Package com.compomics.util.experiment.identification.protein_sequences.digestion.iterators

Class SpecificSingleEnzymeCombinationIterator

java.lang.Object

com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeCombinationIterator

All Implemented Interfaces:

SequenceIterator

public class SpecificSingleEnzymeCombinationIterator
extends Object
implements SequenceIterator

Iterator for enzymatic digestion.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor	Description
SpecificSingleEnzymeCombinationIterator()	Empty default constructor
SpecificSingleEnzymeCombinationIterator(ProteinIteratorUtils proteinIteratorUtils, String proteinSequence, Enzyme enzyme, int nMissedCleavages, double massMin, double massMax)	Constructor.

Method Summary

Modifier and Type	Method	Description
ExtendedPeptide	getNextPeptide()	Returns the next peptide that can be generated from the iterator.

Methods inherited from class java.lang.Object

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

Constructor Details

SpecificSingleEnzymeCombinationIterator

public SpecificSingleEnzymeCombinationIterator()

Empty default constructor

SpecificSingleEnzymeCombinationIterator

public SpecificSingleEnzymeCombinationIterator(ProteinIteratorUtils proteinIteratorUtils,
 String proteinSequence,
 Enzyme enzyme,
 int nMissedCleavages,
 double massMin,
 double massMax)

Constructor.

Parameters:

proteinIteratorUtils - utils for the creation of the peptides

proteinSequence - the sequence to iterate

enzyme - the enzyme to use for digestion

nMissedCleavages - the maximal number of missed cleavages allowed

massMin - the minimal mass of a peptide

massMax - the maximal mass of a peptide

Method Details

getNextPeptide

public ExtendedPeptide getNextPeptide()
                               throws InterruptedException

Description copied from interface: SequenceIterator

Returns the next peptide that can be generated from the iterator. Null if none left.

Specified by:

getNextPeptide in interface SequenceIterator

Returns:

the next peptide that can be generated from the iterator

Throws:

InterruptedException - exception thrown if a thread is interrupted