org.expasy.mzjava.proteomics.ms.dbsearch

Interface DigestDB

All Known Implementing Classes:

ArrayDigestDB

public interface DigestDB

A database that stores digested peptides

Version:

sqrt -1

Author:

Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	DigestDB.AmbiguousAminoAcidAction The action to take if a peptide that have amino acids that are ambiguous (Z, B etc) are returned by the digester

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

Method Detail

getPeptides

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

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

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

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

Parameters:

targetMass - the target mass

tolerance - the tolerance

collection - collection to which the peptides are to be added