Uses of Interface
toxTree.core.IDecisionMethod

Packages that use IDecisionMethod

Package	Description
com.molecularnetworks.start
cramer2	Class CramerRules is the implementation of Cramer rules [Cramer et al,78].
eye	Class SicretRules is the implementation of BfR rules for estimating skin irritation and corrosion potential.
mic
michaelacceptors
mutant
sicret	Class SicretRules is the implementation of BfR rules for estimating skin irritation and corrosion potential.
toxTree.apps.toxForest
toxTree.core	This packages contains only interface definitions, defining essential classes in toxTree application.
toxtree.data
toxTree.io.batch	Batch processing facility.
toxtree.plugins.ames
toxtree.plugins.dnabinding
toxtree.plugins.func
toxtree.plugins.kroes
toxtree.plugins.lewis
toxtree.plugins.moa
toxtree.plugins.proteinbinding
toxtree.plugins.search
toxtree.plugins.skinsensitisation
toxtree.plugins.smartcyp
toxtree.plugins.verhaar2	Class toxtree.plugins.verhaar2.VerhaarScheme is the implementation of modified Verhaar structural scheme, according to recommendation from
toxTree.tree	This packages contains abstract and default classes implementing the interfaces defined in toxTree.core package.
toxTree.tree.cramer	Class CramerRules is the implementation of Cramer rules [Cramer et al,78].
toxtree.tree.cramer3
toxTree.tree.demo	Two simple demo decision trees.
toxTree.ui
toxtree.ui.batch	User interface for toxTree.io.batch
toxtree.ui.editors
toxtree.ui.tree	User interface for viewing and editing a decision tree IDecisionMethod
toxtree.ui.tree.actions	Actions (derived from AbstractAction for the decision tree user interface toxTree.ui.tree
toxtree.ui.wizard	Wizard support.
verhaar	Class VerhaarScheme is the implementation of Verhaar structural scheme for estimating toxicity mode of action.

Uses of IDecisionMethod in com.molecularnetworks.start

Classes in com.molecularnetworks.start that implement IDecisionMethod

Modifier and Type	Class and Description
class	BiodgeradationRules Wrapper class that knows the biodegradation rules that are available in the toxBiodegradation plugin.

Uses of IDecisionMethod in cramer2

Classes in cramer2 that implement IDecisionMethod

Modifier and Type	Class and Description
class	CramerRulesWithExtensions TODO update An UserDefinedTree descendant, implementing the decision tree described in "Cramer G.

Uses of IDecisionMethod in eye

Classes in eye that implement IDecisionMethod

Modifier and Type	Class and Description
class	EyeIrritationRules Decision tree for estimating skin irritation and corrosion potential.

Uses of IDecisionMethod in mic

Classes in mic that implement IDecisionMethod

Modifier and Type	Class and Description
class	MICRules

Uses of IDecisionMethod in michaelacceptors

Classes in michaelacceptors that implement IDecisionMethod

Modifier and Type	Class and Description
class	MichaelAcceptorRules

Uses of IDecisionMethod in mutant

Classes in mutant that implement IDecisionMethod

Modifier and Type	Class and Description
class	BB_CarcMutRules

Uses of IDecisionMethod in sicret

Classes in sicret that implement IDecisionMethod

Modifier and Type	Class and Description
class	SicretRules Decision tree for estimating skin irritation and corrosion potential.

Uses of IDecisionMethod in toxTree.apps.toxForest

Methods in toxTree.apps.toxForest that return IDecisionMethod

Modifier and Type	Method and Description
IDecisionMethod	ToxForestDataModule.getRules()

Methods in toxTree.apps.toxForest with parameters of type IDecisionMethod

Modifier and Type	Method and Description
void	ToxForestDataModule.setRules(IDecisionMethod rules)

Uses of IDecisionMethod in toxTree.core

Fields in toxTree.core declared as IDecisionMethod

Modifier and Type	Field and Description
protected IDecisionMethod	ToxTreeDescriptor.decisionTree

Methods in toxTree.core that return IDecisionMethod

Modifier and Type	Method and Description
IDecisionMethod	IDecisionMethodEditor.edit(Component owner, IDecisionMethod method)
IDecisionMethod	IDecisionResult.getDecisionMethod()
IDecisionMethod	IDecisionMethodEditor.getMethod()
IDecisionMethod	IDecisionMethodsList.getMethod(int index)
static IDecisionMethod	Introspection.loadRules(InputStream stream, String newTitle) Loads a decision tree from an InputStream Uses Java serialization mechanism
static IDecisionMethod	Introspection.loadRulesXML(InputStream stream, String newTitle)

