Package eu.isas.peptideshaker.export.sections

Class PsProteinSection

java.lang.Object
eu.isas.peptideshaker.export.sections.PsProteinSection
public class PsProteinSection extends Object
This class outputs the protein related export features.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Summary

    Constructors
    Constructor
    Description
    PsProteinSection(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.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, int nSurroundingAas, long proteinKey, com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch, com.compomics.util.experiment.identification.peptide_shaker.PSParameter psParameter, com.compomics.util.io.export.features.peptideshaker.PsProteinFeature tempProteinFeatures, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Returns the part of the desired section.
    static String
    getFeature(com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, int nSurroundingAas, long proteinKey, com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch, String fractionName, com.compomics.util.experiment.identification.peptide_shaker.PSParameter psParameter, com.compomics.util.io.export.features.peptideshaker.PsProteinFeature tempProteinFeatures, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Returns the part of the desired section.
    void
    writeHeader(ArrayList<String> fractions)
    Writes the header of the protein 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.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, long[] keys, 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

    • PsProteinSection

      public PsProteinSection(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. ProteinFeatures as main features. If Peptide or protein features are selected, they will be added as sub-sections.
      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.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, long[] keys, int nSurroundingAa, boolean validatedOnly, boolean decoys, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Writes the desired section.
      Parameters:
      identification - The identification of the project.
      identificationFeaturesGenerator - The identification features generator of the project.
      sequenceProvider - The sequence provider.
      proteinDetailsProvider - The protein details provider.
      spectrumProvider - The spectrum provider.
      geneMaps - The gene maps.
      identificationParameters - The identification parameters.
      keys - The keys of the PSM matches to output.
      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:
      IOException - exception thrown whenever an error occurred while writing to the file

    • getFeature

      public static String getFeature(com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, int nSurroundingAas, long proteinKey, com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch, com.compomics.util.experiment.identification.peptide_shaker.PSParameter psParameter, com.compomics.util.io.export.features.peptideshaker.PsProteinFeature tempProteinFeatures, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Returns the part of the desired section.
      Parameters:
      identificationFeaturesGenerator - the identification features generator of the project
      sequenceProvider - the sequence provider
      proteinDetailsProvider - the protein details provider
      geneMaps - the gene maps
      identificationParameters - the identification parameters
      nSurroundingAas - in case a peptide export is included with surrounding amino acids, the number of surrounding amino acids to use
      proteinKey - the key of the protein match being written
      proteinMatch - the protein match, can be null if not needed
      psParameter - the protein match parameter containing the PeptideShaker parameters, can be null if not needed
      tempProteinFeatures - the protein feature to write
      waitingHandler - the waiting handler
      Returns:
      the string to write

    • getFeature

      public static String getFeature(com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, int nSurroundingAas, long proteinKey, com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch, String fractionName, com.compomics.util.experiment.identification.peptide_shaker.PSParameter psParameter, com.compomics.util.io.export.features.peptideshaker.PsProteinFeature tempProteinFeatures, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Returns the part of the desired section.
      Parameters:
      identificationFeaturesGenerator - the identification features generator of the project
      sequenceProvider - the sequence provider
      proteinDetailsProvider - the protein details provider
      geneMaps - the gene maps
      identificationParameters - the identification parameters
      nSurroundingAas - in case a peptide export is included with surrounding amino acids, the number of surrounding amino acids to use
      proteinKey - the key of the protein match being written
      proteinMatch - the protein match, can be null if not needed
      fractionName - the name of the fraction
      psParameter - the protein match parameter containing the PeptideShaker parameters, can be null if not needed
      tempProteinFeatures - the protein feature to write
      waitingHandler - the waiting handler
      Returns:
      the string to write

    • writeHeader

      public void writeHeader(ArrayList<String> fractions) throws IOException
      Writes the header of the protein section.
      Parameters:
      fractions - the fraction names
      Throws:
      IOException - exception thrown whenever an error occurred while writing the file