Uses of Interface
toxTree.core.IDecisionMethod

Packages that use IDecisionMethod
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.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.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
 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
 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
 class EyeIrritationRules
          Decision tree for estimating skin irritation and corrosion potential.
 

Uses of IDecisionMethod in mic
 

Classes in mic that implement IDecisionMethod
 class MICRules
           
 

Uses of IDecisionMethod in michaelacceptors
 

Classes in michaelacceptors that implement IDecisionMethod
 class MichaelAcceptorRules
           
 

Uses of IDecisionMethod in mutant
 

Classes in mutant that implement IDecisionMethod
 class BB_CarcMutRules
           
 

Uses of IDecisionMethod in sicret
 

Classes in sicret that implement IDecisionMethod
 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
 IDecisionMethod ToxForestDataModule.getRules()
           
 

Methods in toxTree.apps.toxForest with parameters of type IDecisionMethod
 void ToxForestDataModule.setRules(IDecisionMethod rules)
           
 

Uses of IDecisionMethod in toxTree.core
 

Fields in toxTree.core declared as IDecisionMethod
protected  IDecisionMethod ToxTreeDescriptor.decisionTree
           
 

Methods in toxTree.core that return IDecisionMethod
 IDecisionMethod IDecisionMethodEditor.edit(java.awt.Component owner, IDecisionMethod method)
           
 IDecisionMethod IDecisionResult.getDecisionMethod()
           
 IDecisionMethod IDecisionMethodEditor.getMethod()
           
 IDecisionMethod IDecisionMethodsList.getMethod(int index)
           
static IDecisionMethod Introspection.loadRules(java.io.InputStream stream, java.lang.String newTitle)
          Loads a decision tree from an InputStream Uses Java serialization mechanism
static IDecisionMethod Introspection.loadRulesXML(java.io.InputStream stream, java.lang.String newTitle)
           
 

Methods in toxTree.core with parameters of type IDecisionMethod
 void IDecisionMethodsList.addDecisionMethod(IDecisionMethod method)
           
 IDecisionMethod IDecisionMethodEditor.edit(java.awt.Component owner, IDecisionMethod method)
           
 void IProcessRule.init(IDecisionMethod method)
           
 java.lang.Object IProcessRule.process(IDecisionMethod method, IDecisionRule rule)
           
static void Introspection.saveRulesXML(IDecisionMethod method, java.io.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
protected  IDecisionMethod DecisionMethodsDataModule.rules
           
 

Methods in toxtree.data that return IDecisionMethod
 IDecisionMethod DecisionMethodsDataModule.getRules()
           
 IDecisionMethod DecisionMethodsDataModule.getSelectedRules()
           
 

Methods in toxtree.data with parameters of type IDecisionMethod
 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
protected  IDecisionMethod ToxTreeBatchProcessing.decisionMethod
           
 

Methods in toxTree.io.batch that return IDecisionMethod
 IDecisionMethod ToxTreeBatchProcessing.getDecisionMethod()
           
 

Methods in toxTree.io.batch with parameters of type IDecisionMethod
 void ToxTreeBatchProcessing.setDecisionMethod(IDecisionMethod decisionMethod)
           
 

Uses of IDecisionMethod in toxtree.plugins.dnabinding
 

Classes in toxtree.plugins.dnabinding that implement IDecisionMethod
 class DNABindingPlugin
          Protein binding
 

Uses of IDecisionMethod in toxtree.plugins.func
 

Classes in toxtree.plugins.func that implement IDecisionMethod
 class FuncRules
           
 

Uses of IDecisionMethod in toxtree.plugins.kroes
 

Classes in toxtree.plugins.kroes that implement IDecisionMethod
 class Kroes1Tree
           
 

Uses of IDecisionMethod in toxtree.plugins.lewis
 

Classes in toxtree.plugins.lewis that implement IDecisionMethod
 class LewisTree
           derived by Weka from table2.
 

Uses of IDecisionMethod in toxtree.plugins.moa
 

Classes in toxtree.plugins.moa that implement IDecisionMethod
 class MOARules
           
 

Uses of IDecisionMethod in toxtree.plugins.proteinbinding
 

Classes in toxtree.plugins.proteinbinding that implement IDecisionMethod
 class ProteinBindingPlugin
          Protein binding
 

Uses of IDecisionMethod in toxtree.plugins.search
 

Classes in toxtree.plugins.search that implement IDecisionMethod
 class CompoundLookup
           
 

Uses of IDecisionMethod in toxtree.plugins.skinsensitisation
 

Classes in toxtree.plugins.skinsensitisation that implement IDecisionMethod
 class SkinSensitisationPlugin
          Skin sensitisation
 

