toxTree.core
Interface IDecisionMethod

All Superinterfaces:
java.lang.Cloneable, IDecisionMethodPrority, ambit2.core.data.IStructureDiagramHighlights, java.io.Serializable
All Known Implementing Classes:
AbstractTree, BatchDecisionResultsList, BB_CarcMutRules, BiodgeradationRules, CompoundLookup, CramerRules, CramerRulesWithExtensions, DNABindingPlugin, EyeIrritationRules, FuncRules, Kroes1Tree, LewisTree, MichaelAcceptorRules, MICRules, MOARules, ProteinBindingPlugin, SicretRules, SkinSensitisationPlugin, SMARTCYPPlugin, SMARTSTree, SubstructureTree, UserDefinedTree, VerhaarScheme, VerhaarScheme2

public interface IDecisionMethod
extends java.io.Serializable, java.lang.Cloneable, IDecisionMethodPrority, ambit2.core.data.IStructureDiagramHighlights

An interface to represent a decision tree. In order to be used as a decision tree in the toxTree application, a class should implement this interface.
The decision method consists of rules, which are classes implementing IDecisionRule.
and transitions IDecisionTransition. The result of applying a decision tree to a compound is assigning IDecisionCategory.
The assigned category and the path followed is represented by IDecisionResult.

Version:
0.1, 2005-4-30
Author:
Nina Jeliazkova

Method Summary
 void addDecisionRule(IDecisionRule rule)
           
 void addPropertyChangeListener(java.beans.PropertyChangeListener l)
           
 boolean classify(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
           
 IDecisionResult createDecisionResult()
           
 java.lang.StringBuffer explainRules(IDecisionResult result, boolean verbose)
           
 IDecisionRule getBranch(IDecisionRule rule, boolean answer)
           
 IDecisionCategories getCategories()
           
 IDecisionCategory getCategory(IDecisionRule rule, boolean answer)
           
 IDecisionMethodEditor getEditor()
          Each rule provides an editor, which is a class implementing IDecisionMethodEditor.
 java.lang.String getExplanation()
           
 int getNumberOfClasses()
           
 int getNumberOfRules()
           
 IDecisionRule getRule(int id)
           
 IDecisionRule getRule(java.lang.String name)
           
 IDecisionRuleList getRules()
           
 java.lang.String getTitle()
           
 IDecisionRule getTopRule()
           
 IDecisionRuleList hasUnreachableRules()
           
 IDecisionCategories hasUnusedCategories()
           
 boolean isEditable()
           
 boolean isModified()
           
 boolean isWeb()
           
 void removePropertyChangeListener(java.beans.PropertyChangeListener l)
           
 void setDecisionRule(IDecisionRule rule)
           
 void setEditable(boolean value)
           
 void setExplanation(java.lang.String value)
           
 void setModified(boolean value)
           
 void setParameters(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 void setTitle(java.lang.String value)
           
 void setWeb(java.lang.Boolean web)
           
 boolean verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
           
 void walkRules(IDecisionRule rule, IProcessRule processor)
           
 
Methods inherited from interface toxTree.core.IDecisionMethodPrority
getPriority, setPriority
 
Methods inherited from interface ambit2.core.data.IStructureDiagramHighlights
getImage, getImage, getImageSize, getLegend, setImageSize
 

Method Detail

getTitle

java.lang.String getTitle()

setTitle

void setTitle(java.lang.String value)

getExplanation

java.lang.String getExplanation()

setExplanation

void setExplanation(java.lang.String value)

getRule

IDecisionRule getRule(int id)

getRule

IDecisionRule getRule(java.lang.String name)

getTopRule

IDecisionRule getTopRule()

getBranch

IDecisionRule getBranch(IDecisionRule rule,
                        boolean answer)

getCategory

IDecisionCategory getCategory(IDecisionRule rule,
                              boolean answer)

getCategories

IDecisionCategories getCategories()

getRules

IDecisionRuleList getRules()

setDecisionRule

void setDecisionRule(IDecisionRule rule)
                     throws DecisionMethodException
Throws:
DecisionMethodException

addDecisionRule

void addDecisionRule(IDecisionRule rule)
                     throws DecisionMethodException
Throws:
DecisionMethodException

explainRules

java.lang.StringBuffer explainRules(IDecisionResult result,
                                    boolean verbose)
                                    throws DecisionMethodException
Throws:
DecisionMethodException

verifyRules

boolean verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol,
                    IDecisionResult result)
                    throws DecisionMethodException
Throws:
DecisionMethodException

classify

boolean classify(org.openscience.cdk.interfaces.IAtomContainer mol,
                 IDecisionResult result)
                 throws DecisionMethodException
Throws:
DecisionMethodException

walkRules

void walkRules(IDecisionRule rule,
               IProcessRule processor)
               throws DecisionMethodException
Throws:
DecisionMethodException

hasUnreachableRules

IDecisionRuleList hasUnreachableRules()

hasUnusedCategories

IDecisionCategories hasUnusedCategories()

getNumberOfRules

int getNumberOfRules()

getNumberOfClasses

int getNumberOfClasses()

addPropertyChangeListener

void addPropertyChangeListener(java.beans.PropertyChangeListener l)

removePropertyChangeListener

void removePropertyChangeListener(java.beans.PropertyChangeListener l)

createDecisionResult

IDecisionResult createDecisionResult()

isEditable

boolean isEditable()

setEditable

void setEditable(boolean value)

isModified

boolean isModified()

setModified

void setModified(boolean value)

getEditor

IDecisionMethodEditor getEditor()
Each rule provides an editor, which is a class implementing IDecisionMethodEditor. The editor shall provide user interface for visualization and modification of various method settings.

Returns:
IDecisionMethodEditor

setParameters

void setParameters(org.openscience.cdk.interfaces.IAtomContainer mol)

setWeb

void setWeb(java.lang.Boolean web)

isWeb

boolean isWeb()


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