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

Class PepXmlWriterBuilder.Builder

java.lang.Object

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

Enclosing class:

PepXmlWriterBuilder

public static class PepXmlWriterBuilder.Builder
extends Object

Build PepXmlWriter

Method Summary

Methods

Modifier and Type	Method and Description
PepXmlWriter	build() Build a PepXmlWriter
PepXmlWriterBuilder.Builder	enzymaticSearchConstraint(int maxNumInternalCleavages, int minNumberTermini) Set the enzymatic_search_constraint child element of search_summary
PepXmlWriterBuilder.Builder	enzyme(MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme enzyme) Set the sample_enzyme element of msms_run_summary (else enzyme by default)
PepXmlWriterBuilder.Builder	fragMassType(MassType massType) Set the fragment_mass_type attribute of element search_summary
PepXmlWriterBuilder.Builder	msDetector(String msDetector) Set the msDetector attribute of element msms_run_summary
PepXmlWriterBuilder.Builder	msIonization(String msIonization) Set the msIonization attribute of element msms_run_summary
PepXmlWriterBuilder.Builder	msManufacturer(String msManufacturer) Set the msManufacturer attribute of element msms_run_summary
PepXmlWriterBuilder.Builder	msMassAnalyzer(String msMassAnalyzer) Set the msMassAnalyzer attribute of element msms_run_summary
PepXmlWriterBuilder.Builder	msModel(String msModel) Set the msModel attribute of element msms_run_summary
PepXmlWriterBuilder.Builder	parameter(String name, String value) Add a parameter element in element search_summary
PepXmlWriterBuilder.Builder	precMassType(MassType massType) Set the precursor_mass_type attribute of element search_summary
PepXmlWriterBuilder.Builder	searchDatabase(File dbFile) Set the search_database element of element search_summary
PepXmlWriterBuilder.Builder	searchHitRank(int rankCount) Set the number of maximum result hits retained

Methods inherited from class java.lang.Object

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

Method Detail

enzyme

public PepXmlWriterBuilder.Builder enzyme(MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme enzyme)

Set the sample_enzyme element of msms_run_summary (else enzyme by default)

Parameters:

enzyme - the sample enzyme element

Returns:

this Builder

enzymaticSearchConstraint

public PepXmlWriterBuilder.Builder enzymaticSearchConstraint(int maxNumInternalCleavages,
                                                    int minNumberTermini)

Set the enzymatic_search_constraint child element of search_summary

Parameters:

maxNumInternalCleavages - Maximum number of enzyme cleavage sites allowable within peptide

minNumberTermini - Minimum number of termini compatible with enzymatic cleavage

Returns:

this Builder

searchHitRank

public PepXmlWriterBuilder.Builder searchHitRank(int rankCount)

Set the number of maximum result hits retained

Parameters:

rankCount - the maximum number of retained results

Returns:

this Builder

msManufacturer

public PepXmlWriterBuilder.Builder msManufacturer(String msManufacturer)

Set the msManufacturer attribute of element msms_run_summary

Parameters:

msManufacturer - Manufacturer of MS/MS instrument

Returns:

this Builder

msModel

public PepXmlWriterBuilder.Builder msModel(String msModel)

Set the msModel attribute of element msms_run_summary

Parameters:

msModel - Instrument model

Returns:

this Builder

msIonization

public PepXmlWriterBuilder.Builder msIonization(String msIonization)

Set the msIonization attribute of element msms_run_summary

Parameters:

msIonization - Ionization type

Returns:

this Builder

msMassAnalyzer

public PepXmlWriterBuilder.Builder msMassAnalyzer(String msMassAnalyzer)

Set the msMassAnalyzer attribute of element msms_run_summary

Parameters:

msMassAnalyzer - Ion trap, etc

Returns:

this Builder

msDetector

public PepXmlWriterBuilder.Builder msDetector(String msDetector)

Set the msDetector attribute of element msms_run_summary

Parameters:

msDetector - EMT, etc

Returns:

this Builder

precMassType

public PepXmlWriterBuilder.Builder precMassType(MassType massType)

Set the precursor_mass_type attribute of element search_summary

Parameters:

massType - precursor mass type (monoisotopic by default)

Returns:

this Builder

fragMassType

public PepXmlWriterBuilder.Builder fragMassType(MassType massType)

Set the fragment_mass_type attribute of element search_summary

Parameters:

massType - fragment mass type (monoisotopic by default)

Returns:

this Builder

searchDatabase

public PepXmlWriterBuilder.Builder searchDatabase(File dbFile)

Set the search_database element of element search_summary

Parameters:

dbFile - full path file of database on local computer

Returns:

this Builder

parameter

public PepXmlWriterBuilder.Builder parameter(String name,
                                    String value)

Add a parameter element in element search_summary

Parameters:

name - the parameter name

value - the parameter value

Returns:

this Builder

build

public PepXmlWriter build()

Build a PepXmlWriter

Returns:

a new instance of PepXmlWriter