toxTree.apps
Class ToxTreeApp

java.lang.Object
  extended by toxTree.apps.AbstractApplication
      extended by toxTree.apps.CompoundMethodApplication
          extended by toxTree.apps.ToxTreeApp

public class ToxTreeApp
extends CompoundMethodApplication

ToxTreeApp is a full-featured and flexible user-friendly open source application, which is able to estimate toxic hazard by applying a decision tree approach. Currently it encodes the Cramer scheme (Cramer G. M., R. A. Ford, R. L. Hall, Estimation of Toxic Hazard - A Decision Tree Approach, J. Cosmet. Toxicol., Vol.16, pp. 255-276, Pergamon Press, 1978) and could be applied to datasets from various compatible file types (MOL, MOL2, SDF, CML, XYZ, PDB, HIN, CDX and SMI). User-defined molecular structures are also supported - they could be entered by SMILES or by JChemPaint structure diagram editor TODO Prevent multiple instances: http://www.rgagnon.com/javadetails/java-0288.html

Author:
Nina Jeliazkova
Modified 2008-03-17

Field Summary
protected  java.io.File file4Batch
           
 
Fields inherited from class toxTree.apps.CompoundMethodApplication
compoundPanel, dataModulePanel, fileToOpen, mainPanel, splitPanel, strucEntryPanel
 
Fields inherited from class toxTree.apps.AbstractApplication
cmdArgs, dataModule, logger, mainFrame
 
Constructor Summary
ToxTreeApp()
           
 
Method Summary
protected static void createAndShowGUI()
          Create the GUI and show it.
protected  DataModule createDataModule()
           
protected  DataModulePanel createDataModulePanel(DataModule dataModule)
           
protected  javax.swing.ImageIcon getIcon()
           
protected  java.lang.String getTitle()
           
static void main(java.lang.String[] args)
          Command line options:
java -jar toxTree.jar -f input_file_for_normal_open
java -jar toxTree.jar -b input_file_for_batch_processing
protected  void parseCmdArgs(java.lang.String[] args)
           
 
Methods inherited from class toxTree.apps.CompoundMethodApplication
createCompoundPanel, createSplitPanel, createStatusBar
 
Methods inherited from class toxTree.apps.AbstractApplication
centerScreen, createMenuBar, exit, initLookAndFeel, setEditorFactory
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

file4Batch

protected java.io.File file4Batch
Constructor Detail

ToxTreeApp

public ToxTreeApp()
Method Detail

getTitle

protected java.lang.String getTitle()
Specified by:
getTitle in class CompoundMethodApplication

createDataModule

protected DataModule createDataModule()
Overrides:
createDataModule in class CompoundMethodApplication

createAndShowGUI

protected static void createAndShowGUI()
Create the GUI and show it. For thread safety, this method should be invoked from the event-dispatching thread.


main

public static void main(java.lang.String[] args)
Command line options:
java -jar toxTree.jar -f input_file_for_normal_open
java -jar toxTree.jar -b input_file_for_batch_processing

Parameters:
args -

parseCmdArgs

protected void parseCmdArgs(java.lang.String[] args)
Overrides:
parseCmdArgs in class CompoundMethodApplication

getIcon

protected javax.swing.ImageIcon getIcon()
Overrides:
getIcon in class CompoundMethodApplication

createDataModulePanel

protected DataModulePanel createDataModulePanel(DataModule dataModule)
Specified by:
createDataModulePanel in class CompoundMethodApplication


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