eu.isas.peptideshaker.export.sections

Class PsFragmentSection

java.lang.Object

eu.isas.peptideshaker.export.sections.PsFragmentSection

public class PsFragmentSection
extends Object

This class outputs the PSM related export features.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
PsFragmentSection(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
void	writeHeader() Writes the header of this section.
void	writeSection(String spectrumFile, String spectrumTitle, com.compomics.util.experiment.identification.SpectrumIdentificationAssumption spectrumIdentificationAssumption, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, String linePrefix, 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

PsFragmentSection

public PsFragmentSection(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 indicates whether the table header should be written.

writer - The writer which will write to the file.

Method Detail

writeSection

public void writeSection(String spectrumFile,
                         String spectrumTitle,
                         com.compomics.util.experiment.identification.SpectrumIdentificationAssumption spectrumIdentificationAssumption,
                         com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                         com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                         com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                         String linePrefix,
                         com.compomics.util.waiting.WaitingHandler waitingHandler)
                  throws IOException

Writes the desired section.

Parameters:

spectrumFile - The file name of the spectrum.

spectrumTitle - The title of the spectrum.

spectrumIdentificationAssumption - The spectrum identification of interest.

sequenceProvider - The sequence provider.

spectrumProvider - The spectrum provider.

identificationParameters - The identification parameters.

linePrefix - The line prefix.

waitingHandler - The waiting handler.

Throws:

IOException - exception thrown whenever an error occurred while writing the 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