org.expasy.mzjava.proteomics.ms.dbsearch

Interface PeptideSpectrumDB.DigestDSL

Enclosing class:

PeptideSpectrumDB

public static interface PeptideSpectrumDB.DigestDSL

Fluent interface for configuring the protein digestion and fragmentation.

Method Summary

Methods

Modifier and Type	Method and Description
PeptideSpectrumDB.DigestDSL	digestWith(Protease protease) Set the Protease that is used to digest the proteins.
PeptideSpectrumDB.DigestDSL	onAmbiguousAminoAcid(DigestDB.AmbiguousAminoAcidAction ambiguousAminoAcidAction) Set what happens when an ambiguous amino acid is found.
PeptideSpectrumDB.DigestDSL	retainPeptidesOfLength(int min, int max) Only retain peptides that have a length >= min and <= max
PeptideSpectrumDB.FragmentDSL	setMissedCleavagesTo(int missedCleavages) Set the number of missed cleavages that is allowed by the digester.
PeptideSpectrumDB.DigestDSL	useDigestionController(DigestionController digestionController) Set the digestion controller that is used by the digester

Method Detail

digestWith

PeptideSpectrumDB.DigestDSL digestWith(Protease protease)

Set the Protease that is used to digest the proteins.

Parameters:

protease - the Protease

Returns:

dsl with methods to configure digest and fragmentation

setMissedCleavagesTo

PeptideSpectrumDB.FragmentDSL setMissedCleavagesTo(int missedCleavages)

Set the number of missed cleavages that is allowed by the digester.

Parameters:

missedCleavages - the number of missed cleavages

Returns:

dsl with methods to configure digest and fragmentation

retainPeptidesOfLength

PeptideSpectrumDB.DigestDSL retainPeptidesOfLength(int min,
                                                 int max)

Only retain peptides that have a length >= min and <= max

Parameters:

min - the minimum peptide length, inclusive

max - the maximum peptide length, inclusive

Returns:

dsl with methods to configure digest and fragmentation

onAmbiguousAminoAcid

PeptideSpectrumDB.DigestDSL onAmbiguousAminoAcid(DigestDB.AmbiguousAminoAcidAction ambiguousAminoAcidAction)

Set what happens when an ambiguous amino acid is found.

Parameters:

ambiguousAminoAcidAction - the fail behaviour

Returns:

dsl with methods to configure digest and fragmentation

useDigestionController

PeptideSpectrumDB.DigestDSL useDigestionController(DigestionController digestionController)

Set the digestion controller that is used by the digester

Parameters:

digestionController - the digestion controller

Returns:

dsl with methods to configure digest and fragmentation