eu.isas.peptideshaker.export.sections

Class PsPsmSection

java.lang.Object

eu.isas.peptideshaker.export.sections.PsPsmSection

public class PsPsmSection
extends Object

This class outputs the PSM level export features.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor and Description
PsPsmSection(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	getFeature(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, String linePrefix, com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, com.compomics.util.experiment.identification.peptide_shaker.PSParameter psParameter, com.compomics.util.io.export.features.peptideshaker.PsPsmFeature psmFeature, boolean validatedOnly, boolean decoys, com.compomics.util.waiting.WaitingHandler waitingHandler) Writes the given feature of the current section.
static String	getPeptideModificationLocationConfidence(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters) Returns the peptide modification location confidence as a string.
static String	getProteinGroupText(long proteinGroupKey, com.compomics.util.experiment.identification.Identification identification) Returns a description of the given protein group in the form proteinA,proteinB(confidence).
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, 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 Detail

PsPsmSection

public PsPsmSection(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,
                         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.

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:

IOException - exception thrown if an error occurred while writing to the file.

getFeature

public static String getFeature(com.compomics.util.experiment.identification.Identification identification,
                                com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                                com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                                String linePrefix,
                                com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch,
                                com.compomics.util.experiment.identification.peptide_shaker.PSParameter psParameter,
                                com.compomics.util.io.export.features.peptideshaker.PsPsmFeature psmFeature,
                                boolean validatedOnly,
                                boolean decoys,
                                com.compomics.util.waiting.WaitingHandler waitingHandler)

Writes the given feature of the current section.

Parameters:

identification - the identification of the project

identificationFeaturesGenerator - the identification features generator of the project

identificationParameters - the identification parameters

linePrefix - the line prefix

spectrumMatch - the spectrum match inspected

psParameter - the PeptideShaker parameter of the match

psmFeature - the feature to export

validatedOnly - indicates whether only validated hits should be exported

decoys - indicates whether decoys should be included in the export

waitingHandler - the waiting handler

Returns:

the content corresponding to the given feature of the current section

getProteinGroupText

public static String getProteinGroupText(long proteinGroupKey,
                                         com.compomics.util.experiment.identification.Identification identification)

Returns a description of the given protein group in the form proteinA,proteinB(confidence).

Parameters:

proteinGroupKey - the key of the protein group

identification - the identification object

Returns:

a description of the given protein group

getPeptideModificationLocationConfidence

public static String getPeptideModificationLocationConfidence(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch,
                                                              com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters)

Returns the peptide modification location confidence as a string.

Parameters:

spectrumMatch - the spectrum match

modificationParameters - the PTM profile

Returns:

the peptide modification location confidence as a string

writeHeader

public void writeHeader()
                 throws IOException

Writes the header of this section.

Throws:

IOException - exception thrown whenever an error occurred while writing the file