bounds.

Digestion workflow

Internally ProteinDigester generates a sequence of pairs of these bounds for the digested protein given the number of potential cleavage sites and the maximum number of missed cleavages. A protein with n potential cleavage sites will potentially produce (n+1)(n+2)/2 potential digests. Each pair of bounds then pass a series of process that lead to the production of a peptide digest and its storing.

Callbacks

The following callbacks can affect these processes at different control point:

1. interruptDigestion(): the first control point where digestion can potentially stop
2. makeDigest(): this second control point lead to the potential building of the current peptide digest
3. retainDigest(): this third control point potentially stores the digest

The last method retainSemiDigest() is potentially called back when semi-digests are generated after the previous digests have been produced.

Author:

fnikitin Date: 10/29/13

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.

Method Detail

interruptDigestion

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

Control digestion flow given the potential digest bounds

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

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

Make a peptide digest from the given protein.

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

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

Process DigestedPeptide with/without missed cleavages

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

boolean retainSemiDigest(Peptide digest)

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

Parameters:

digest - the actual semi digest

Returns:

true if this semi digest is kept