Uses of Class
org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Packages that use PepXmlWriterBuilder.Builder

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

Uses of PepXmlWriterBuilder.Builder in org.expasy.mzjava.proteomics.io.ms.ident

Methods in org.expasy.mzjava.proteomics.io.ms.ident that return PepXmlWriterBuilder.Builder

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

Constructors in org.expasy.mzjava.proteomics.io.ms.ident with parameters of type PepXmlWriterBuilder.Builder

Constructor and Description
PepXmlWriter(PepXmlWriterBuilder.Builder builder)