org.expasy.mzjava.proteomics.mol.digest

Class ProteinDigester

java.lang.Object

org.expasy.mzjava.proteomics.mol.digest.ProteinDigester

public class ProteinDigester
extends Object

A ProteinDigester is defined by a name and a cleavage site matcher that match the sites to be digested.

Terminal Modification

In rare case, a peptidase may modify the extremity of released digests. As an example, CNBr modify the end terminal Methionine of the C-terminal digest in homoserine lactone.

This object is immutable. There are 2 modes of digestion:

Mode.STANDARD

no-missed-cleavage and missed-cleavage digests produced depending on MC param

Mode.SEMI

a supplementary step generates all the semi digests from the no-missed-cleavage digests (http://thegpm.org/TANDEM/api/pcsemi.html)

Author:

nikitin, Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ProteinDigester.Builder
static class	ProteinDigester.CleavageSiteIteration

Constructor Summary

Constructors

Constructor and Description
ProteinDigester(ProteinDigester.Builder builder)

Method Summary

Methods

Modifier and Type	Method and Description
int	countCleavageSites(SymbolSequence<AminoAcid> aaSeq)
List<Peptide>	digest(Protein protein) Digest protein
Collection<Peptide>	digest(Protein protein, Collection<Peptide> digests) Digest protein given a container for digests

Methods inherited from class java.lang.Object

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

Constructor Detail

ProteinDigester

public ProteinDigester(ProteinDigester.Builder builder)

Method Detail

digest

public List<Peptide> digest(Protein protein)

Digest protein

Parameters:

protein - the protein to digest.

Returns:

the digests.

digest

public Collection<Peptide> digest(Protein protein,
                         Collection<Peptide> digests)

Digest protein given a container for digests

Parameters:

protein - the protein to digest

digests - a list of digests

Returns:

the digests.

countCleavageSites

public int countCleavageSites(SymbolSequence<AminoAcid> aaSeq)