Uses of Interface
org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.DigestDSL

Packages that use PeptideSpectrumDB.DigestDSL

Package	Description
org.expasy.mzjava.proteomics.ms.dbsearch

Uses of PeptideSpectrumDB.DigestDSL in org.expasy.mzjava.proteomics.ms.dbsearch

Methods in org.expasy.mzjava.proteomics.ms.dbsearch that return PeptideSpectrumDB.DigestDSL

Modifier and Type	Method and Description
PeptideSpectrumDB.DigestDSL	PeptideSpectrumDB.DigestDSL.digestWith(Protease protease) Set the Protease that is used to digest the proteins.
PeptideSpectrumDB.DigestDSL	PeptideSpectrumDB.DigestDSL.onAmbiguousAminoAcid(DigestDB.AmbiguousAminoAcidAction ambiguousAminoAcidAction) Set what happens when an ambiguous amino acid is found.
PeptideSpectrumDB.DigestDSL	PeptideSpectrumDB.DigestDSL.retainPeptidesOfLength(int min, int max) Only retain peptides that have a length >= min and <= max
PeptideSpectrumDB.DigestDSL	PeptideSpectrumDB.DigestSourceDSL.setProteinSource(File fastaFile) Set the fasta format protein file.
PeptideSpectrumDB.DigestDSL	PeptideSpectrumDB.DigestSourceDSL.setProteinSource(IterativeReader<Protein> reader) Set the IterativeReader reader as the protein source.
PeptideSpectrumDB.DigestDSL	PeptideSpectrumDB.DigestDSL.useDigestionController(DigestionController digestionController) Set the digestion controller that is used by the digester