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

Class MgfFileWriter

java.lang.Object

com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileWriter

All Implemented Interfaces:

AutoCloseable

public class MgfFileWriter
extends Object
implements AutoCloseable

This class writes spectrum files in Mascot Generic File (mgf) format.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor	Description
MgfFileWriter()	Empty default constructor.
MgfFileWriter(File destinationFile)	Constructor.

Method Summary

Modifier and Type	Method	Description
static String	asMgf(String spectrumTitle, Spectrum spectrum)	Returns the spectrum as an mgf bloc.
static String	asMgf(String spectrumTitle, Spectrum spectrum, TreeMap<String,String> additionalTags)	Returns the spectrum as an mgf bloc.
void	close()
void	writeSpectrum(String spectrumTitle, Spectrum spectrum)	Writes the given spectrum to the file.

Methods inherited from class java.lang.Object

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

Constructor Details

MgfFileWriter

public MgfFileWriter()

Empty default constructor.

MgfFileWriter

public MgfFileWriter(File destinationFile)

Constructor.

Parameters:

destinationFile - The file where to write.

Method Details

writeSpectrum

public void writeSpectrum(String spectrumTitle,
 Spectrum spectrum)

Writes the given spectrum to the file.

Parameters:

spectrumTitle - The title of the spectrum to write.

spectrum - The spectrum to write.

close

public void close()

Specified by:

close in interface AutoCloseable

asMgf

public static String asMgf(String spectrumTitle,
 Spectrum spectrum)

Returns the spectrum as an mgf bloc.

Parameters:

spectrumTitle - The title of the spectrum.

spectrum - The spectrum.

Returns:

the spectrum as an mgf bloc

asMgf

public static String asMgf(String spectrumTitle,
 Spectrum spectrum,
 TreeMap<String,String> additionalTags)

Returns the spectrum as an mgf bloc.

Parameters:

spectrumTitle - The title of the spectrum.

spectrum - The spectrum.

additionalTags - additional tags which will be added after the BEGIN IONS tag in alphabetic order

Returns:

the peak list as an mgf bloc