Uses of IDecisionMethod in toxtree.plugins.smartcyp
 

Classes in toxtree.plugins.smartcyp that implement IDecisionMethod
 class SMARTCYPPlugin
           
 

Uses of IDecisionMethod in toxtree.plugins.verhaar2
 

Classes in toxtree.plugins.verhaar2 that implement IDecisionMethod
 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
 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
protected  IDecisionMethod TreeResult.decisionMethod
           
 

Methods in toxTree.tree that return IDecisionMethod
 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
 void DecisionResultsList.addDecisionMethod(IDecisionMethod method)
           
 void DecisionMethodsList.addDecisionMethod(IDecisionMethod method)
           
 void Tree2PrefuseGraph.init(IDecisionMethod method)
           
 void SimpleTreePrinter.init(IDecisionMethod tree)
           
 void ReportTreePrinter.init(IDecisionMethod tree)
           
 void PDFTreePrinter.init(IDecisionMethod method)
           
 java.lang.Object Tree2PrefuseGraph.process(IDecisionMethod method, IDecisionRule rule)
           
 java.lang.Object SimpleTreePrinter.process(IDecisionMethod method, IDecisionRule rule)
           
 java.lang.Object ReportTreePrinter.process(IDecisionMethod method, IDecisionRule rule)
           
 java.lang.Object PDFTreePrinter.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, java.util.ArrayList<java.lang.Integer> visited)
           
 

Uses of IDecisionMethod in toxTree.tree.cramer
 

Classes in toxTree.tree.cramer that implement IDecisionMethod
 class CramerRules
          An UserDefinedTree descendant, implementing the decision tree described in "Cramer G.
 

Uses of IDecisionMethod in toxTree.tree.demo
 

Classes in toxTree.tree.demo that implement IDecisionMethod
 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
 IDecisionMethodEditor IEditorFactory.createTreeEditor(IDecisionMethod method)
           
 IDecisionMethodEditor EditorFactory.createTreeEditor(IDecisionMethod method)
           
 javax.swing.JComponent IEditorFactory.optionsPanel(IDecisionMethod method, org.openscience.cdk.interfaces.IAtomContainer atomContainer)
           
 javax.swing.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
 IDecisionMethod BatchProcessingDialog.getDecisionMethod()
           
 

Methods in toxtree.ui.batch with parameters of type IDecisionMethod
 void BatchProcessingDialog.setDecisionMethod(IDecisionMethod decisionMethod)
           
 

Uses of IDecisionMethod in toxtree.ui.editors
 

Methods in toxtree.ui.editors with parameters of type IDecisionMethod
 IDecisionMethodEditor SwingEditorFactory.createTreeEditor(IDecisionMethod method)
           
 javax.swing.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
protected  IDecisionMethod DecisionTreeModel.decisionMethod
           
protected  IDecisionMethod TreeLayout.method
           
protected  IDecisionMethod TreeEditorPanel.method
           
protected  IDecisionMethod TreePrefuse.tree
           
protected  IDecisionMethod EditTreeActions.tree
           
 

Methods in toxtree.ui.tree that return IDecisionMethod
 IDecisionMethod TreeEditorPanel.edit(java.awt.Component owner, IDecisionMethod method)
           
 IDecisionMethod TreePrefuse.getDecisionMethod()
           
 IDecisionMethod TreeDrawing.getDecisionMethod()
           
 IDecisionMethod JCustomTreeComponent.getDecisionMethod()
           
 IDecisionMethod ITreeView.getDecisionMethod()
           
 IDecisionMethod TreeLayout.getMethod()
           
 IDecisionMethod TreeEditorPanel.getMethod()
           
static IDecisionMethod SelectListDialog.selectNewTree(java.awt.Component parent, java.lang.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
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(java.awt.Component owner, IDecisionMethod method)
           
 void TreePrefuse.setDecisionMethod(IDecisionMethod decisionMethod)
           
 void TreePanel.setDecisionMethod(IDecisionMethod decisionMethod)
           
 void TreeFrame.setDecisionMethod(IDecisionMethod decisionMethod)
           
 void TreeDrawing.setDecisionMethod(IDecisionMethod method)
           
 void JCustomTreeComponent.setDecisionMethod(IDecisionMethod method)
           
 void ITreeView.setDecisionMethod(IDecisionMethod decisionMethod)
           
 void DecisionTreeModel.setDecisionMethod(IDecisionMethod decisionMethod)
           
 java.awt.Dimension TreeLayout.setMethod(IDecisionMethod method)
           
 void TreeEditorPanel.setMethod(IDecisionMethod method)
           
