Package eu.isas.peptideshaker.followup

Class ProgenesisExport

java.lang.Object
eu.isas.peptideshaker.followup.ProgenesisExport
public class ProgenesisExport extends Object
This class exports identifications for post-processing with Non-Linear Progenesis.
Author:
Marc Vaudel

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    static enum 
    ProgenesisExport.ExportType
    Enum of the different types of export implemented.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final char
    SEPARATOR
    The separator (tab by default).

  • Constructor Summary

    Constructors
    Constructor
    Description
    ProgenesisExport()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    writeProgenesisExport(File destinationFile, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.identification.Identification identification, ProgenesisExport.ExportType exportType, com.compomics.util.waiting.WaitingHandler waitingHandler, HashSet<String> targetedModifications, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences)
    Writes a file containing the PSMs in a Progenesis compatible format.

    Methods inherited from class java.lang.Object

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

  • Field Details

    • SEPARATOR

      public static final char SEPARATOR
      The separator (tab by default).
      See Also:

  • Constructor Details

    • ProgenesisExport

      public ProgenesisExport()

  • Method Details

    • writeProgenesisExport

      public static void writeProgenesisExport(File destinationFile, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.identification.Identification identification, ProgenesisExport.ExportType exportType, com.compomics.util.waiting.WaitingHandler waitingHandler, HashSet<String> targetedModifications, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences) throws IOException
      Writes a file containing the PSMs in a Progenesis compatible format.
      Parameters:
      destinationFile - the destination file
      sequenceProvider - a sequence provider
      proteinDetailsProvider - the protein details provider
      identification - the identification
      exportType - the type of export
      waitingHandler - waiting handler displaying progress to the user and allowing canceling the process
      targetedModifications - the modifications of interest in case of a PTM export. Ignored otherwise.
      sequenceMatchingPreferences - the sequence matching preferences
      Throws:
      IOException - thrown if an error occurred while writing the file