eu.isas.peptideshaker.export

Class MzIdentMLExport

java.lang.Object

eu.isas.peptideshaker.export.MzIdentMLExport

public class MzIdentMLExport
extends Object

The class that takes care of converting the data to mzIdentML.

Author:

Harald Barsnes, Marc Vaudel

Constructor Summary

Constructors

Constructor and Description

MzIdentMLExport(String peptideShakerVersion, com.compomics.util.experiment.identification.Identification identification, ProjectDetails projectDetails, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider, com.compomics.util.experiment.io.biology.protein.FastaSummary fastaSummary, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, File outputFile, boolean includeProteinSequences, com.compomics.util.waiting.WaitingHandler waitingHandler, boolean gzip) Constructor.

Method Summary

Modifier and Type	Method and Description
void	createMzIdentMLFile(com.compomics.util.experiment.io.identification.MzIdentMLVersion mzIdentMLVersion) Creates the mzIdentML file.
static String	getPeptideEvidenceKey(String accession, int peptideStart, long peptideKey) Returns the peptide evidence key as string for the given peptide attributes.

Methods inherited from class java.lang.Object

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

Constructor Detail

MzIdentMLExport

public MzIdentMLExport(String peptideShakerVersion,
                       com.compomics.util.experiment.identification.Identification identification,
                       ProjectDetails projectDetails,
                       com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                       com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                       com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                       com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                       com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider,
                       com.compomics.util.experiment.io.biology.protein.FastaSummary fastaSummary,
                       com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                       File outputFile,
                       boolean includeProteinSequences,
                       com.compomics.util.waiting.WaitingHandler waitingHandler,
                       boolean gzip)

Constructor.

Parameters:

peptideShakerVersion - The PeptideShaker version.

identification - The identification object.

projectDetails - The project details.

identificationParameters - The identification parameters.

sequenceProvider - The sequence provider.

fastaSummary - The summary information on the protein sequences file.

proteinDetailsProvider - The protein details provider.

spectrumProvider - The spectrum provider.

modificationProvider - The modifications provider.

identificationFeaturesGenerator - The identification features generator.

outputFile - The output file.

includeProteinSequences - If true, the protein sequences are included in the output.

waitingHandler - The waiting handler used to display progress to the user and interrupt the process.

gzip - If true export as gzipped file.

Method Detail

createMzIdentMLFile

public void createMzIdentMLFile(com.compomics.util.experiment.io.identification.MzIdentMLVersion mzIdentMLVersion)

Creates the mzIdentML file.

Parameters:

mzIdentMLVersion - The version of mzIdentML to use.

getPeptideEvidenceKey

public static String getPeptideEvidenceKey(String accession,
                                           int peptideStart,
                                           long peptideKey)

Returns the peptide evidence key as string for the given peptide attributes.

Parameters:

accession - the protein accession

peptideStart - the index of the peptide on the protein sequence

peptideKey - the peptide match key

Returns:

the peptide evidence key as string for the given peptide attributes