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java.lang.Objectjava.lang.Thread
biggests.gui.ThreadFunctionAnalysis
public class ThreadFunctionAnalysis
Title: Function analysis thread.
Description: Thread to compute function analysis (long time consuming task) while displaying a progress bar dialog to the user.
Copyright: Copyright (C) 2007 Joana Gonçalves This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
| Nested Class Summary |
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| Nested classes/interfaces inherited from class java.lang.Thread |
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java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler |
| Field Summary |
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| Fields inherited from class java.lang.Thread |
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MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY |
| Constructor Summary | |
|---|---|
ThreadFunctionAnalysis(BiggestsFrame frame,
Biclustering biclustering,
javax.swing.tree.TreePath selectionPath,
de.schlichtherle.io.File[] goFiles,
de.schlichtherle.io.File directoryFunctionResults,
float pvalue)
Creates a new ThreadFunctionAnalysis. |
|
ThreadFunctionAnalysis(BiggestsFrame frame,
Biclustering biclustering,
javax.swing.tree.TreePath selectionPath,
java.lang.String pathToGeneOntologyFile,
java.lang.String pathToGeneAssociationFile,
de.schlichtherle.io.File directoryFunctionResults,
float pvalue)
Creates a new ThreadFunctionAnalysis. |
|
ThreadFunctionAnalysis(BiggestsFrame frame,
Bicluster bicluster,
javax.swing.tree.TreePath selectionPath,
java.lang.String pathToGeneOntologyFile,
java.lang.String pathToGeneAssociationFile,
java.lang.String directoryFunctionResults,
float pvalue)
Creates a new Function Analysis Thread to perform function analysis over a matrix. |
|
ThreadFunctionAnalysis(BiggestsFrame frame,
IMatrix matrix,
javax.swing.tree.TreePath selectionPath,
de.schlichtherle.io.File[] goFiles,
de.schlichtherle.io.File directoryFunctionResults,
java.lang.String filenameDOT,
float pvalue)
Creates a new Function Analysis Thread to perform function analysis over a matrix. |
|
ThreadFunctionAnalysis(BiggestsFrame frame,
IMatrix matrix,
javax.swing.tree.TreePath selectionPath,
java.lang.String pathToGeneOntologyFile,
java.lang.String pathToGeneAssociationFile,
de.schlichtherle.io.File directoryFunctionResults,
java.lang.String filenameDOT,
float pvalue)
Creates a new Function Analysis Thread to perform function analysis over a matrix. |
|
| Method Summary | |
|---|---|
void |
run()
Overrides Thread's run method. |
| Methods inherited from class java.lang.Thread |
|---|
activeCount, checkAccess, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield |
| Methods inherited from class java.lang.Object |
|---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
| Constructor Detail |
|---|
public ThreadFunctionAnalysis(BiggestsFrame frame,
Biclustering biclustering,
javax.swing.tree.TreePath selectionPath,
de.schlichtherle.io.File[] goFiles,
de.schlichtherle.io.File directoryFunctionResults,
float pvalue)
throws java.lang.Exception
ThreadFunctionAnalysis.
frame - the main BiggestsFramebiclustering - Biclustering object to perform
function analysis on toselectionPath - the TreePath which corresponds to
biclustering place in the dataset treegoFiles - File[] gene ontology filesdirectoryFunctionResults - File directory
to store the files resulting from function analysispvalue - float
java.lang.Exception
public ThreadFunctionAnalysis(BiggestsFrame frame,
Biclustering biclustering,
javax.swing.tree.TreePath selectionPath,
java.lang.String pathToGeneOntologyFile,
java.lang.String pathToGeneAssociationFile,
de.schlichtherle.io.File directoryFunctionResults,
float pvalue)
throws java.lang.Exception
ThreadFunctionAnalysis.
frame - the main BiggestsFramebiclustering - Biclustering object to perform
function analysis on toselectionPath - the TreePath which corresponds to
biclustering place in the dataset treepathToGeneOntologyFile - String the path to gene
ontology filepathToGeneAssociationFile - String the path to
gene association filedirectoryFunctionResults - File directory
to store the files resulting from function analysispvalue - float
java.lang.Exception
public ThreadFunctionAnalysis(BiggestsFrame frame,
IMatrix matrix,
javax.swing.tree.TreePath selectionPath,
de.schlichtherle.io.File[] goFiles,
de.schlichtherle.io.File directoryFunctionResults,
java.lang.String filenameDOT,
float pvalue)
throws java.lang.Exception
frame - the main BiggestsFramematrix - the IMatrix over which function
analysis will be performedselectionPath - the TreePath which corresponds to
biclustering place in the dataset treegoFiles - File[] gene ontology filesdirectoryFunctionResults - File directory
to store the files resulting from function analysisfilenameDOT - String the name for the resulting DOT file
(graph of significant terms)pvalue - float the p-value threshold for
significant terms
java.lang.Exception
public ThreadFunctionAnalysis(BiggestsFrame frame,
IMatrix matrix,
javax.swing.tree.TreePath selectionPath,
java.lang.String pathToGeneOntologyFile,
java.lang.String pathToGeneAssociationFile,
de.schlichtherle.io.File directoryFunctionResults,
java.lang.String filenameDOT,
float pvalue)
throws java.lang.Exception
frame - the main BiggestsFramematrix - the IMatrix over which function
analysis will be performedselectionPath - the TreePath which corresponds to
biclustering place in the dataset treepathToGeneOntologyFile - String the path to gene
ontology filepathToGeneAssociationFile - String the path to
gene association filedirectoryFunctionResults - File directory
to store the files resulting from function analysisfilenameDOT - String the name for the resulting DOT file
(graph of significant terms)pvalue - float the p-value threshold for
significant terms
java.lang.Exception
public ThreadFunctionAnalysis(BiggestsFrame frame,
Bicluster bicluster,
javax.swing.tree.TreePath selectionPath,
java.lang.String pathToGeneOntologyFile,
java.lang.String pathToGeneAssociationFile,
java.lang.String directoryFunctionResults,
float pvalue)
throws java.lang.Exception
frame - the main BiggestsFramebicluster - the Bicluster on which function
analysis has to be performedselectionPath - the selected TreePath in the
dataset tree (corresponding to the bicluster nodepathToGeneOntologyFile - String the path to gene ontology file
(OBO file)pathToGeneAssociationFile - String the path to gene
association file (organism specific file)directoryFunctionResults - File directory
to store the files resulting from function analysispvalue - float the p-value threshold for
significant terms
java.lang.Exception| Method Detail |
|---|
public void run()
Thread's run method. Performs the
actual task of this working thread (performing function analysis on
a given biclusters group).
run in interface java.lang.Runnablerun in class java.lang.ThreadThread.run()
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