Methods in toxTree.core with parameters of type IDecisionMethod

Modifier and Type	Method and Description
void	IDecisionMethodsList.addDecisionMethod(IDecisionMethod method)
IDecisionMethod	IDecisionMethodEditor.edit(Component owner, IDecisionMethod method)
void	IProcessRule.init(IDecisionMethod method)
Object	IProcessRule.process(IDecisionMethod method, IDecisionRule rule)
static void	Introspection.saveRulesXML(IDecisionMethod method, OutputStream out)
void	IDecisionResult.setDecisionMethod(IDecisionMethod method)
void	IDecisionMethodEditor.setMethod(IDecisionMethod method) Each method IDecisionMethod should provides an editor, which is a class, implementing this interface.

Uses of IDecisionMethod in toxtree.data

Fields in toxtree.data declared as IDecisionMethod

Modifier and Type	Field and Description
protected IDecisionMethod	DecisionMethodsDataModule.rules

Methods in toxtree.data that return IDecisionMethod

Modifier and Type	Method and Description
IDecisionMethod	DecisionMethodsDataModule.getRules()
IDecisionMethod	DecisionMethodsDataModule.getSelectedRules()

Methods in toxtree.data with parameters of type IDecisionMethod

Modifier and Type	Method and Description
void	ToxTreeModule.setRules(IDecisionMethod rules)
void	DecisionMethodsDataModule.setRules(IDecisionMethod rules)
void	DecisionMethodsDataModule.viewMethod(IDecisionMethod method, boolean editable)
abstract void	DataModule.viewMethod(IDecisionMethod method, boolean editable)

Uses of IDecisionMethod in toxTree.io.batch

Fields in toxTree.io.batch declared as IDecisionMethod

Modifier and Type	Field and Description
protected IDecisionMethod	ToxTreeBatchProcessing.decisionMethod

Methods in toxTree.io.batch that return IDecisionMethod

Modifier and Type	Method and Description
IDecisionMethod	ToxTreeBatchProcessing.getDecisionMethod()

Methods in toxTree.io.batch with parameters of type IDecisionMethod

Modifier and Type	Method and Description
void	ToxTreeBatchProcessing.setDecisionMethod(IDecisionMethod decisionMethod)

Uses of IDecisionMethod in toxtree.plugins.ames

Classes in toxtree.plugins.ames that implement IDecisionMethod

Modifier and Type	Class and Description
class	AmesMutagenicityRules

Uses of IDecisionMethod in toxtree.plugins.dnabinding

Classes in toxtree.plugins.dnabinding that implement IDecisionMethod

Modifier and Type	Class and Description
class	DNABindingPlugin Protein binding

Uses of IDecisionMethod in toxtree.plugins.func

Classes in toxtree.plugins.func that implement IDecisionMethod

Modifier and Type	Class and Description
class	FuncRules

Uses of IDecisionMethod in toxtree.plugins.kroes

Classes in toxtree.plugins.kroes that implement IDecisionMethod

Modifier and Type	Class and Description
class	Kroes1Tree

Uses of IDecisionMethod in toxtree.plugins.lewis

Classes in toxtree.plugins.lewis that implement IDecisionMethod

Modifier and Type	Class and Description
class	LewisTree derived by Weka from table2.

Uses of IDecisionMethod in toxtree.plugins.moa

Classes in toxtree.plugins.moa that implement IDecisionMethod

Modifier and Type	Class and Description
class	MOARules

Uses of IDecisionMethod in toxtree.plugins.proteinbinding

Classes in toxtree.plugins.proteinbinding that implement IDecisionMethod

Modifier and Type	Class and Description
class	ProteinBindingPlugin Protein binding

Uses of IDecisionMethod in toxtree.plugins.search

Classes in toxtree.plugins.search that implement IDecisionMethod

Modifier and Type	Class and Description
class	CompoundLookup

Uses of IDecisionMethod in toxtree.plugins.skinsensitisation

Classes in toxtree.plugins.skinsensitisation that implement IDecisionMethod

Modifier and Type	Class and Description
class	SkinSensitisationPlugin Skin sensitisation

Uses of IDecisionMethod in toxtree.plugins.smartcyp

Classes in toxtree.plugins.smartcyp that implement IDecisionMethod

Modifier and Type	Class and Description
class	SMARTCYPPlugin

Uses of IDecisionMethod in toxtree.plugins.verhaar2

Classes in toxtree.plugins.verhaar2 that implement IDecisionMethod

Modifier and Type	Class and Description
class	VerhaarScheme2 An implementaton of Verhaar scheme for predicting toxicity mode of action.

