Package eu.isas.searchgui.processbuilders

Class TandemProcessBuilder

java.lang.Object

eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

eu.isas.searchgui.processbuilders.TandemProcessBuilder

All Implemented Interfaces:

Runnable

public class TandemProcessBuilder
extends SearchGUIProcessBuilder

This class will build files and start a process to perform an X!Tandem search.

Author:

Marc Vaudel, Harald Barsnes

Field Summary

Fields

Modifier and Type	Field	Description
static final String	EXECUTABLE_FILE_NAME	The name of the X!Tandem executable.

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

exceptionHandler, waitingHandler

Constructor Summary

Constructors

Constructor	Description
TandemProcessBuilder(File xTandem_directory, File xTandemTempFolder, File mgfFile, File fastaFile, String outputPath, 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	getASelected()	Returns yes if the a ions are selected, no otherwise.
String	getBSelected()	Returns yes if the b ions are selected, no otherwise.
String	getCSelected()	Returns yes if the c ions are selected, no otherwise.
String	getCurrentlyProcessedFileName()	Returns the file name of the currently processed file.
String	getType()	Returns the type of the process.
String	getXSelected()	Returns yes if the x ions are selected, no otherwise.
String	getYSelected()	Returns yes if the y ions are selected, no otherwise.
String	getZSelected()	Returns yes if the z ions are selected, no otherwise.

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 X!Tandem executable.

See Also:

• Constant Field Values

Constructor Details

TandemProcessBuilder

public TandemProcessBuilder(File xTandem_directory,
 File xTandemTempFolder,
 File mgfFile,
 File fastaFile,
 String outputPath,
 com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.exceptions.ExceptionHandler exceptionHandler,
 int nThreads)

Constructor.

Parameters:

xTandem_directory - directory location of tandem.exe

xTandemTempFolder - folder for XTandem temp files

mgfFile - the spectrum file

fastaFile - the FASTA file

outputPath - path 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

getXSelected

public String getXSelected()

Returns yes if the x ions are selected, no otherwise.

Returns:

whether the x ions are to be searched for.

getYSelected

public String getYSelected()

Returns yes if the y ions are selected, no otherwise.

Returns:

whether the y ions are to be searched for.

getZSelected

public String getZSelected()

Returns yes if the z ions are selected, no otherwise.

Returns:

whether the z ions are to be searched for.

getASelected

public String getASelected()

Returns yes if the a ions are selected, no otherwise.

Returns:

whether the a ions are to be searched for.

getBSelected

public String getBSelected()

Returns yes if the b ions are selected, no otherwise.

Returns:

whether the b ions are to be searched for.

getCSelected

public String getCSelected()

Returns yes if the c ions are selected, no otherwise.

Returns:

whether the c ions are to be searched for.