org.expasy.mzjava.proteomics.ms.dbsearch

Class PeptideSpectrumDB

java.lang.Object

org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB

public class PeptideSpectrumDB
extends Object

PeptideSpectrumDB is a facade that collects together all the classes that are required by a peptide spectrum database. The spectrum database is backed by a protein database, a PeptideFragmenter to generate theoretical spectra and a PeptideSpectrumCache to allow the generated spectra to be cached.

PeptideSpectrumDB can be built by using the constructor and by using the Builder class for configuring a database by calling PeptideSpectrumDB.newBuilder()

Version:

sqrt -1

Author:

Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	PeptideSpectrumDB.DigestDSL Fluent interface for configuring the protein digestion and fragmentation.
static interface	PeptideSpectrumDB.DigestSourceDSL Fluent interface for configuring the protein source
static interface	PeptideSpectrumDB.EndDSL
static interface	PeptideSpectrumDB.FragmentDSL Fluent interface for configuring the protein digestion and fragmentation.
static interface	PeptideSpectrumDB.StartDSL Fluent interface that starts the build.

Constructor Summary

Constructors

Constructor and Description
PeptideSpectrumDB(Tolerance precursorTolerance, PeptideFragmenter fragmenter, DigestDB digestDB, PeptideSpectrumCache peptideSpectrumCache, PeakProcessorChain<PepFragAnnotation> processorChain) Construct a PeptideSpectrumDB backed by the fragmenter, proteinDB and peptideSpectrumCache.

Method Summary

Methods

Modifier and Type	Method and Description
List<PeptideSpectrum>	getSpectra(Peak precursor) Collect all peptide spectra with mass closed to the given precursor peak
void	getSpectra(Peak precursor, Collection<PeptideSpectrum> spectrumCollection) Add all peptide spectra contained in this database that are within tolerance of the precursor to spectrumCollection
static PeptideSpectrumDB.StartDSL	newBuilder() Factory method for creating a builder that can be used to configure and build an in memory PeptideSpectrumDB.

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideSpectrumDB

public PeptideSpectrumDB(Tolerance precursorTolerance,
                 PeptideFragmenter fragmenter,
                 DigestDB digestDB,
                 PeptideSpectrumCache peptideSpectrumCache,
                 PeakProcessorChain<PepFragAnnotation> processorChain)

Construct a PeptideSpectrumDB backed by the fragmenter, proteinDB and peptideSpectrumCache.

Parameters:

precursorTolerance - the precursor tolerance

fragmenter - the class that is used to generate theoretical spectra

digestDB - the peptide database

peptideSpectrumCache - the spectrum cache

processorChain - the processor chain that is used to process the generated spectra

Method Detail

getSpectra

public List<PeptideSpectrum> getSpectra(Peak precursor)

Collect all peptide spectra with mass closed to the given precursor peak

Parameters:

precursor - the peak precursor query

Returns:

a list of PeptideSpectrum

getSpectra

public void getSpectra(Peak precursor,
              Collection<PeptideSpectrum> spectrumCollection)

Add all peptide spectra contained in this database that are within tolerance of the precursor to spectrumCollection

Parameters:

precursor - the precursor

spectrumCollection - to collection to which the spectra re to be added

newBuilder

public static PeptideSpectrumDB.StartDSL newBuilder()

Factory method for creating a builder that can be used to configure and build an in memory PeptideSpectrumDB.

Returns:

the new builder.