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 and 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 and 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 Detail

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 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.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