org.expasy.mzjava.proteomics.ms.dbsearch

Class ArrayDigestDB.Builder

java.lang.Object

org.expasy.mzjava.proteomics.ms.dbsearch.ArrayDigestDB.Builder

Enclosing class:

ArrayDigestDB

public static class ArrayDigestDB.Builder
extends Object

Builder

Constructor Summary

Constructors

Constructor and Description
ArrayDigestDB.Builder(IterativeReader<Protein> reader, Protease protease, int missedCleavages) Create a bulder that build a ArrayDigestDB that digests proteins from the reader using the protease with missedCleavages missed cleavages.

Method Summary

Methods

Modifier and Type	Method and Description
ArrayDigestDB	build() Build the ArrayDigestDB
ArrayDigestDB.Builder	setAmbiguousAminoAcidAction(DigestDB.AmbiguousAminoAcidAction ambiguousAminoAcidAction) Set what action the ArrayDigestDB is to take if ambiguous amino acids are encountered.
ArrayDigestDB.Builder	setDigestionController(DigestionController digestionController) Set the controller for the digest.

Methods inherited from class java.lang.Object

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

Constructor Detail

ArrayDigestDB.Builder

public ArrayDigestDB.Builder(IterativeReader<Protein> reader,
                     Protease protease,
                     int missedCleavages)

Create a bulder that build a ArrayDigestDB that digests proteins from the reader using the protease with missedCleavages missed cleavages.

Parameters:

reader - the reader

protease - the protease

missedCleavages - the number of mised cleavages

Method Detail

build

public ArrayDigestDB build()

Build the ArrayDigestDB

Returns:

the new ArrayDigestDB

setDigestionController

public ArrayDigestDB.Builder setDigestionController(DigestionController digestionController)

Set the controller for the digest.

Parameters:

digestionController - the controller for the digest

Returns:

the builder

setAmbiguousAminoAcidAction

public ArrayDigestDB.Builder setAmbiguousAminoAcidAction(DigestDB.AmbiguousAminoAcidAction ambiguousAminoAcidAction)

Set what action the ArrayDigestDB is to take if ambiguous amino acids are encountered.

Parameters:

ambiguousAminoAcidAction - the action that is be take if the ArrayDigestDB encounters ambiguous amino acids

Returns:

the builder