Uses of IDecisionMethod in toxTree.tree

Classes in toxTree.tree that implement IDecisionMethod

Modifier and Type	Class and Description
class	AbstractTree An astract class, implementing IDecisionMethod interface.
class	BatchDecisionResultsList Encapsulates DecisionResultsList as IDecisionMethod.
class	UserDefinedTree A default decision tree class, implementing IDecisionMethod interface.

Fields in toxTree.tree declared as IDecisionMethod

Modifier and Type	Field and Description
protected IDecisionMethod	TreeResult.decisionMethod

Methods in toxTree.tree that return IDecisionMethod

Modifier and Type	Method and Description
IDecisionMethod	TreeResult.getDecisionMethod()
IDecisionMethod	BatchDecisionResultsList.getDecisionMethod()
IDecisionMethod	DecisionResultsList.getMethod(int index)
IDecisionMethod	DecisionMethodsList.getMethod(int index)

Methods in toxTree.tree with parameters of type IDecisionMethod

Modifier and Type	Method and Description
void	DecisionResultsList.addDecisionMethod(IDecisionMethod method)
void	DecisionMethodsList.addDecisionMethod(IDecisionMethod method)
void	Tree2PrefuseGraph.init(IDecisionMethod method)
void	ReportTreePrinter.init(IDecisionMethod tree)
void	PDFTreePrinter.init(IDecisionMethod method)
void	SimpleTreePrinter.init(IDecisionMethod tree)
Object	Tree2PrefuseGraph.process(IDecisionMethod method, IDecisionRule rule)
Object	ReportTreePrinter.process(IDecisionMethod method, IDecisionRule rule)
Object	PDFTreePrinter.process(IDecisionMethod method, IDecisionRule rule)
Object	SimpleTreePrinter.process(IDecisionMethod method, IDecisionRule rule)
void	TreeResult.setDecisionMethod(IDecisionMethod decisionMethod)
void	BatchDecisionResultsList.setDecisionMethod(IDecisionMethod method)
prefuse.data.Node	Tree2PrefuseGraph.walkRules(IDecisionMethod tree)
protected prefuse.data.Node	Tree2PrefuseGraph.walkRules(IDecisionMethod tree, IDecisionRule rule, ArrayList<Integer> visited)
protected String	ReportTreePrinter.writeMolecule(IDecisionMethod tree, IDecisionRule rule, boolean answer)
protected void	AbstractTreePrinter.writeMolecule(IDecisionMethod tree, IDecisionRule rule, boolean answer, OutputStream out)

Uses of IDecisionMethod in toxTree.tree.cramer

Classes in toxTree.tree.cramer that implement IDecisionMethod

Modifier and Type	Class and Description
class	CramerRules An UserDefinedTree descendant, implementing the decision tree described in "Cramer G.

Uses of IDecisionMethod in toxtree.tree.cramer3

Classes in toxtree.tree.cramer3 that implement IDecisionMethod

Modifier and Type	Class and Description
class	RevisedCramerDecisionTree Assigns categories: toxTree.tree.cramer3.CramerClass1 toxTree.tree.cramer3.CramerClass2 toxTree.tree.cramer3.CramerClass2

Uses of IDecisionMethod in toxTree.tree.demo

Classes in toxTree.tree.demo that implement IDecisionMethod

Modifier and Type	Class and Description
class	SMARTSTree
class	SubstructureTree A demo decision tree consisting of a single decision rule , which checks for the presence of benzene ring.

Uses of IDecisionMethod in toxTree.ui

Methods in toxTree.ui with parameters of type IDecisionMethod

Modifier and Type	Method and Description
IDecisionMethodEditor	IEditorFactory.createTreeEditor(IDecisionMethod method)
IDecisionMethodEditor	EditorFactory.createTreeEditor(IDecisionMethod method)
JComponent	IEditorFactory.optionsPanel(IDecisionMethod method, org.openscience.cdk.interfaces.IAtomContainer atomContainer)
JComponent	EditorFactory.optionsPanel(IDecisionMethod method, org.openscience.cdk.interfaces.IAtomContainer atomContainer)

