org.expasy.mzjava.proteomics.io.ms.ident

Class PepXmlWriterBuilder

java.lang.Object

org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder

public class PepXmlWriterBuilder
extends Object

This builder Builds PepXmlWriter instances.

Proper Usage

Use one of the static methods create(), set your identifications parameters and terminate with build() to create a new instance of PepXmlWriter.

Internal SampleEnzyme builder

This class also contains static factory methods createEnzyme(String name) and createTrypsin() to create SampleEnzyme needed as a parameter of Builder.enzyme(sampleEnzyme)

Remark

This written PepXml format has been simplified as it may only contain one search_summary by msms_run_summary. Elements aminoacid_modification of search_summary will be automatically deduced from PeptideMatch collected. Moreover msms_run_summary are also will be automatically deduced from identified MsnSpectrum.

Author:

fnikitin Date: 1/14/14

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PepXmlWriterBuilder.Builder Build PepXmlWriter
static interface	PepXmlWriterBuilder.EnzymeEnd
static class	PepXmlWriterBuilder.SampleEnzymeBuilder
static class	PepXmlWriterBuilder.SpecificityBuilder

Constructor Summary

Constructors

Constructor and Description
PepXmlWriterBuilder()

Method Summary

Methods

Modifier and Type	Method and Description
static PepXmlWriterBuilder.Builder	create(EngineType engineType, Comparator<PeptideMatch> peptideMatchComparator) Main entry point to build PepXmlWriter
static PepXmlWriterBuilder.Builder	create(EngineType engineType, String scoreName) Main entry point to build PepXmlWriter
static PepXmlWriterBuilder.SampleEnzymeBuilder	createEnzyme(String name) Static factory method that create a SampleEnzyme builder
static MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme	createTrypsin() Static factory method that create the default SampleEnzyme

Methods inherited from class java.lang.Object

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

Constructor Detail

PepXmlWriterBuilder

public PepXmlWriterBuilder()

Method Detail

create

public static PepXmlWriterBuilder.Builder create(EngineType engineType,
                                 String scoreName)

Main entry point to build PepXmlWriter

Parameters:

engineType - the engine type

scoreName - the score name as a criterium to sort result hits

Returns:

an instance of Builder

create

public static PepXmlWriterBuilder.Builder create(EngineType engineType,
                                 Comparator<PeptideMatch> peptideMatchComparator)

Main entry point to build PepXmlWriter

Parameters:

engineType - the engine type

peptideMatchComparator - the comparator to sort result hits

Returns:

an instance of Builder

createEnzyme

public static PepXmlWriterBuilder.SampleEnzymeBuilder createEnzyme(String name)

Static factory method that create a SampleEnzyme builder

Parameters:

name - mandatory enzyme name

Returns:

SampleEnzymeBuilder

createTrypsin

public static MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme createTrypsin()

Static factory method that create the default SampleEnzyme

Returns:

a new trypsin SampleEnzyme