Package com.compomics.util.experiment.io.mass_spectrometry

Class MsFileExporter

java.lang.Object

com.compomics.util.experiment.io.mass_spectrometry.MsFileExporter

public class MsFileExporter
extends Object

This class writes ms files in various formats.

Author:

Marc Vaudel, Harald Barsnes

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	MsFileExporter.Format	Enum of the supported export formats.

Constructor Summary

Constructors

Constructor	Description
MsFileExporter()

Method Summary

Modifier and Type	Method	Description
static void	writeAplFile(SpectrumProvider spectrumProvider, boolean includeAllSpectrumLevels, String fileNameWithoutExtension, File destinationFile, SearchParameters searchParameters, WaitingHandler waitingHandler)	Writes the spectra of a file in the Andromeda peak list (apl) format.
static void	writeMgfFile(SpectrumProvider spectrumProvider, boolean includeAllSpectrumLevels, String fileNameWithoutExtension, File destinationFile, WaitingHandler waitingHandler)	Writes the spectra of a file in the Mascot Generic File (mgf) format.
static void	writeMs2File(SpectrumProvider spectrumProvider, boolean includeAllSpectrumLevels, String fileNameWithoutExtension, File destinationFile, WaitingHandler waitingHandler)	Writes the spectra of a file in the ms2 format.
static void	writeMsFile(SpectrumProvider spectrumProvider, boolean includeAllSpectrumLevels, String fileNameWithoutExtension, File destinationFile, MsFileExporter.Format format, SearchParameters searchParameters, WaitingHandler waitingHandler)	Writes the spectra of a file in the given format.

Methods inherited from class java.lang.Object

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

Constructor Details

MsFileExporter

public MsFileExporter()

Method Details

writeMsFile

public static void writeMsFile(SpectrumProvider spectrumProvider,
 boolean includeAllSpectrumLevels,
 String fileNameWithoutExtension,
 File destinationFile,
 MsFileExporter.Format format,
 SearchParameters searchParameters,
 WaitingHandler waitingHandler)

Writes the spectra of a file in the given format.

Parameters:

spectrumProvider - The spectrum provider to use to get the spectra.

includeAllSpectrumLevels - If true, all spectrum levels will be included, if false only MS2 spectra are included.

fileNameWithoutExtension - The name of the file to export.

destinationFile - The file where to write.

format - The format to write in.

searchParameters - The search parameters.

waitingHandler - The waiting handler to use to inform on progress and allow cancelling.

writeAplFile

public static void writeAplFile(SpectrumProvider spectrumProvider,
 boolean includeAllSpectrumLevels,
 String fileNameWithoutExtension,
 File destinationFile,
 SearchParameters searchParameters,
 WaitingHandler waitingHandler)

Writes the spectra of a file in the Andromeda peak list (apl) format.

Parameters:

spectrumProvider - The spectrum provider to use to get the spectra.

includeAllSpectrumLevels - If true, all spectrum levels will be included, if false only MS2 spectra are included.

fileNameWithoutExtension - The name of the file to export.

destinationFile - The file where to write.

searchParameters - The search parameters.

waitingHandler - The waiting handler to use to inform on progress and allow cancelling.

writeMgfFile

public static void writeMgfFile(SpectrumProvider spectrumProvider,
 boolean includeAllSpectrumLevels,
 String fileNameWithoutExtension,
 File destinationFile,
 WaitingHandler waitingHandler)

Writes the spectra of a file in the Mascot Generic File (mgf) format.

Parameters:

spectrumProvider - The spectrum provider to use to get the spectra.

includeAllSpectrumLevels - If true, all spectrum levels will be included, if false only MS2 spectra are included.

fileNameWithoutExtension - The name of the file to export.

destinationFile - The file where to write.

waitingHandler - The waiting handler to use to inform on progress and allow cancelling.

writeMs2File

public static void writeMs2File(SpectrumProvider spectrumProvider,
 boolean includeAllSpectrumLevels,
 String fileNameWithoutExtension,
 File destinationFile,
 WaitingHandler waitingHandler)

Writes the spectra of a file in the ms2 format.

Parameters:

spectrumProvider - The spectrum provider to use to get the spectra.

includeAllSpectrumLevels - If true, all spectrum levels will be included, if false only MS2 spectra are included.

fileNameWithoutExtension - The name of the file to export.

destinationFile - The file where to write.

waitingHandler - The waiting handler to use to inform on progress and allow cancelling.