com.compomics.util.experiment.io.massspectrometry

Class MgfReader

java.lang.Object

com.compomics.util.experiment.io.massspectrometry.MgfReader

public class MgfReader
extends Object

This class will read an MGF file.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor and Description
MgfReader() General constructor for an mgf reader.

Method Summary

Modifier and Type	Method and Description
static void	addMissingPrecursorCharges(File mgfFile, WaitingHandler waitingHandler) Add missing precursor charges.
static void	addMissingSpectrumTitles(File mgfFile, WaitingHandler waitingHandler) Adds missing spectrum titles.
static MgfIndex	getIndexMap(File mgfFile) Returns the index of all spectra in the given mgf file.
static MgfIndex	getIndexMap(File mgfFile, WaitingHandler waitingHandler) Returns the index of all spectra in the given MGF file.
static Precursor	getPrecursor(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile, Long index, String fileName) Returns the next precursor starting from the given index.
ArrayList<MSnSpectrum>	getSpectra(File aFile) Reads an MGF file and retrieves a list of spectra.
static MSnSpectrum	getSpectrum(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile, long index, String fileName) Returns the next spectrum starting from the given index.
static MSnSpectrum	getSpectrum(BufferedReader br, String fileName) Returns the next spectrum found in the mgf file.
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.
ArrayList<MgfIndex>	splitFile(File mgfFile, int nSpectra, WaitingHandler waitingHandler) Splits an mgf file into smaller ones and returns the indexes of the generated files.
static void	writeAplFile(File mgfFile, File aplFile, String fragmentation) Writes an apl file from an MGF file.

Methods inherited from class java.lang.Object

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

Constructor Detail

MgfReader

public MgfReader()

General constructor for an mgf reader.

Method Detail

getSpectrum

public static MSnSpectrum getSpectrum(BufferedReader br,
                                      String fileName)
                               throws IOException

Returns the next spectrum found in the mgf file. Null if none found.

Parameters:

br - a buffered reader

fileName - the name of the mgf file

Returns:

the next spectrum found in the mgf file

Throws:

IOException - if an IOException occurs

getSpectra

public ArrayList<MSnSpectrum> getSpectra(File aFile)
                                  throws FileNotFoundException,
                                         IOException,
                                         IllegalArgumentException

Reads an MGF file and retrieves a list of spectra.

Parameters:

aFile - the mgf file

Returns:

list of MSnSpectra imported from the file

Throws:

FileNotFoundException - Exception thrown if a problem is encountered reading the file

IOException - Exception thrown if a problem is encountered reading the file

IllegalArgumentException - thrown when a parameter in the file cannot be parsed correctly

getIndexMap

public static MgfIndex getIndexMap(File mgfFile)
                            throws FileNotFoundException,
                                   IOException

Returns the index of all spectra in the given mgf file.

Parameters:

mgfFile - the given mgf file

Returns:

the index of all spectra

Throws:

FileNotFoundException - Exception thrown whenever the file is not found

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

getIndexMap

public static MgfIndex getIndexMap(File mgfFile,
                                   WaitingHandler waitingHandler)
                            throws FileNotFoundException,
                                   IOException

Returns the index of all spectra in the given MGF file.

Parameters:

mgfFile - the given MGF file

waitingHandler - a waitingHandler showing the progress

Returns:

the index of all spectra

Throws:

FileNotFoundException - Exception thrown whenever the file is not found

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

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 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

getSpectrum

public static MSnSpectrum getSpectrum(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile,
                                      long index,
                                      String fileName)
                               throws IOException,
                                      IllegalArgumentException

Returns the next spectrum starting from the given index.

Parameters:

bufferedRandomAccessFile - The random access file of the inspected mgf file

index - The index where to start looking for the spectrum

fileName - The name of the MGF file

Returns:

The next spectrum encountered

Throws:

IOException - Exception thrown whenever an error is encountered while reading the spectrum

IllegalArgumentException - Exception thrown whenever the file is not of a compatible format

getPrecursor

public static Precursor getPrecursor(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile,
                                     Long index,
                                     String fileName)
                              throws IOException,
                                     IllegalArgumentException

Returns the next precursor starting from the given index.

Parameters:

bufferedRandomAccessFile - The random access file of the inspected mgf file

index - The index where to start looking for the spectrum

fileName - The name of the mgf file

Returns:

The next spectrum encountered

Throws:

IOException - Exception thrown whenever an error is encountered while reading the spectrum

IllegalArgumentException - Exception thrown whenever the file is not of a compatible format

writeAplFile

public static void writeAplFile(File mgfFile,
                                File aplFile,
                                String fragmentation)
                         throws FileNotFoundException,
                                IOException,
                                IllegalArgumentException

Writes an apl file from an MGF file. @TODO: move to massspectrometry.export

Parameters:

mgfFile - the mgf file

aplFile - the target apl file

fragmentation - the fragmentation method used

Throws:

FileNotFoundException - exception thrown whenever a file was not found

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

IllegalArgumentException - exception thrown whenever the mgf file is truncated in the middle of a spectrum