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

Class MgfFileUtils

java.lang.Object

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

public class MgfFileUtils
extends Object

Utilities for the handling of mgf files.

Author:

Marc Vaudel, Harald Barsnes

Field Summary

Fields

Modifier and Type	Field	Description
static final String[]	EXTENSIONS	The file extension for mgf files.

Constructor Summary

Constructors

Constructor	Description
MgfFileUtils()

Method Summary

Modifier and Type	Method	Description
static void	addMissingPrecursorCharges(File mgfFile, WaitingHandler waitingHandler)	Add missing precursor charges.
static void	addMissingSpectrumTitles(File mgfFile, WaitingHandler waitingHandler)	Adds missing spectrum titles.
static void	removeDuplicateSpectrumTitles(File mgfFile, WaitingHandler waitingHandler)	Removes duplicate spectrum titles (the first occurrence is kept).
static void	removeZeroes(File mgfFile, WaitingHandler waitingHandler)	Removes zero intensity peaks.
static void	renameDuplicateSpectrumTitles(File mgfFile, WaitingHandler waitingHandler)	Renames duplicate spectrum titles.
static ArrayList<MgfIndex>	splitFile(File mgfFile, int nSpectra, WaitingHandler waitingHandler)	Splits an mgf file into smaller ones and returns the indexes of the generated files.

Methods inherited from class java.lang.Object

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

Field Details

EXTENSIONS

public static final String[] EXTENSIONS

The file extension for mgf files.

Constructor Details

MgfFileUtils

public MgfFileUtils()

Method Details

removeDuplicateSpectrumTitles

public static void removeDuplicateSpectrumTitles(File mgfFile,
 WaitingHandler waitingHandler)
                                          throws FileNotFoundException,
IOException,
UnsupportedEncodingException

Removes duplicate spectrum titles (the first occurrence is kept).

Parameters:

mgfFile - the MGF file to validate

waitingHandler - a waitingHandler showing the progress, can be null

Throws:

FileNotFoundException - Exception thrown whenever the file is not found

IOException - Exception thrown whenever an error occurs while reading the file

UnsupportedEncodingException - if the decoding of a spectrum title fails

addMissingSpectrumTitles

public static void addMissingSpectrumTitles(File mgfFile,
 WaitingHandler waitingHandler)
                                     throws FileNotFoundException,
IOException,
UnsupportedEncodingException

Adds missing spectrum titles.

Parameters:

mgfFile - the MGF file to fix

waitingHandler - a waitingHandler showing the progress, can be null

Throws:

FileNotFoundException - Exception thrown whenever the file is not found

IOException - Exception thrown whenever an error occurs while reading the file

UnsupportedEncodingException - if the decoding of a spectrum title fails

addMissingPrecursorCharges

public static void addMissingPrecursorCharges(File mgfFile,
 WaitingHandler waitingHandler)
                                       throws FileNotFoundException,
IOException,
UnsupportedEncodingException

Add missing precursor charges.

Parameters:

mgfFile - the MGF file to fix

waitingHandler - a waitingHandler showing the progress, can be null

Throws:

FileNotFoundException - Exception thrown whenever the file is not found

IOException - Exception thrown whenever an error occurs while reading the file

UnsupportedEncodingException - if the decoding of a spectrum title fails

removeZeroes

public static void removeZeroes(File mgfFile,
 WaitingHandler waitingHandler)
                         throws FileNotFoundException,
IOException,
UnsupportedEncodingException

Removes zero intensity peaks.

Parameters:

mgfFile - the MGF file to fix

waitingHandler - a waitingHandler showing the progress, can be null

Throws:

FileNotFoundException - Exception thrown whenever the file is not found

IOException - Exception thrown whenever an error occurs while reading the file

UnsupportedEncodingException - if the decoding of a spectrum title fails

renameDuplicateSpectrumTitles

public static void renameDuplicateSpectrumTitles(File mgfFile,
 WaitingHandler waitingHandler)
                                          throws FileNotFoundException,
IOException,
UnsupportedEncodingException

Renames duplicate spectrum titles. Adds (2), (3) etc, behind the duplicate spectrum titles.

Parameters:

mgfFile - the MGF file to validate

waitingHandler - a waitingHandler showing the progress

Throws:

FileNotFoundException - Exception thrown whenever the file is not found

IOException - Exception thrown whenever an error occurs while reading the file

UnsupportedEncodingException - if the decoding of a spectrum title fails

splitFile

public static ArrayList<MgfIndex> splitFile(File mgfFile,
 int nSpectra,
 WaitingHandler waitingHandler)
                                     throws FileNotFoundException,
IOException

Splits an mgf file into smaller ones and returns the indexes of the generated files.

Parameters:

mgfFile - the mgf file to split

nSpectra - the number of spectra allowed in the smaller files

waitingHandler - the waitingHandler showing the progress

Returns:

a list of indexes of the generated files

Throws:

FileNotFoundException - exception thrown whenever a file was not found

IOException - exception thrown whenever a problem occurred while reading/writing a file