biggests.gui
Class ThreadFunctionAnalysis

java.lang.Object
  extended by java.lang.Thread
      extended by biggests.gui.ThreadFunctionAnalysis
All Implemented Interfaces:
java.lang.Runnable

public class ThreadFunctionAnalysis
extends java.lang.Thread

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
 
Nested classes/interfaces inherited from class java.lang.Thread
java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler
 
Field Summary
 
Fields inherited from class java.lang.Thread
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

ThreadFunctionAnalysis

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
Creates a new ThreadFunctionAnalysis.

Parameters:
frame - the main BiggestsFrame
biclustering - Biclustering object to perform function analysis on to
selectionPath - the TreePath which corresponds to biclustering place in the dataset tree
goFiles - File[] gene ontology files
directoryFunctionResults - File directory to store the files resulting from function analysis
pvalue - float
Throws:
java.lang.Exception

ThreadFunctionAnalysis

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
Creates a new ThreadFunctionAnalysis.

Parameters:
frame - the main BiggestsFrame
biclustering - Biclustering object to perform function analysis on to
selectionPath - the TreePath which corresponds to biclustering place in the dataset tree
pathToGeneOntologyFile - String the path to gene ontology file
pathToGeneAssociationFile - String the path to gene association file
directoryFunctionResults - File directory to store the files resulting from function analysis
pvalue - float
Throws:
java.lang.Exception

ThreadFunctionAnalysis

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
Creates a new Function Analysis Thread to perform function analysis over a matrix.

Parameters:
frame - the main BiggestsFrame
matrix - the IMatrix over which function analysis will be performed
selectionPath - the TreePath which corresponds to biclustering place in the dataset tree
goFiles - File[] gene ontology files
directoryFunctionResults - File directory to store the files resulting from function analysis
filenameDOT - String the name for the resulting DOT file (graph of significant terms)
pvalue - float the p-value threshold for significant terms
Throws:
java.lang.Exception

ThreadFunctionAnalysis

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
Creates a new Function Analysis Thread to perform function analysis over a matrix.

Parameters:
frame - the main BiggestsFrame
matrix - the IMatrix over which function analysis will be performed
selectionPath - the TreePath which corresponds to biclustering place in the dataset tree
pathToGeneOntologyFile - String the path to gene ontology file
pathToGeneAssociationFile - String the path to gene association file
directoryFunctionResults - File directory to store the files resulting from function analysis
filenameDOT - String the name for the resulting DOT file (graph of significant terms)
pvalue - float the p-value threshold for significant terms
Throws:
java.lang.Exception

ThreadFunctionAnalysis

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
Creates a new Function Analysis Thread to perform function analysis over a matrix.

Parameters:
frame - the main BiggestsFrame
bicluster - the Bicluster on which function analysis has to be performed
selectionPath - the selected TreePath in the dataset tree (corresponding to the bicluster node
pathToGeneOntologyFile - 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 analysis
pvalue - float the p-value threshold for significant terms
Throws:
java.lang.Exception
Method Detail

run

public void run()
Overrides Thread's run method. Performs the actual task of this working thread (performing function analysis on a given biclusters group).

Specified by:
run in interface java.lang.Runnable
Overrides:
run in class java.lang.Thread
See Also:
Thread.run()