Package 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
    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
    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 Details

    • 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.
      proteinDetailsProvider - The protein details provider.
      spectrumProvider - The spectrum provider.
      modificationProvider - The modifications provider.
      fastaSummary - The summary information on the protein sequences file.
      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 Details

    • 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