Package eu.isas.searchgui.processbuilders

Class MyriMatchProcessBuilder

java.lang.Object

eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

eu.isas.searchgui.processbuilders.MyriMatchProcessBuilder

All Implemented Interfaces:

Runnable

public class MyriMatchProcessBuilder
extends SearchGUIProcessBuilder

This class will set up and start a process to perform a MyriMatch search.

Author:

Harald Barsnes, Marc Vaudel

Field Summary

Fields

Modifier and Type	Field	Description
static final String	EXECUTABLE_FILE_NAME	The name of the MyriMatch executable.

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

exceptionHandler, waitingHandler

Constructor Summary

Constructors

Constructor	Description
MyriMatchProcessBuilder(File myriMatchDirectory, File mgfFile, File fastaFile, File outputFolder, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, int nThreads)	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 MyriMatch executable.

See Also:

• Constant Field Values

Constructor Details

MyriMatchProcessBuilder

public MyriMatchProcessBuilder(File myriMatchDirectory,
 File mgfFile,
 File fastaFile,
 File outputFolder,
 com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.exceptions.ExceptionHandler exceptionHandler,
 int nThreads)

Constructor.

Parameters:

myriMatchDirectory - directory location of MyriMatch executable

mgfFile - the file containing the spectra

fastaFile - the FASTA file

outputFolder - folder where to output the results

searchParameters - the search parameters

waitingHandler - the waiting handler

exceptionHandler - the handler of exceptions

nThreads - the number of threads to use

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