org.expasy.mzjava.proteomics.ms.dbsearch

Interface PeptideSpectrumDB.DigestSourceDSL

Enclosing class:

PeptideSpectrumDB

public static interface PeptideSpectrumDB.DigestSourceDSL

Fluent interface for configuring the protein source

Method Summary

Methods

Modifier and Type	Method and Description
PeptideSpectrumDB.FragmentDSL	setDigestDB(DigestDB digestDB)
PeptideSpectrumDB.DigestDSL	setProteinSource(File fastaFile) Set the fasta format protein file.
PeptideSpectrumDB.DigestDSL	setProteinSource(IterativeReader<Protein> reader) Set the IterativeReader reader as the protein source.

Method Detail

setProteinSource

PeptideSpectrumDB.DigestDSL setProteinSource(File fastaFile)

Set the fasta format protein file. This uses a FastaStreamReader.

Parameters:

fastaFile - the file contining the protins

Returns:

dsl with methods to configure digesting and fragmenting

setProteinSource

PeptideSpectrumDB.DigestDSL setProteinSource(IterativeReader<Protein> reader)

Set the IterativeReader reader as the protein source.

Parameters:

reader - the protein source

Returns:

dsl with methods to configure digest and fragmentation

setDigestDB

PeptideSpectrumDB.FragmentDSL setDigestDB(DigestDB digestDB)