Package eu.isas.searchgui.processbuilders

Class NovorProcessBuilder

java.lang.Object

eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

eu.isas.searchgui.processbuilders.NovorProcessBuilder

All Implemented Interfaces:

Runnable

public class NovorProcessBuilder
extends SearchGUIProcessBuilder

This class will set up and start a process to run Novor.

Author:

Harald Barsnes, Marc Vaudel

Field Summary

Fields

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

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

exceptionHandler, waitingHandler

Constructor Summary

Constructors

Constructor	Description
NovorProcessBuilder(File novorFolder, File novorTempFolder, File mgfFile, File outputFile, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, boolean isCommandLine, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)	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 Novor executable.

See Also:

• Constant Field Values

Constructor Details

NovorProcessBuilder

public NovorProcessBuilder(File novorFolder,
 File novorTempFolder,
 File mgfFile,
 File outputFile,
 com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
 boolean isCommandLine,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
                    throws IOException,
ClassNotFoundException

Constructor.

Parameters:

novorFolder - the path to the Novor executable

novorTempFolder - the folder for Novor temp files

mgfFile - the spectrum MGF file

outputFile - the output file

searchParameters - the search parameters

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

waitingHandler - the waiting handler

exceptionHandler - the exception handler

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

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

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