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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 | |
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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 . |
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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 . |
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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. |
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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. |
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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 | |
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void |
run()
Overrides Thread 's run method. |
Methods inherited from class java.lang.Thread |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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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 BiggestsFrame
biclustering
- 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 BiggestsFrame
biclustering
- 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 BiggestsFrame
matrix
- 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 BiggestsFrame
matrix
- 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 BiggestsFrame
bicluster
- 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 |
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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.Runnable
run
in class java.lang.Thread
Thread.run()
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