Package eu.isas.peptideshaker.followup

Class Ms2PipExport

java.lang.Object
eu.isas.peptideshaker.followup.Ms2PipExport
public class Ms2PipExport extends Object
Export training files for ms2pip.
Author:
Marc Vaudel, Dafni Skiadopoulou

  • Constructor Summary

    Constructors
    Constructor
    Description
    Ms2PipExport()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    ms2pipExport(File peprecFile, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Exports a ms2pip training file for the given spectrum file.
    static ArrayList<File>
    ms2pipExport(File peprecFile, String[] models, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Exports ms2pip config and peprec files.
    static void
    writeConfigFile(File configFile, String model, com.compomics.util.parameters.identification.search.SearchParameters searchParameters)
    Writes a config file for a given model.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • Ms2PipExport

      public Ms2PipExport()

  • Method Details

    • ms2pipExport

      public static ArrayList<File> ms2pipExport(File peprecFile, String[] models, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Exports ms2pip config and peprec files. Returns an ArrayList of the files written.
      Parameters:
      peprecFile - The file where to write the peptides.
      models - The names of the models to write config files for.
      identification - The identification object containing the matches.
      searchParameters - The search parameters.
      sequenceMatchingParameters - The sequence matching parameters.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      waitingHandler - The waiting handler.
      Returns:
      An ArrayList of the files exported.

    • writeConfigFile

      public static void writeConfigFile(File configFile, String model, com.compomics.util.parameters.identification.search.SearchParameters searchParameters)
      Writes a config file for a given model.
      Parameters:
      configFile - The file where to write.
      model - The name of the model.
      searchParameters - The search parameters.

    • ms2pipExport

      public static void ms2pipExport(File peprecFile, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Exports a ms2pip training file for the given spectrum file.
      Parameters:
      peprecFile - The file where to write the export.
      identification - The identification object containing the matches.
      modificationParameters - The modification parameters.
      sequenceMatchingParameters - The sequence matching parameters.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      waitingHandler - The waiting handler.