Uses of IDecisionMethod in toxtree.ui.batch

Methods in toxtree.ui.batch that return IDecisionMethod

Modifier and Type	Method and Description
IDecisionMethod	BatchProcessingDialog.getDecisionMethod()

Methods in toxtree.ui.batch with parameters of type IDecisionMethod

Modifier and Type	Method and Description
void	BatchProcessingDialog.setDecisionMethod(IDecisionMethod decisionMethod)

Uses of IDecisionMethod in toxtree.ui.editors

Methods in toxtree.ui.editors with parameters of type IDecisionMethod

Modifier and Type	Method and Description
IDecisionMethodEditor	SwingEditorFactory.createTreeEditor(IDecisionMethod method)
JComponent	SwingEditorFactory.optionsPanel(IDecisionMethod method, org.openscience.cdk.interfaces.IAtomContainer atomContainer)

Uses of IDecisionMethod in toxtree.ui.tree

Fields in toxtree.ui.tree declared as IDecisionMethod

Modifier and Type	Field and Description
protected IDecisionMethod	DecisionTreeModel.decisionMethod
protected IDecisionMethod	TreeEditorPanel.method
protected IDecisionMethod	TreeLayout.method
protected IDecisionMethod	TreePrefuse.tree
protected IDecisionMethod	EditTreeActions.tree

Methods in toxtree.ui.tree that return IDecisionMethod

Modifier and Type	Method and Description
IDecisionMethod	TreeEditorPanel.edit(Component owner, IDecisionMethod method)
IDecisionMethod	TreePrefuse.getDecisionMethod()
IDecisionMethod	TreeDrawing.getDecisionMethod()
IDecisionMethod	ITreeView.getDecisionMethod()
IDecisionMethod	JCustomTreeComponent.getDecisionMethod()
IDecisionMethod	TreeEditorPanel.getMethod()
IDecisionMethod	TreeLayout.getMethod()
static IDecisionMethod	SelectListDialog.selectNewTree(Component parent, ClassLoader classLoader) Provides a list of names of the classes implementing IDecisionMethod If the user selects a name, the tree is created and returned Uses Introspection.getAvailableTreeTypes(ClassLoader)

Methods in toxtree.ui.tree with parameters of type IDecisionMethod

Modifier and Type	Method and Description
protected void	TreePanel.addWidgets(IDecisionMethod treeMethod)
protected void	TreeFrame.addWidgets(IDecisionMethod treeMethod)
protected void	TreeDrawing.addWidgets(IDecisionMethod treeMethod, EditTreeActions actions)
protected int[]	TreePrefuse.createPalette(IDecisionMethod tree)
IDecisionMethod	TreeEditorPanel.edit(Component owner, IDecisionMethod method)
void	TreePanel.setDecisionMethod(IDecisionMethod decisionMethod)
void	TreePrefuse.setDecisionMethod(IDecisionMethod decisionMethod)
void	TreeDrawing.setDecisionMethod(IDecisionMethod method)
void	ITreeView.setDecisionMethod(IDecisionMethod decisionMethod)
void	TreeFrame.setDecisionMethod(IDecisionMethod decisionMethod)
void	DecisionTreeModel.setDecisionMethod(IDecisionMethod decisionMethod)
void	JCustomTreeComponent.setDecisionMethod(IDecisionMethod method)
void	TreeEditorPanel.setMethod(IDecisionMethod method)
Dimension	TreeLayout.setMethod(IDecisionMethod method)

Constructors in toxtree.ui.tree with parameters of type IDecisionMethod

Constructor and Description
DecisionTreeModel(IDecisionMethod decisionMethod)
EditTreeActions(IDecisionMethod tree)
JCustomTreeComponent(IDecisionMethod method, ActionMap actions)
TreeDrawing(IDecisionMethod treeMethod, EditTreeActions actions)
TreeEditorPanel(IDecisionMethod method)
TreeFrame(IDecisionMethod treeMethod)
TreeLayout(IDecisionMethod method)
TreeOptions(IDecisionMethod tree, org.openscience.cdk.interfaces.IAtomContainer atomcontainer)
TreePanel(IDecisionMethod treeMethod)
TreePrefuse(IDecisionMethod tree, EditTreeActions actions)
TreePrefuse(IDecisionMethod tree, EditTreeActions actions, boolean forcefieldLayout)

Uses of IDecisionMethod in toxtree.ui.tree.actions

Fields in toxtree.ui.tree.actions declared as IDecisionMethod

Modifier and Type	Field and Description
protected IDecisionMethod	AbstractTreeAction.tree

