Package eu.isas.searchgui.processbuilders

Class MsgfProcessBuilder

java.lang.Object

eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

eu.isas.searchgui.processbuilders.MsgfProcessBuilder

All Implemented Interfaces:

Runnable

public class MsgfProcessBuilder
extends SearchGUIProcessBuilder

This class will set up and start a process to perform an MS-GF+ search.

Author:

Harald Barsnes, Marc Vaudel

Field Summary

Fields

Modifier and Type	Field	Description
static final String	EXECUTABLE_FILE_NAME	The name of the MS-GF+ executable.

Fields inherited from class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

exceptionHandler, waitingHandler

Constructor Summary

Constructors

Constructor	Description
MsgfProcessBuilder(File msgfDirectory, File msgfTempFolder, File mgfFile, File fastaFile, File outputFile, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, int nThreads, boolean isCommandLine)	Constructor.

Method Summary

Modifier and Type	Method	Description
String	getCurrentlyProcessedFileName()	Returns the file name of the currently processed file.
String	getType()	Returns the type of the process.

Methods inherited from class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

endProcess, run, startProcess

Methods inherited from class java.lang.Object

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

Field Details

EXECUTABLE_FILE_NAME

public static final String EXECUTABLE_FILE_NAME

The name of the MS-GF+ executable.

See Also:

• Constant Field Values

Constructor Details

MsgfProcessBuilder

public MsgfProcessBuilder(File msgfDirectory,
 File msgfTempFolder,
 File mgfFile,
 File fastaFile,
 File outputFile,
 com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.exceptions.ExceptionHandler exceptionHandler,
 int nThreads,
 boolean isCommandLine)
                   throws IOException,
ClassNotFoundException

Constructor.

Parameters:

msgfDirectory - directory location of MSGFPlus.jar

msgfTempFolder - the temp folder for MSGF+

mgfFile - the file containing the spectra

fastaFile - the FASTA file

outputFile - the output file

searchParameters - the search parameters

waitingHandler - the waiting handler

exceptionHandler - the handler of exceptions

nThreads - the number of threads to use

isCommandLine - true if run from the command line, false if GUI

Throws:

IOException - exception thrown whenever an error occurred while getting the Java home

ClassNotFoundException - exception thrown whenever an error occurred while getting the SearchGUI path

Method Details

getType

public String getType()

Description copied from class: SearchGUIProcessBuilder

Returns the type of the process.

Specified by:

getType in class SearchGUIProcessBuilder

Returns:

the type of the process

getCurrentlyProcessedFileName

public String getCurrentlyProcessedFileName()

Description copied from class: SearchGUIProcessBuilder

Returns the file name of the currently processed file.

Specified by:

getCurrentlyProcessedFileName in class SearchGUIProcessBuilder

Returns:

the file name of the currently processed file