eu.isas.peptideshaker.followup

Class SpectrumExporter

java.lang.Object

eu.isas.peptideshaker.followup.SpectrumExporter

public class SpectrumExporter
extends Object

This class can be used to export spectra.

Author:

Marc Vaudel

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SpectrumExporter.ExportType Enum of the different types of export implemented.

Constructor Summary

Constructors

Constructor and Description
SpectrumExporter(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider) Constructor.

Method Summary

Modifier and Type	Method and Description
ArrayList<File>	exportSpectra(File destinationFolder, com.compomics.util.waiting.WaitingHandler waitingHandler, SpectrumExporter.ExportType exportType, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences) Exports the spectra from different categories of PSMs according to the export type.
static File	getDestinationFile(File destinationFolder, String originalFileName, SpectrumExporter.ExportType exportType) Returns the destination file for the given export.
static String	getSuffix(SpectrumExporter.ExportType exportType) Returns the suffix for a spectrum file name.
static boolean	include(String spectrumFile, String spectrumTitle, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, SpectrumExporter.ExportType exportType) Indicates whether a spectrum should be exported.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SpectrumExporter

public SpectrumExporter(com.compomics.util.experiment.identification.Identification identification,
                        com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)

Constructor.

Parameters:

identification - The identification object.

spectrumProvider - The spectrum provider.

Method Detail

exportSpectra

public ArrayList<File> exportSpectra(File destinationFolder,
                                     com.compomics.util.waiting.WaitingHandler waitingHandler,
                                     SpectrumExporter.ExportType exportType,
                                     com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences)
                              throws IOException

Exports the spectra from different categories of PSMs according to the export type. Export format is mgf.

Parameters:

destinationFolder - the folder where to write the spectra

waitingHandler - waiting handler used to display progress and cancel the process. Can be null.

exportType - the type of PSM to export

sequenceMatchingPreferences - the sequence matching preferences

Returns:

ArrayList files containing exported spectra

Throws:

IOException - thrown if an error occurred while writing the file

getDestinationFile

public static File getDestinationFile(File destinationFolder,
                                      String originalFileName,
                                      SpectrumExporter.ExportType exportType)

Returns the destination file for the given export.

Parameters:

destinationFolder - the destination folder

originalFileName - the original file name

exportType - the export type

Returns:

the destination file

include

public static boolean include(String spectrumFile,
                              String spectrumTitle,
                              com.compomics.util.experiment.identification.Identification identification,
                              com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters,
                              SpectrumExporter.ExportType exportType)

Indicates whether a spectrum should be exported.

Parameters:

spectrumFile - the name of the file of the spectrum

spectrumTitle - the spectrum title

identification - the identification object

sequenceMatchingParameters - the sequence matching preferences

exportType - the export type

Returns:

a boolean indicating whether a spectrum should be exported

getSuffix

public static String getSuffix(SpectrumExporter.ExportType exportType)

Returns the suffix for a spectrum file name.

Parameters:

exportType - the type of PSM to be exported

Returns:

the suffix for a spectrum file name