eu.isas.peptideshaker.export.sections

Class PsPeptideSection

java.lang.Object

eu.isas.peptideshaker.export.sections.PsPeptideSection

public class PsPeptideSection
extends Object

This class outputs the peptide related export features.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
PsPeptideSection(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.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, int nSurroundingAA, String linePrefix, com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch, com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature peptideFeature, boolean validatedOnly, boolean decoys, com.compomics.util.waiting.WaitingHandler waitingHandler) Returns the component of the section corresponding to the given feature.
static String	getPeptideLocalizationText(String proteinAccession, int[] sites) Returns the peptide localization on the given protein as text in the form accession (site1,site2).
static String	getPeptideModificationLocationConfidence(com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch, 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 title of the 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, int nSurroundingAA, String linePrefix, 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

PsPeptideSection

public PsPeptideSection(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 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,
                         int nSurroundingAA,
                         String linePrefix,
                         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 reading or writing a file

getfeature

public static String getfeature(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.parameters.identification.IdentificationParameters identificationParameters,
                                int nSurroundingAA,
                                String linePrefix,
                                com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch,
                                com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature peptideFeature,
                                boolean validatedOnly,
                                boolean decoys,
                                com.compomics.util.waiting.WaitingHandler waitingHandler)

Returns the component of the section corresponding to the given feature.

Parameters:

identification - the identification of the project

identificationFeaturesGenerator - the identification features generator of the project

sequenceProvider - a provider for the protein sequences

proteinDetailsProvider - a provider for protein details

identificationParameters - the identification parameters

nSurroundingAA - the number of surrounding amino acids to export

linePrefix - the line prefix to use.

peptideMatch - the peptide match

peptideFeature - the peptide feature to export

validatedOnly - whether only validated matches should be exported

decoys - whether decoy matches should be exported as well

waitingHandler - the waiting handler

Returns:

the component of the section corresponding to the given feature

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

getPeptideLocalizationText

public static String getPeptideLocalizationText(String proteinAccession,
                                                int[] sites)

Returns the peptide localization on the given protein as text in the form accession (site1,site2).

Parameters:

proteinAccession - the protein accession

sites - the position of the peptide on the protein

Returns:

the peptide localization on the given protein as text

getPeptideModificationLocationConfidence

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

Returns the peptide modification location confidence as a string.

Parameters:

peptideMatch - the peptide match

modificationParameters - the modification parameters

Returns:

the peptide modification location confidence as a string

writeHeader

public void writeHeader()
                 throws IOException

Writes the title of the section.

Throws:

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