 

Constructors in toxtree.ui.tree with parameters of type IDecisionMethod
DecisionTreeModel(IDecisionMethod decisionMethod)
           
EditTreeActions(IDecisionMethod tree)
           
JCustomTreeComponent(IDecisionMethod method, javax.swing.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
protected  IDecisionMethod AbstractTreeAction.tree
           
 

Methods in toxtree.ui.tree.actions that return IDecisionMethod
 IDecisionMethod ITreeAction.getTree()
           
 IDecisionMethod AbstractTreeAction.getTree()
           
static IDecisionMethod NewRuleAction.treeFromRule(IDecisionRule rule)
           
 

Methods in toxtree.ui.tree.actions with parameters of type IDecisionMethod
 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
AbstractTreeAction(IDecisionMethod tree)
           
AbstractTreeAction(IDecisionMethod tree, java.lang.String name)
           
AbstractTreeAction(IDecisionMethod tree, java.lang.String name, javax.swing.Icon icon)
           
EditCategoryAction(IDecisionMethod tree)
           
EditCategoryAction(IDecisionMethod tree, java.lang.String name)
           
EditCategoryAction(IDecisionMethod tree, java.lang.String name, javax.swing.Icon icon)
           
EditRuleAction(IDecisionMethod tree)
           
EditRuleAction(IDecisionMethod tree, java.lang.String arg0)
           
EditRuleAction(IDecisionMethod tree, java.lang.String arg0, javax.swing.Icon arg1)
           
EditTreeExplanation(IDecisionMethod tree)
           
EditTreeExplanation(IDecisionMethod tree, java.lang.String name)
           
EditTreeExplanation(IDecisionMethod tree, java.lang.String name, javax.swing.Icon icon)
           
NewRuleAction(IDecisionMethod tree)
           
NewRuleAction(IDecisionMethod tree, java.lang.String name)
           
NewRuleAction(IDecisionMethod tree, java.lang.String name, javax.swing.Icon icon)
           
SaveTreeAction(IDecisionMethod tree)
           
SaveTreeAction(IDecisionMethod tree, java.lang.String name)
           
SaveTreeAction(IDecisionMethod tree, java.lang.String name, javax.swing.Icon icon)
           
SelectCategoryFromListAction(IDecisionMethod tree)
           
SelectCategoryFromListAction(IDecisionMethod tree, java.lang.String name)
           
SelectCategoryFromListAction(IDecisionMethod tree, java.lang.String name, javax.swing.Icon icon)
           
SetBranchAction(IDecisionMethod tree, boolean answer)
           
SetBranchAction(IDecisionMethod tree, boolean answer, java.lang.String name)
           
SetBranchAction(IDecisionMethod tree, boolean answer, java.lang.String name, javax.swing.Icon icon)
           
VerifyUnreachableRulesAction(IDecisionMethod tree)
           
VerifyUnreachableRulesAction(IDecisionMethod tree, java.lang.String name)
           
VerifyUnreachableRulesAction(IDecisionMethod tree, java.lang.String name, javax.swing.Icon icon)
           
VerifyUnusedCategories(IDecisionMethod tree)
           
VerifyUnusedCategories(IDecisionMethod tree, java.lang.String name)
           
VerifyUnusedCategories(IDecisionMethod tree, java.lang.String name, javax.swing.Icon icon)
           
 

Uses of IDecisionMethod in toxtree.ui.wizard
 

Fields in toxtree.ui.wizard declared as IDecisionMethod
protected  IDecisionMethod DecisionTreeWizard.tree
           
 

Methods in toxtree.ui.wizard with parameters of type IDecisionMethod
static DecisionNodeWizard DecisionNodeWizard.createWizard(java.awt.Frame frame, IDecisionMethod tree, int start)
           
 

Constructors in toxtree.ui.wizard with parameters of type IDecisionMethod
DecisionNodeWizard(java.awt.Dialog arg0, IDecisionMethod tree, ListPanel[] panels)
           
DecisionNodeWizard(java.awt.Frame frame, IDecisionMethod tree, ListPanel[] panels)
           
DecisionNodeWizard(IDecisionMethod tree, ListPanel[] panels)
           
DecisionTreeWizard(java.awt.Dialog arg0, IDecisionMethod tree)
           
DecisionTreeWizard(java.awt.Frame frame, IDecisionMethod tree)
           
DecisionTreeWizard(IDecisionMethod tree)
           
 

Uses of IDecisionMethod in verhaar
 

Classes in verhaar that implement IDecisionMethod
 class VerhaarScheme
          An implementaton of Verhaar scheme for predicting toxicity mode of action.
 



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