eu.isas.peptideshaker.export.sections

Class PsIdentificationAlgorithmMatchesSection

java.lang.Object

eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection

public class PsIdentificationAlgorithmMatchesSection
extends Object

This report section contains the results of the identification algorithms.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor and Description
PsIdentificationAlgorithmMatchesSection(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 and Description
static String	getPeptideAssumptionFeature(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.parameters.identification.IdentificationParameters identificationParameters, String linePrefix, int nSurroundingAA, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, String spectrumFile, String spectrumTitle, com.compomics.util.experiment.identification.peptide_shaker.PSParameter psParameter, com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature exportFeature, com.compomics.util.waiting.WaitingHandler waitingHandler) Writes the feature associated to the match of the given peptide assumption.
static String	getTagAssumptionFeature(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, String linePrefix, com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption tagAssumption, String spectrumFile, String spectrumTitle, com.compomics.util.experiment.identification.peptide_shaker.PSParameter psParameter, com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature exportFeature, com.compomics.util.waiting.WaitingHandler waitingHandler) Writes the feature associated to the match of the given tag assumption.
void	writeHeader() 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.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, long[] keys, String linePrefix, int nSurroundingAA, 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 Detail

PsIdentificationAlgorithmMatchesSection

public PsIdentificationAlgorithmMatchesSection(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 indicating whether the table header should be written.

writer - The writer which will write to the file.

Method Detail

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.parameters.identification.IdentificationParameters identificationParameters,
                         long[] keys,
                         String linePrefix,
                         int nSurroundingAA,
                         com.compomics.util.waiting.WaitingHandler waitingHandler)
                  throws IOException

Writes the desired section. Exports all algorithm assumptions including the decoy and non-validated matches.

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.

identificationParameters - The identification parameters.

keys - The keys of the spectrum matches to output.

linePrefix - The line prefix.

nSurroundingAA - The number of surrounding amino acids to export.

waitingHandler - The waiting handler.

Throws:

IOException - exception thrown whenever an error occurred while interacting with a 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

getPeptideAssumptionFeature

public static String getPeptideAssumptionFeature(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.parameters.identification.IdentificationParameters identificationParameters,
                                                 String linePrefix,
                                                 int nSurroundingAA,
                                                 com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption,
                                                 String spectrumFile,
                                                 String spectrumTitle,
                                                 com.compomics.util.experiment.identification.peptide_shaker.PSParameter psParameter,
                                                 com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature exportFeature,
                                                 com.compomics.util.waiting.WaitingHandler waitingHandler)

Writes the feature associated to the match of the given peptide assumption.

Parameters:

identification - The identification of the project.

identificationFeaturesGenerator - The identification features generator of the project.

sequenceProvider - The provider for the protein sequences.

proteinDetailsProvider - The provider for protein details.

spectrumProvider - The spectrum provider.

identificationParameters - The identification parameters.

linePrefix - The line prefix.

nSurroundingAA - The number of surrounding amino acids to export.

peptideAssumption - The assumption for the match to inspect.

spectrumFile - The name of the file of the spectrum.

spectrumTitle - The title of the spectrum.

psParameter - The PeptideShaker parameter of the match.

exportFeature - The feature to export.

waitingHandler - The waiting handler.

Returns:

The content corresponding to the given feature of the current section.

getTagAssumptionFeature

public static String getTagAssumptionFeature(com.compomics.util.experiment.identification.Identification identification,
                                             com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                                             com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                             com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                                             String linePrefix,
                                             com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption tagAssumption,
                                             String spectrumFile,
                                             String spectrumTitle,
                                             com.compomics.util.experiment.identification.peptide_shaker.PSParameter psParameter,
                                             com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature exportFeature,
                                             com.compomics.util.waiting.WaitingHandler waitingHandler)

Writes the feature associated to the match of the given tag assumption.

Parameters:

identification - The identification of the project.

identificationFeaturesGenerator - The identification features generator of the project.

spectrumProvider - the spectrum provider

identificationParameters - The identification parameters.

linePrefix - The line prefix.

spectrumFile - The name of the file of the spectrum.

spectrumTitle - The title of the spectrum.

tagAssumption - The assumption for the match to inspect.

psParameter - The PeptideShaker parameter of the match.

exportFeature - The feature to export.

waitingHandler - The waiting handler.

Returns:

The content corresponding to the given feature of the current section.