Package eu.isas.searchgui.processbuilders

Class MetaMorpheusProcessBuilder

java.lang.Object

eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

eu.isas.searchgui.processbuilders.MetaMorpheusProcessBuilder

All Implemented Interfaces:

Runnable

public class MetaMorpheusProcessBuilder
extends SearchGUIProcessBuilder

ProcessBuilder for the MetaMorpheus search engine.

Author:

Harald Barsnes

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	MetaMorpheusProcessBuilder.MetaMorpheusTaskType	The available MetaMorpheus task types.

Field Summary

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

exceptionHandler, waitingHandler

Constructor Summary

Constructors

Constructor	Description
MetaMorpheusProcessBuilder(File metaMorpheusFolder, boolean metaMorpheusLocationSetByUser, File metaMorpheusTempFolder, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, File spectrumFile, int threads, File fastaFile, File outputFile, 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.
static String	getExecutableFileName(boolean local)	Returns the name of the MetaMorpheus 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

MetaMorpheusProcessBuilder

public MetaMorpheusProcessBuilder(File metaMorpheusFolder,
 boolean metaMorpheusLocationSetByUser,
 File metaMorpheusTempFolder,
 com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
 File spectrumFile,
 int threads,
 File fastaFile,
 File outputFile,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
                           throws IOException

Constructor.

Parameters:

metaMorpheusFolder - the MetaMorpheus folder

metaMorpheusLocationSetByUser - boolean indicating whether the location of MetaMorpheus was set by the user

metaMorpheusTempFolder - the MetaMorpheus temp folder

searchParameters - the search parameters

spectrumFile - the spectrum file

threads - the number of threads to use

fastaFile - the FASTA file

outputFile - the output file

waitingHandler - the waiting handler

exceptionHandler - the handler of exceptions

Throws:

IOException - thrown whenever an IO error occurs

Method Details

getExecutableFileName

public static String getExecutableFileName(boolean local)

Returns the name of the MetaMorpheus executable.

Parameters:

local - if true, the execution will be expected to run locally

Returns:

the name of the MetaMorpheus executable

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