Package eu.isas.searchgui.processbuilders

Class PeptideShakerProcessBuilder

java.lang.Object

eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

eu.isas.searchgui.processbuilders.PeptideShakerProcessBuilder

All Implemented Interfaces:

Runnable

public class PeptideShakerProcessBuilder
extends SearchGUIProcessBuilder

This process builder runs PeptideShaker.

Author:

Marc Vaudel, Harald Barsnes

Field Summary

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

exceptionHandler, waitingHandler

Constructor Summary

Constructors

Constructor

Description

PeptideShakerProcessBuilder(com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, String reference, ArrayList<File> spectrumFiles, File fastaFile, ArrayList<File> identificationFiles, File identificationParametersFile, File psdbFile, boolean showGuiProgress, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, boolean includeData)

Constructor for the process builder.

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

Constructor Details

PeptideShakerProcessBuilder

public PeptideShakerProcessBuilder(com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.exceptions.ExceptionHandler exceptionHandler,
 String reference,
 ArrayList<File> spectrumFiles,
 File fastaFile,
 ArrayList<File> identificationFiles,
 File identificationParametersFile,
 File psdbFile,
 boolean showGuiProgress,
 com.compomics.util.parameters.tools.ProcessingParameters processingParameters,
 boolean includeData)
                            throws IOException,
ClassNotFoundException

Constructor for the process builder.

Parameters:

waitingHandler - the waiting handler

exceptionHandler - the handler of exceptions

reference - the name of the experiment

spectrumFiles - the spectrum files

fastaFile - the FASTA file

identificationFiles - the search engines result files

identificationParametersFile - the file where to save the search parameters

psdbFile - the psdb file

showGuiProgress - a boolean indicating whether the progress shall be displayed in a GUI

processingParameters - the processing parameters

includeData - Indicates whether the mass spectrum and FASTA file should be included in the output

Throws:

IOException - thrown if there are problems accessing the files

ClassNotFoundException - thrown if a class cannot be found

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