Package eu.isas.searchgui.processbuilders

Class MsAmandaProcessBuilder

java.lang.Object

eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

eu.isas.searchgui.processbuilders.MsAmandaProcessBuilder

All Implemented Interfaces:

Runnable

public class MsAmandaProcessBuilder
extends SearchGUIProcessBuilder

This class will build files and start a process to perform an MS Amanda 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 Amanda executable.

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

exceptionHandler, waitingHandler

Constructor Summary

Constructors

Constructor

Description

MsAmandaProcessBuilder(File msAmandaDirectory, File msAmandaTempFolder, File mgfFile, File fastaFile, String outputPath, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, 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.
boolean	reportBothBestHitsForTD()	Returns true if target and decoy are ranked separately, false if shared rank.
void	setReportBothBestHitsForTD(boolean reportBothBestHitsForTD)	Set if target and decoy are ranked separately or shared.

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 Amanda executable.

See Also:

• Constant Field Values

Constructor Details

MsAmandaProcessBuilder

public MsAmandaProcessBuilder(File msAmandaDirectory,
 File msAmandaTempFolder,
 File mgfFile,
 File fastaFile,
 String outputPath,
 com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
 com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.exceptions.ExceptionHandler exceptionHandler,
 int nThreads)
                       throws IOException

Constructor.

Parameters:

msAmandaDirectory - directory location of MSAmanda.exe

msAmandaTempFolder - the folder for temp MS Amanda files

mgfFile - the spectrum file

fastaFile - the FASTA file

outputPath - path where to output the results

searchParameters - the search parameters

fastaParameters - the FASTA parameters

waitingHandler - the waiting handler

exceptionHandler - the handler of exceptions

nThreads - the number of threads to use (not supported by ms amanda)

Throws:

IOException - thrown whenever an IO error occurs

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

reportBothBestHitsForTD

public boolean reportBothBestHitsForTD()

Returns true if target and decoy are ranked separately, false if shared rank.

Returns:

true if target and decoy are ranked separately, false if shared rank

setReportBothBestHitsForTD

public void setReportBothBestHitsForTD(boolean reportBothBestHitsForTD)

Set if target and decoy are ranked separately or shared.

Parameters:

reportBothBestHitsForTD - the reportBothBestHitsForTD to set