Methods in toxtree.ui.tree.actions that return IDecisionMethod

Modifier and Type	Method and Description
IDecisionMethod	ITreeAction.getTree()
IDecisionMethod	AbstractTreeAction.getTree()
static IDecisionMethod	NewRuleAction.treeFromRule(IDecisionRule rule)

Methods in toxtree.ui.tree.actions with parameters of type IDecisionMethod

Modifier and Type	Method and Description
void	SelectTreeAction.addTree(IDecisionMethod tree)
static DecisionMethodsList	NewRuleAction.forestFromTree(IDecisionMethod tree) Creates forest of trees, each tree consists of a single rule.
void	EditDecisionMethodAction.launchEditor(IDecisionMethod method)
void	ITreeAction.setTree(IDecisionMethod tree)
void	AbstractTreeAction.setTree(IDecisionMethod tree)
static DecisionNode	NewRuleAction.updateNode(IDecisionMethod tree, DecisionNode node)

Constructors in toxtree.ui.tree.actions with parameters of type IDecisionMethod

Constructor and Description
AbstractTreeAction(IDecisionMethod tree)
AbstractTreeAction(IDecisionMethod tree, String name)
AbstractTreeAction(IDecisionMethod tree, String name, Icon icon)
EditCategoryAction(IDecisionMethod tree)
EditCategoryAction(IDecisionMethod tree, String name)
EditCategoryAction(IDecisionMethod tree, String name, Icon icon)
EditRuleAction(IDecisionMethod tree)
EditRuleAction(IDecisionMethod tree, String arg0)
EditRuleAction(IDecisionMethod tree, String arg0, Icon arg1)
EditTreeExplanation(IDecisionMethod tree)
EditTreeExplanation(IDecisionMethod tree, String name)
EditTreeExplanation(IDecisionMethod tree, String name, Icon icon)
NewRuleAction(IDecisionMethod tree)
NewRuleAction(IDecisionMethod tree, String name)
NewRuleAction(IDecisionMethod tree, String name, Icon icon)
SaveTreeAction(IDecisionMethod tree)
SaveTreeAction(IDecisionMethod tree, String name)
SaveTreeAction(IDecisionMethod tree, String name, Icon icon)
SelectCategoryFromListAction(IDecisionMethod tree)
SelectCategoryFromListAction(IDecisionMethod tree, String name)
SelectCategoryFromListAction(IDecisionMethod tree, String name, Icon icon)
SetBranchAction(IDecisionMethod tree, boolean answer)
SetBranchAction(IDecisionMethod tree, boolean answer, String name)
SetBranchAction(IDecisionMethod tree, boolean answer, String name, Icon icon)
VerifyUnreachableRulesAction(IDecisionMethod tree)
VerifyUnreachableRulesAction(IDecisionMethod tree, String name)
VerifyUnreachableRulesAction(IDecisionMethod tree, String name, Icon icon)
VerifyUnusedCategories(IDecisionMethod tree)
VerifyUnusedCategories(IDecisionMethod tree, String name)
VerifyUnusedCategories(IDecisionMethod tree, String name, Icon icon)

Uses of IDecisionMethod in toxtree.ui.wizard

Fields in toxtree.ui.wizard declared as IDecisionMethod

Modifier and Type	Field and Description
protected IDecisionMethod	DecisionTreeWizard.tree

Methods in toxtree.ui.wizard with parameters of type IDecisionMethod

Modifier and Type	Method and Description
static DecisionNodeWizard	DecisionNodeWizard.createWizard(Frame frame, IDecisionMethod tree, int start)

Constructors in toxtree.ui.wizard with parameters of type IDecisionMethod

Constructor and Description
DecisionNodeWizard(Dialog arg0, IDecisionMethod tree, ListPanel[] panels)
DecisionNodeWizard(Frame frame, IDecisionMethod tree, ListPanel[] panels)
DecisionNodeWizard(IDecisionMethod tree, ListPanel[] panels)
DecisionTreeWizard(Dialog arg0, IDecisionMethod tree)
DecisionTreeWizard(Frame frame, IDecisionMethod tree)
DecisionTreeWizard(IDecisionMethod tree)

Uses of IDecisionMethod in verhaar

Classes in verhaar that implement IDecisionMethod

Modifier and Type	Class and Description
class	VerhaarScheme An implementaton of Verhaar scheme for predicting toxicity mode of action.