Package eu.isas.peptideshaker.followup

Class SpectrumExporter

java.lang.Object
eu.isas.peptideshaker.followup.SpectrumExporter
public class SpectrumExporter extends Object
This class can be used to export spectra.
Author:
Marc Vaudel

  • Nested Class Summary

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

  • Constructor Summary

    Constructors
    Constructor
    Description
    SpectrumExporter(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    ArrayList<File>
    exportSpectra(File destinationFolder, com.compomics.util.waiting.WaitingHandler waitingHandler, SpectrumExporter.ExportType exportType, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences)
    Exports the spectra from different categories of PSMs according to the export type.
    static File
    getDestinationFile(File destinationFolder, String originalFileName, SpectrumExporter.ExportType exportType)
    Returns the destination file for the given export.
    static String
    getSuffix(SpectrumExporter.ExportType exportType)
    Returns the suffix for a spectrum file name.
    static boolean
    include(String spectrumFile, String spectrumTitle, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, SpectrumExporter.ExportType exportType)
    Indicates whether a spectrum should be exported.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • SpectrumExporter

      public SpectrumExporter(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)
      Constructor.
      Parameters:
      identification - The identification object.
      spectrumProvider - The spectrum provider.

  • Method Details

    • exportSpectra

      public ArrayList<File> exportSpectra(File destinationFolder, com.compomics.util.waiting.WaitingHandler waitingHandler, SpectrumExporter.ExportType exportType, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences) throws IOException
      Exports the spectra from different categories of PSMs according to the export type. Export format is mgf and only MS2 spectra are included.
      Parameters:
      destinationFolder - the folder where to write the spectra
      waitingHandler - waiting handler used to display progress and cancel the process. Can be null.
      exportType - the type of PSM to export
      sequenceMatchingPreferences - the sequence matching preferences
      Returns:
      ArrayList files containing exported spectra
      Throws:
      IOException - thrown if an error occurred while writing the file

    • getDestinationFile

      public static File getDestinationFile(File destinationFolder, String originalFileName, SpectrumExporter.ExportType exportType)
      Returns the destination file for the given export.
      Parameters:
      destinationFolder - the destination folder
      originalFileName - the original file name
      exportType - the export type
      Returns:
      the destination file

    • include

      public static boolean include(String spectrumFile, String spectrumTitle, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, SpectrumExporter.ExportType exportType)
      Indicates whether a spectrum should be exported.
      Parameters:
      spectrumFile - the name of the file of the spectrum
      spectrumTitle - the spectrum title
      identification - the identification object
      sequenceMatchingParameters - the sequence matching preferences
      exportType - the export type
      Returns:
      a boolean indicating whether a spectrum should be exported

    • getSuffix

      public static String getSuffix(SpectrumExporter.ExportType exportType)
      Returns the suffix for a spectrum file name.
      Parameters:
      exportType - the type of PSM to be exported
      Returns:
      the suffix for a spectrum file name