toxTree.tree

Class DecisionNode

java.lang.Object

java.util.Observable

toxTree.tree.DecisionNode

All Implemented Interfaces:

Serializable, Cloneable, Observer, IDecisionRule, IDecisionTransition

Direct Known Subclasses:

MultiLabelDecisionNode

public class DecisionNode
extends Observable
implements IDecisionRule, IDecisionTransition, Observer

A decision node to be used in UserDefinedTree. Implements IDecisionRule and IDecisionTransition.

A decision node consists of a rule IDecisionRule and decision nodes DecisionNode to be followed, or categories IDecisionCategory to be assigned if the rule provides YES or NO answer.

Version:

0.1, 2005-5-2

Author:

Nina Jeliazkova

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected IDecisionCategory[]	categories
protected DecisionNode[]	nodes
protected IDecisionRule	rule
protected boolean	visited

Constructor Summary

Constructors

Constructor and Description
DecisionNode() Constructor
DecisionNode(IDecisionRule rule) Constructs a decision node with rule, null next nodes.
DecisionNode(IDecisionRule rule, DecisionNode nodeNo, DecisionNode nodeYes) Constructs a decision node with rule, nodeNo at branch NO and nodeYes at branch YES.
DecisionNode(IDecisionRule rule, DecisionNode nodeNo, DecisionNode nodeYes, IDecisionCategory categoryNo, IDecisionCategory categoryYes)

Method Summary

Modifier and Type	Method and Description
void	addPropertyChangeListener(PropertyChangeListener l)
void	clearFlags(org.openscience.cdk.interfaces.IAtomContainer mol) When rules analyze a molecule, a set of properties are set.
Object	clone()
boolean	equals(Object obj)
IDecisionRule	getBranch(boolean answer) returns the decision rule at the branch No if answer==false or the decision rule at the branch Yes if answer =true
IDecisionCategory[]	getCategories()
IDecisionCategory	getCategory(boolean answer) returns the decision category at the branch No if answer==false or the category at the branch Yes if answer =true
IDecisionRuleEditor	getEditor() Each rule provides an editor, which is a class implementing IDecisionRuleEditor.
org.openscience.cdk.interfaces.IAtomContainer	getExampleMolecule(boolean ruleResult) if ruleResult is TRUE, returns the example molecule if the rule is answered YES if ruleResult is FALSE, returns the example molecule if the rule is answered NO
String	getExplanation() Rule explanation is an arbitrary text, could be multiline and may contain html tags.
String	getID() Rule identifier is an arbitrary string, preferably short one
DecisionNode[]	getNodes()
int	getNum()
IDecisionRule	getRule()
ambit2.rendering.IAtomContainerHighlights	getSelector()
String	getTitle() Rule name is an arbitrary string, preferably one line, reflecting the essence of the rule (e.g.
void	hideResiduesID(boolean hide)
boolean	isEditable()
boolean	isImplemented()
boolean	isResidueIDHidden()
boolean	isVisited()
void	removePropertyChangeListener(PropertyChangeListener l)
void	setBranch(boolean answer, IDecisionRule node) Sets the decision rule at the branch No if answer==false or the decision rule at the branch Yes if answer =true
void	setCategories(IDecisionCategory[] categories)
void	setCategory(boolean answer, IDecisionCategory category) /** Sets the category at the branch No if answer==false or the category at the branch Yes if answer =true
void	setEditable(boolean value)
void	setExampleMolecule(org.openscience.cdk.interfaces.IAtomContainer mol, boolean ruleResult) Sets example molecule for the YES or NO answer of the rule
void	setExplanation(String message) Sets rule explanation
void	setID(String id) Sets rule identifier
void	setNodes(DecisionNode[] nodes)
void	setNum(int no)
void	setRule(IDecisionRule rule) Sets rule
void	setTitle(String name) Sets rule name
void	setVisited(boolean visited)
String	toString()
String	toString(boolean verbose) Returns string representation of the decision node if (verbose) returns getId() + "." + getName() else returns "Q"+getId();
void	update(Observable arg0, Object arg1)
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) This is the core of a IDecisionRule behaviour.

Methods inherited from class java.util.Observable

addObserver, clearChanged, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers, setChanged

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

rule

protected IDecisionRule rule

nodes

protected DecisionNode[] nodes

categories

protected IDecisionCategory[] categories

visited

protected transient boolean visited

Constructor Detail

DecisionNode

public DecisionNode()

Constructor

DecisionNode

public DecisionNode(IDecisionRule rule)

Constructs a decision node with rule, null next nodes.

Parameters:

rule -

DecisionNode

public DecisionNode(IDecisionRule rule,
                    DecisionNode nodeNo,
                    DecisionNode nodeYes)

Constructs a decision node with rule, nodeNo at branch NO and nodeYes at branch YES. Categories are assigned null value.

Parameters:

rule -

nodeNo -

nodeYes -

DecisionNode

public DecisionNode(IDecisionRule rule,
                    DecisionNode nodeNo,
                    DecisionNode nodeYes,
                    IDecisionCategory categoryNo,
                    IDecisionCategory categoryYes)

Parameters:

rule - - the rule

nodeNo - - the node at branch "No"

nodeYes - - the node at branch "Yes"

categoryNo - - the Category at branch "No"

categoryYes - - the Category at branch "Yes"

Method Detail

isEditable

public boolean isEditable()

Specified by:

isEditable in interface IDecisionRule

setEditable

public void setEditable(boolean value)

Specified by:

setEditable in interface IDecisionRule

getRule

public IDecisionRule getRule()

Returns:

rule

setRule

public void setRule(IDecisionRule rule)

