Package eu.isas.reporter.export.report.sections

Class ReporterPsmSection

java.lang.Object
eu.isas.reporter.export.report.sections.ReporterPsmSection
public class ReporterPsmSection extends Object
This class outputs the PSM level quantification export features.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Summary

    Constructors
    Constructor
    Description
    ReporterPsmSection(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
    static String
    getFeature(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterSettings reporterSettings, long matchKey, com.compomics.util.io.export.features.reporter.ReporterPsmFeatures psmFeatures, String sampleIndex)
    Returns the report component corresponding to a feature at a given channel.
    void
    writeHeader(com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification)
    Writes the header of this section.
    void
    writeSection(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterSettings reporterSettings, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, long[] keys, String linePrefix, int nSurroundingAA, boolean validatedOnly, boolean decoys, 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

    • ReporterPsmSection

      public ReporterPsmSection(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 - indicates whether the line index should be written
      header - indicates whether the table header should be written
      writer - the writer which will write to the file

  • Method Details

    • writeSection

      public void writeSection(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterSettings reporterSettings, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, long[] keys, String linePrefix, int nSurroundingAA, boolean validatedOnly, boolean decoys, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException, InterruptedException, org.apache.commons.math.MathException
      Writes the desired section.
      Parameters:
      identification - the identification of the project
      identificationFeaturesGenerator - the identification features generator of the project
      sequenceProvider - the sequence provider
      spectrumProvider - the spectrum provider
      proteinDetailsProvider - the protein details provider
      quantificationFeaturesGenerator - the quantification features generator containing the quantification information
      reporterIonQuantification - the reporter ion quantification object containing the quantification configuration
      reporterSettings - the reporter settings
      identificationParameters - the identification parameters
      keys - the keys of the PSM matches to output
      linePrefix - the line prefix
      nSurroundingAA - the number of surrounding amino acids to export
      validatedOnly - whether only validated matches should be exported
      decoys - whether decoy matches should be exported as well
      waitingHandler - the waiting handler
      Throws:
      SQLException - exception thrown whenever an error occurred while interacting with the database
      IOException - exception thrown whenever an error occurred while interacting with a file
      ClassNotFoundException - exception thrown whenever an error occurred while deserializing an object
      InterruptedException - exception thrown whenever a threading error occurred
      org.apache.commons.math.MathException - exception thrown whenever an error occurred while transforming the ratios
      IllegalArgumentException

    • getFeature

      public static String getFeature(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterSettings reporterSettings, long matchKey, com.compomics.util.io.export.features.reporter.ReporterPsmFeatures psmFeatures, String sampleIndex) throws SQLException, IOException, ClassNotFoundException, InterruptedException
      Returns the report component corresponding to a feature at a given channel.
      Parameters:
      identification - the identification of the project
      spectrumProvider - the spectrum provider
      quantificationFeaturesGenerator - the quantification features generator
      reporterIonQuantification - the reporter ion quantification object containing the quantification configuration
      reporterSettings - the reporter settings
      matchKey - the match key
      psmFeatures - the PSM feature to export
      sampleIndex - the index of the sample in case the feature is channel dependent, ignored otherwise
      Returns:
      the report component corresponding to a feature at a given channel
      Throws:
      SQLException - exception thrown whenever an error occurred while interacting with the database
      IOException - exception thrown whenever an error occurred while interacting with a file
      ClassNotFoundException - exception thrown whenever an error occurred while deserializing an object
      InterruptedException - exception thrown whenever a threading error occurred

    • writeHeader

      public void writeHeader(com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification) throws IOException
      Writes the header of this section.
      Parameters:
      reporterIonQuantification - the reporter ion quantification object containing the quantification configuration
      Throws:
      IOException - exception thrown whenever an error occurred while interacting with a file