com.compomics.util.experiment.io.massspectrometry.export

Class Ms2Exporter

java.lang.Object

com.compomics.util.experiment.io.massspectrometry.export.Ms2Exporter

public class Ms2Exporter
extends Object

This converter writes spectrum files in MS2 format.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor and Description
Ms2Exporter()

Method Summary

Modifier and Type	Method and Description
static void	mgfToMs2(File mgfFile, File destinationFile, boolean resetScanNumbers) Writes the content of the given file name into the destination file in the ms2 format.
static void	writeHeader(BufferedWriter bw) Writes the header of the file.
static void	writeSpectrum(BufferedWriter bw, MSnSpectrum spectrum, Integer defaultScanNumber) Writes the given spectrum in ms2 format.

Methods inherited from class java.lang.Object

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

Constructor Detail

Ms2Exporter

public Ms2Exporter()

Method Detail

mgfToMs2

public static void mgfToMs2(File mgfFile,
                            File destinationFile,
                            boolean resetScanNumbers)
                     throws IOException

Writes the content of the given file name into the destination file in the ms2 format. The spectra must be loaded in the factory.

Parameters:

mgfFile - the original mgf file

destinationFile - the destination file where to write the spectra

resetScanNumbers - If true the scan numbers are reset to simply indicate the spectrum indexes, first spectrum is scan 1, second is scan 2, etc. Required in order to map back to the mgf.

Throws:

IOException - exception thrown whenever an error occurred while reading or writing a file

writeHeader

public static void writeHeader(BufferedWriter bw)
                        throws IOException

Writes the header of the file.

Parameters:

bw - a buffered writer where to write

Throws:

IOException - exception thrown whenever an error occurred while reading or writing a file

writeSpectrum

public static void writeSpectrum(BufferedWriter bw,
                                 MSnSpectrum spectrum,
                                 Integer defaultScanNumber)
                          throws IOException

Writes the given spectrum in ms2 format.

Parameters:

bw - a buffered writer where to write the spectrum

spectrum - the spectrum of interest

defaultScanNumber - if not null, overrides the scan number given in the file (needed when converting mgf to ms2)

Throws:

IOException - exception thrown whenever an error occurred while reading or writing a file