biggests.gui
Class ThreadBiclustering

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

public class ThreadBiclustering
extends java.lang.Thread

Title: Biclustering and function analysis thread.

Description: Thread to apply biclustering algorithms and 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
ThreadBiclustering(BiggestsFrame frame, Biclustering biclustering, javax.swing.tree.TreePath selectionPath)
          Creates a new ThreadBiclusteringFunctionAnalysis
 
Method Summary
 void biclusteringError(java.lang.String message)
          Displays an error message when something went wrong with biclustering algorithm.
 GOFrontEnd computeBiclusters()
          Computes biclusters and GO frontend for function analysis.
 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

ThreadBiclustering

public ThreadBiclustering(BiggestsFrame frame,
                          Biclustering biclustering,
                          javax.swing.tree.TreePath selectionPath)
Creates a new ThreadBiclusteringFunctionAnalysis

Parameters:
frame - the BiGGEsTS main window
biclustering - Biclustering object to apply biclustering algorithm and function analysis on to
selectionPath - the selected TreePath (path to biclustering node in the dataset tree)
Method Detail

run

public void run()
Overrides Thread's run method. Performs the actual task of this working thread (applying the required biclustering algorithm and 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()

computeBiclusters

public GOFrontEnd computeBiclusters()
                             throws java.lang.Exception,
                                    java.lang.StackOverflowError,
                                    java.lang.OutOfMemoryError
Computes biclusters and GO frontend for function analysis.

Returns:
GOFrontEnd the GO frontend for function analysis
Throws:
java.lang.Exception - if biclusters cannot be computed
java.lang.StackOverflowError - if there is a stack overflow
java.lang.OutOfMemoryError - if runs out of memory

biclusteringError

public void biclusteringError(java.lang.String message)
Displays an error message when something went wrong with biclustering algorithm.

Parameters:
message - String