Package eu.isas.reporter.export.report.sections

Class ReporterProteinSection

java.lang.Object

eu.isas.reporter.export.report.sections.ReporterProteinSection

public class ReporterProteinSection
extends Object

This class outputs the protein related export features.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor	Description
ReporterProteinSection(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.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, long proteinKey, com.compomics.util.io.export.features.reporter.ReporterProteinFeatures proteinFeatures, String sampleIndex, com.compomics.util.waiting.WaitingHandler waitingHandler)	Returns the report component corresponding to a feature at a given channel.
void	writeHeader(com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification)	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.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterSettings reporterSettings, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, long[] keys, int nSurroundingAas, 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

ReporterProteinSection

public ReporterProteinSection(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.mass_spectrometry.SpectrumProvider spectrumProvider,
 com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
 com.compomics.util.experiment.biology.genes.GeneMaps geneMaps,
 QuantificationFeaturesGenerator quantificationFeaturesGenerator,
 com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification,
 ReporterSettings reporterSettings,
 com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
 long[] keys,
 int nSurroundingAas,
 boolean validatedOnly,
 boolean decoys,
 com.compomics.util.waiting.WaitingHandler waitingHandler)
                  throws IOException,
IllegalArgumentException,
SQLException,
ClassNotFoundException,
InterruptedException,
org.apache.commons.math.MathException

Writes the desired section.

Parameters:

identification - the identification of the project

identificationFeaturesGenerator - the identification features generator of the project

sequenceProvider - the sequence provider

spectrumProvider - the spectrum provider

proteinDetailsProvider - the protein details provider

geneMaps - the gene maps

quantificationFeaturesGenerator - the quantification features generator containing the quantification information

reporterIonQuantification - the reporter ion quantification object containing the quantification configuration

reporterSettings - the reporter settings

identificationParameters - the identification parameters

keys - the keys of the protein matches to output. if null all proteins will be exported.

nSurroundingAas - in case a peptide export is included with surrounding amino-acids, the number of surrounding amino acids to use

validatedOnly - whether only validated matches should be exported

decoys - whether decoy matches should be exported as well

waitingHandler - the waiting handler

Throws:

SQLException - exception thrown whenever an error occurred while interacting with the database

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

ClassNotFoundException - exception thrown whenever an error occurred while deserializing an object

InterruptedException - exception thrown whenever a threading error occurred

org.apache.commons.math.MathException - exception thrown whenever an error occurred while transforming the ratios

IllegalArgumentException

getFeature

public static String getFeature(com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
 QuantificationFeaturesGenerator quantificationFeaturesGenerator,
 com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification,
 long proteinKey,
 com.compomics.util.io.export.features.reporter.ReporterProteinFeatures proteinFeatures,
 String sampleIndex,
 com.compomics.util.waiting.WaitingHandler waitingHandler)
                         throws SQLException,
IOException,
ClassNotFoundException,
InterruptedException

Returns the report component corresponding to a feature at a given channel.

Parameters:

spectrumProvider - the spectrum provider

quantificationFeaturesGenerator - the quantification features generator

reporterIonQuantification - the reporter ion quantification object containing the quantification configuration

proteinKey - the protein key

proteinFeatures - the protein feature to export

sampleIndex - the index of the sample in case the feature is channel dependent, ignored otherwise

waitingHandler - the waiting handler

Returns:

the report component corresponding to a feature at a given channel

Throws:

SQLException - exception thrown whenever an error occurred while interacting with the database

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

ClassNotFoundException - exception thrown whenever an error occurred while deserializing an object

InterruptedException - exception thrown whenever a threading error occurred

writeHeader

public void writeHeader(com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification)
                 throws IOException

Writes the header of the protein section.

Parameters:

reporterIonQuantification - the reporter ion quantification object containing the quantification configuration

Throws:

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