org.expasy.mzjava.proteomics.ms.dbsearch

Class ArrayDigestDB

java.lang.Object

org.expasy.mzjava.proteomics.ms.dbsearch.ArrayDigestDB

All Implemented Interfaces:

DigestDB

public class ArrayDigestDB
extends Object
implements DigestDB

A peptide digest db that stores peptide digests in ram and is backed by an array.

Version:

sqrt -1

Author:

Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ArrayDigestDB.Builder Builder

Nested classes/interfaces inherited from interface org.expasy.mzjava.proteomics.ms.dbsearch.DigestDB

DigestDB.AmbiguousAminoAcidAction

Constructor Summary

Constructors

Constructor and Description
ArrayDigestDB(IterativeReader<Protein> proteinReader, ProteinDigester proteinDigester, DigestDB.AmbiguousAminoAcidAction ambiguousAminoAcidAction) Construct a new ArrayDigestDB.

Method Summary

Methods

Modifier and Type	Method and Description
Set<Digest>	getPeptides(double targetMass, Tolerance tolerance) Retrieves all the peptides that have a mass that is within tolerance of targetMass
void	getPeptides(double targetMass, Tolerance tolerance, Collection<Digest> collection) Add all the peptides that have a mass that is within tolerance of targetMass to the peptides collection
int	size() Return the number of digests that this DigestDB contains

Methods inherited from class java.lang.Object

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

Constructor Detail

ArrayDigestDB

public ArrayDigestDB(IterativeReader<Protein> proteinReader,
             ProteinDigester proteinDigester,
             DigestDB.AmbiguousAminoAcidAction ambiguousAminoAcidAction)

Construct a new ArrayDigestDB. Proteins are read from the proteinRead and digested using the proteinDigester.

Parameters:

proteinReader - the source of the proteins

proteinDigester - the protein digester

ambiguousAminoAcidAction - the action to take if any paptides contain ambiguous amino acids such as (X, B, etc.)

Method Detail

getPeptides

public Set<Digest> getPeptides(double targetMass,
                      Tolerance tolerance)

Description copied from interface: DigestDB

Retrieves all the peptides that have a mass that is within tolerance of targetMass

Specified by:

getPeptides in interface DigestDB

Parameters:

targetMass - the target mass

tolerance - the tolerance

Returns:

a set containing all the peptides that have a mass that is within tolerance of targetMass

getPeptides

public void getPeptides(double targetMass,
               Tolerance tolerance,
               Collection<Digest> collection)

Description copied from interface: DigestDB

Add all the peptides that have a mass that is within tolerance of targetMass to the peptides collection

Specified by:

getPeptides in interface DigestDB

Parameters:

targetMass - the target mass

tolerance - the tolerance

collection - collection to which the peptides are to be added

size

public int size()

Return the number of digests that this DigestDB contains

Returns:

the number of digests that this DigestDB contains