Sets rule

Parameters:

rule -

getBranch

public IDecisionRule getBranch(boolean answer)

returns the decision rule at the branch No if answer==false or the decision rule at the branch Yes if answer =true

Specified by:

getBranch in interface IDecisionTransition

setBranch

public void setBranch(boolean answer,
                      IDecisionRule node)

Sets the decision rule at the branch No if answer==false or the decision rule at the branch Yes if answer =true

Parameters:

answer - - selects which branch to be set

node - - the next node to set

getCategory

public IDecisionCategory getCategory(boolean answer)

returns the decision category at the branch No if answer==false or the category at the branch Yes if answer =true

Specified by:

getCategory in interface IDecisionTransition

setCategory

public void setCategory(boolean answer,
                        IDecisionCategory category)

/** Sets the category at the branch No if answer==false or the category at the branch Yes if answer =true

Parameters:

answer -

category -

toString

public String toString(boolean verbose)

Returns string representation of the decision node if (verbose) returns getId() + "." + getName() else returns "Q"+getId();

Parameters:

verbose -

Returns:

String

toString

public String toString()

Specified by:

toString in interface IDecisionRule

Overrides:

toString in class Object

getExampleMolecule

public org.openscience.cdk.interfaces.IAtomContainer getExampleMolecule(boolean ruleResult)
                                                                 throws DecisionMethodException

Description copied from interface: IDecisionRule

if ruleResult is TRUE, returns the example molecule if the rule is answered YES if ruleResult is FALSE, returns the example molecule if the rule is answered NO

Specified by:

getExampleMolecule in interface IDecisionRule

Returns:

org.openscience.cdk.interfaces.Molecule

Throws:

DecisionMethodException

getExplanation

public String getExplanation()

Description copied from interface: IDecisionRule

Rule explanation is an arbitrary text, could be multiline and may contain html tags.

Specified by:

getExplanation in interface IDecisionRule

Returns:

explanation

getID

public String getID()

Description copied from interface: IDecisionRule

Rule identifier is an arbitrary string, preferably short one

Specified by:

getID in interface IDecisionRule

Returns:

the rule identifier

getTitle

public String getTitle()

Description copied from interface: IDecisionRule

Rule name is an arbitrary string, preferably one line, reflecting the essence of the rule
(e.g. "Is aromatic")

Specified by:

getTitle in interface IDecisionRule

Returns:

rule name

getNum

public int getNum()

Specified by:

getNum in interface IDecisionRule

isImplemented

public boolean isImplemented()

Specified by:

isImplemented in interface IDecisionRule

Returns:

false if the rule is not implemented and true if it is

setExampleMolecule

public void setExampleMolecule(org.openscience.cdk.interfaces.IAtomContainer mol,
                               boolean ruleResult)

Description copied from interface: IDecisionRule

Sets example molecule for the YES or NO answer of the rule

Specified by:

setExampleMolecule in interface IDecisionRule

Parameters:

mol - org.openscience.cdk.interfaces.Molecule

addPropertyChangeListener

public void addPropertyChangeListener(PropertyChangeListener l)

Specified by:

addPropertyChangeListener in interface IDecisionRule

removePropertyChangeListener

public void removePropertyChangeListener(PropertyChangeListener l)

Specified by:

removePropertyChangeListener in interface IDecisionRule

setExplanation

public void setExplanation(String message)

Description copied from interface: IDecisionRule

Sets rule explanation

Specified by:

setExplanation in interface IDecisionRule

setID

public void setID(String id)

Description copied from interface: IDecisionRule

Sets rule identifier

Specified by:

setID in interface IDecisionRule

setTitle

public void setTitle(String name)

Description copied from interface: IDecisionRule

Sets rule name

Specified by:

setTitle in interface IDecisionRule

setNum

public void setNum(int no)

Specified by:

setNum in interface IDecisionRule

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
                   throws DecisionMethodException

Description copied from interface: IDecisionRule

This is the core of a IDecisionRule behaviour. The method returns true if the answer of the rule is YES for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer and FALSE if the answer of the rule is NO for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer??

Specified by:

verifyRule in interface IDecisionRule

Parameters:

mol - org.openscience.cdk.interfaces.AtomContainer

Returns:

rule result, boolean

Throws:

DecisionMethodException

isVisited

public boolean isVisited()

Returns:

Returns the visited.

setVisited

public void setVisited(boolean visited)

Parameters:

visited - The visited to set.

clearFlags

public void clearFlags(org.openscience.cdk.interfaces.IAtomContainer mol)

Description copied from interface: IDecisionRule

When rules analyze a molecule, a set of properties are set. This method provides a way to clear the properties. Could be moved in a different class in a later release

Specified by:

clearFlags in interface IDecisionRule

Parameters:

mol - org.openscience.cdk.interfaces.Molecule

hideResiduesID

public void hideResiduesID(boolean hide)

Specified by:

hideResiduesID in interface IDecisionRule

isResidueIDHidden

public boolean isResidueIDHidden()

Specified by:

isResidueIDHidden in interface IDecisionRule

getEditor

public IDecisionRuleEditor getEditor()

Description copied from interface: IDecisionRule

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

Specified by:

getEditor in interface IDecisionRule

Returns:

IDecisionRuleEditor

clone

public Object clone()
             throws CloneNotSupportedException

Specified by:

clone in interface IDecisionRule

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

update

public void update(Observable arg0,
                   Object arg1)

Specified by:

update in interface Observer

getCategories

public IDecisionCategory[] getCategories()

setCategories

public void setCategories(IDecisionCategory[] categories)

getNodes

public DecisionNode[] getNodes()

setNodes

public void setNodes(DecisionNode[] nodes)

getSelector

public ambit2.rendering.IAtomContainerHighlights getSelector()

Specified by:

getSelector in interface IDecisionRule