Package eu.isas.searchgui.processbuilders

Class CometProcessBuilder

java.lang.Object

eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

eu.isas.searchgui.processbuilders.CometProcessBuilder

All Implemented Interfaces:

Runnable

public class CometProcessBuilder
extends SearchGUIProcessBuilder

ProcessBuilder for the Comet search engine.

Author:

Marc Vaudel, Harald Barsnes

Field Summary

Fields

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

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

exceptionHandler, waitingHandler

Constructor Summary

Constructors

Constructor	Description
CometProcessBuilder(File cometFolder, File cometTempFolder, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, File spectrumFile, File fastaFile, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, int nThreads, Double refMass)	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 Comet executable.

See Also:

• Constant Field Values

Constructor Details

CometProcessBuilder

public CometProcessBuilder(File cometFolder,
 File cometTempFolder,
 com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
 File spectrumFile,
 File fastaFile,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.exceptions.ExceptionHandler exceptionHandler,
 int nThreads,
 Double refMass)
                    throws IOException

Constructor.

Parameters:

cometFolder - the Comet folder

cometTempFolder - the temp folder for Comet files

searchParameters - the search parameters

spectrumFile - the spectrum file

fastaFile - the FASTA file

waitingHandler - the waiting handler

exceptionHandler - the handler of exceptions

nThreads - the number of threads

refMass - a reference mass to convert fragment ion tolerance from ppm to Dalton

Throws:

IOException - thrown if there are problems creating the Comet parameter file

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