Package eu.isas.searchgui.processbuilders

Class SageProcessBuilder

java.lang.Object

eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

eu.isas.searchgui.processbuilders.SageProcessBuilder

All Implemented Interfaces:

Runnable

public class SageProcessBuilder
extends SearchGUIProcessBuilder

ProcessBuilder for the Sage search engine.

Author:

Harald Barsnes

Field Summary

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

exceptionHandler, waitingHandler

Constructor Summary

Constructors

Constructor	Description
SageProcessBuilder(File sageFolder, File sageTempFolder, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, File spectrumFile, File fastaFile, String decoyTag, 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.
static String	getExecutableFileName()	Returns the name of the Sage executable.
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

Constructor Details

SageProcessBuilder

public SageProcessBuilder(File sageFolder,
 File sageTempFolder,
 com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
 File spectrumFile,
 File fastaFile,
 String decoyTag,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.exceptions.ExceptionHandler exceptionHandler,
 int nThreads)
                   throws IOException

Constructor.

Parameters:

sageFolder - the Sage folder

sageTempFolder - the temp folder for Sage files

searchParameters - the search parameters

spectrumFile - the spectrum file

fastaFile - the FASTA file

decoyTag - the FASTA file decoy tag

waitingHandler - the waiting handler

exceptionHandler - the handler of exceptions

nThreads - the number of threads

Throws:

IOException - thrown if there are problems creating the Sage 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

getExecutableFileName

public static String getExecutableFileName()

Returns the name of the Sage executable.

Returns:

the name of the Sage executable