toxTree.apps

Class ToxTreeApp

java.lang.Object

toxTree.apps.AbstractApplication

toxTree.apps.CompoundMethodApplication

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

Author:

Nina Jeliazkova
Modified 2008-03-17

Field Summary

Fields

Modifier and Type	Field and Description
protected File	file4Batch

Fields inherited from class toxTree.apps.CompoundMethodApplication

compoundPanel, dataModulePanel, fileToOpen, mainPanel, splitPanel, strucEntryPanel

Fields inherited from class toxTree.apps.AbstractApplication

dataModule, logger, mainFrame, options

Constructor Summary

Constructors

Constructor and Description
ToxTreeApp()

Method Summary

Modifier and Type	Method and Description
protected static void	createAndShowGUI() Create the GUI and show it.
protected DataModule	createDataModule()
protected DataModulePanel	createDataModulePanel(DataModule dataModule)
protected ImageIcon	getIcon()
protected String	getTitle()
protected void	insecureConfig()
static void	main(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 ToxtreeOptions	parseCmdArgs(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 File file4Batch

Constructor Detail

ToxTreeApp

public ToxTreeApp()

Method Detail

getTitle

protected 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(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 ToxtreeOptions parseCmdArgs(String[] args)
                               throws Exception

Overrides:

parseCmdArgs in class CompoundMethodApplication

Throws:

Exception

getIcon

protected ImageIcon getIcon()

Overrides:

getIcon in class CompoundMethodApplication

createDataModulePanel

protected DataModulePanel createDataModulePanel(DataModule dataModule)

Specified by:

createDataModulePanel in class CompoundMethodApplication

insecureConfig

protected void insecureConfig()