org.expasy.mzjava.proteomics.ms.dbsearch

Interface PeptideSpectrumDB.FragmentDSL

Enclosing class:

PeptideSpectrumDB

public static interface PeptideSpectrumDB.FragmentDSL

Fluent interface for configuring the protein digestion and fragmentation.

Method Summary

Methods

Modifier and Type	Method and Description
PeptideSpectrumDB.FragmentDSL	cachePeptideSpectrumWith(PeptideSpectrumCache cache)
PeptideSpectrumDB.EndDSL	generateSequestCidSpectra(PeakList.Precision precision) Creates a new PeptideFragmenter that generates theoretical spectra like SEQUEST does.
PeptideSpectrumDB.EndDSL	generateSpectra(PeakList.Precision precision, IonType first, IonType... rest) Set the precision of the spectra and ion types that are generated when a theoretical spectrum is created.
PeptideSpectrumDB.EndDSL	generateSpectraWith(PeptideFragmenter peptideFragmenter) Set the PeptideFragmenter that is used to generate the theoretical spectra.
PeptideSpectrumDB.EndDSL	generateSpectraWithIons(IonType first, IonType... rest) Creates a new PeptideFragmenter that generates theoretical spectra using the provided ions.
PeptideSpectrumDB.FragmentDSL	processGeneratedSpectraWith(PeakProcessorChain<PepFragAnnotation> processorChain) Set the processorChain that is used to process the generated spectra

Method Detail

cachePeptideSpectrumWith

PeptideSpectrumDB.FragmentDSL cachePeptideSpectrumWith(PeptideSpectrumCache cache)

generateSpectraWith

PeptideSpectrumDB.EndDSL generateSpectraWith(PeptideFragmenter peptideFragmenter)

Set the PeptideFragmenter that is used to generate the theoretical spectra.

Parameters:

peptideFragmenter - the fragmenter to use

Returns:

dsl with method to build the PeptideSpectrumDB

generateSpectraWithIons

PeptideSpectrumDB.EndDSL generateSpectraWithIons(IonType first,
                                               IonType... rest)

Creates a new PeptideFragmenter that generates theoretical spectra using the provided ions.

Parameters:

first - the first ion type

rest - the rest

Returns:

dsl with method to build the PeptideSpectrumDB

generateSequestCidSpectra

PeptideSpectrumDB.EndDSL generateSequestCidSpectra(PeakList.Precision precision)

Creates a new PeptideFragmenter that generates theoretical spectra like SEQUEST does. The generated spectra have peaks from backbone and neutral loss ions. Backbone peaks are generated for b and y ions. Ammonium and water loss peaks are generated for both b and y ions and carbon monoxide losses are generated for b ions.

The intensity of the backbone ions is 50 and the intensity of the neutral loss ions is set to 10

Parameters:

precision -

Returns:

dsl with method to build the PeptideSpectrumDB

generateSpectra

PeptideSpectrumDB.EndDSL generateSpectra(PeakList.Precision precision,
                                       IonType first,
                                       IonType... rest)

Set the precision of the spectra and ion types that are generated when a theoretical spectrum is created.

Parameters:

precision - the spectrum precision

first - the first ion type

rest - the rest

Returns:

dsl with method to build the PeptideSpectrumDB

processGeneratedSpectraWith

PeptideSpectrumDB.FragmentDSL processGeneratedSpectraWith(PeakProcessorChain<PepFragAnnotation> processorChain)

Set the processorChain that is used to process the generated spectra

Parameters:

processorChain - the processor chain

Returns:

dsl with methods to configure digest and fragmentation