toxTree.core

Interface IDecisionMethod

All Superinterfaces:

Cloneable, IDecisionMethodPrority, ambit2.core.data.IStructureDiagramDepiction<BufferedImage>, ambit2.core.data.IStructureDiagramHighlights, Serializable

All Known Implementing Classes:

AbstractTree, AmesMutagenicityRules, BatchDecisionResultsList, BB_CarcMutRules, BiodgeradationRules, CompoundLookup, CramerRules, CramerRulesWithExtensions, DNABindingPlugin, EyeIrritationRules, FuncRules, Kroes1Tree, LewisTree, MichaelAcceptorRules, MICRules, MOARules, ProteinBindingPlugin, RevisedCramerDecisionTree, SicretRules, SkinSensitisationPlugin, SMARTCYPPlugin, SMARTSTree, SubstructureTree, UserDefinedTree, VerhaarScheme, VerhaarScheme2

public interface IDecisionMethod
extends Serializable, 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

Modifier and Type	Method and Description
void	addDecisionRule(IDecisionRule rule)
void	addPropertyChangeListener(PropertyChangeListener l)
boolean	classify(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
IDecisionResult	createDecisionResult()
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.
String	getExplanation()
int	getNumberOfClasses()
int	getNumberOfRules()
IDecisionRule	getRule(int id)
IDecisionRule	getRule(String name)
IDecisionRuleList	getRules()
String	getTitle()
IDecisionRule	getTopRule()
IDecisionRuleList	hasUnreachableRules()
IDecisionCategories	hasUnusedCategories()
boolean	isEditable()
boolean	isModified()
boolean	isWeb()
void	removePropertyChangeListener(PropertyChangeListener l)
void	setDecisionRule(IDecisionRule rule)
void	setEditable(boolean value)
void	setExplanation(String value)
void	setModified(boolean value)
void	setParameters(org.openscience.cdk.interfaces.IAtomContainer mol)
void	setTitle(String value)
void	setWeb(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.IStructureDiagramDepiction

getImage, getImage, getImageSize, getLegend, setImageSize

Method Detail

getTitle

String getTitle()

setTitle

void setTitle(String value)

getExplanation

String getExplanation()

setExplanation

void setExplanation(String value)

getRule

IDecisionRule getRule(int id)

getRule

IDecisionRule getRule(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

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(PropertyChangeListener l)

removePropertyChangeListener

void removePropertyChangeListener(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(Boolean web)

isWeb

boolean isWeb()