org.expasy.mzjava.proteomics.mol.digest

Class CleavageSiteFinderImpl

java.lang.Object

org.expasy.mzjava.proteomics.mol.digest.CleavageSiteFinderImpl

All Implemented Interfaces:

CleavageSiteFinder

public class CleavageSiteFinderImpl
extends Object
implements CleavageSiteFinder

The default implementation of CleavageSiteFinder

Author:

fnikitin

Constructor Summary

Constructors

Constructor and Description
CleavageSiteFinderImpl(CleavageSiteMatcher cs)

Method Summary

Methods

Modifier and Type	Method and Description
int	countCleavageSites(SymbolSequence<AminoAcid> aaSeq) Get the number of potential cleavage sites
int	find(SymbolSequence<AminoAcid> aaSeq, com.google.common.base.Optional<CleavageSiteVisitor> visitor) Find potential cleavage sites over the given amino-acid sequence
void	find(SymbolSequence<AminoAcid> aaSeq, gnu.trove.list.TIntList sites) Find potential cleavage sites over the given amino-acid sequence
CleavageSiteMatcher	getCleavageSiteMatcher() Get the cleavage site matcher

Methods inherited from class java.lang.Object

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

Constructor Detail

CleavageSiteFinderImpl

public CleavageSiteFinderImpl(CleavageSiteMatcher cs)

Method Detail

find

public void find(SymbolSequence<AminoAcid> aaSeq,
        gnu.trove.list.TIntList sites)

Description copied from interface: CleavageSiteFinder

Find potential cleavage sites over the given amino-acid sequence

Specified by:

find in interface CleavageSiteFinder

countCleavageSites

public int countCleavageSites(SymbolSequence<AminoAcid> aaSeq)

Description copied from interface: CleavageSiteFinder

Get the number of potential cleavage sites

Specified by:

countCleavageSites in interface CleavageSiteFinder

getCleavageSiteMatcher

public final CleavageSiteMatcher getCleavageSiteMatcher()

Description copied from interface: CleavageSiteFinder

Get the cleavage site matcher

Specified by:

getCleavageSiteMatcher in interface CleavageSiteFinder

find

public int find(SymbolSequence<AminoAcid> aaSeq,
       com.google.common.base.Optional<CleavageSiteVisitor> visitor)

Find potential cleavage sites over the given amino-acid sequence

Parameters:

aaSeq - an amino-acid sequence

visitor - an optional CleavageSiteVisitor

Returns:

the number of cleavage sites