Package eu.isas.peptideshaker.export.sections

Class PsFragmentSection

java.lang.Object
eu.isas.peptideshaker.export.sections.PsFragmentSection
public class PsFragmentSection extends Object
This class outputs the PSM related export features.
Author:
Marc Vaudel

  • Constructor Summary

    Constructors
    Constructor
    Description
    PsFragmentSection(ArrayList<com.compomics.util.io.export.ExportFeature> exportFeatures, boolean indexes, boolean header, com.compomics.util.io.export.ExportWriter writer)
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    writeHeader()
    Writes the header of this section.
    void
    writeSection(String spectrumFile, String spectrumTitle, com.compomics.util.experiment.identification.SpectrumIdentificationAssumption spectrumIdentificationAssumption, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, String linePrefix, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Writes the desired section.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • PsFragmentSection

      public PsFragmentSection(ArrayList<com.compomics.util.io.export.ExportFeature> exportFeatures, boolean indexes, boolean header, com.compomics.util.io.export.ExportWriter writer)
      Constructor.
      Parameters:
      exportFeatures - The features to export in this section.
      indexes - A boolean indicating whether the line index should be written.
      header - A boolean indicates whether the table header should be written.
      writer - The writer which will write to the file.

  • Method Details

    • writeSection

      public void writeSection(String spectrumFile, String spectrumTitle, com.compomics.util.experiment.identification.SpectrumIdentificationAssumption spectrumIdentificationAssumption, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, String linePrefix, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Writes the desired section.
      Parameters:
      spectrumFile - The file name of the spectrum.
      spectrumTitle - The title of the spectrum.
      spectrumIdentificationAssumption - The spectrum identification of interest.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      identificationParameters - The identification parameters.
      linePrefix - The line prefix.
      waitingHandler - The waiting handler.
      Throws:
      IOException - exception thrown whenever an error occurred while writing the file

    • writeHeader

      public void writeHeader() throws IOException
      Writes the header of this section.
      Throws:
      IOException - exception thrown whenever an error occurred while writing the file