toxTree.tree

Class UserDefinedTree

java.lang.Object

java.util.Observable

toxTree.tree.AbstractTree

toxTree.tree.UserDefinedTree

All Implemented Interfaces:

ambit2.core.data.IObject2Properties<UserDefinedTree>, ambit2.core.data.IStructureDiagramDepiction<BufferedImage>, ambit2.core.data.IStructureDiagramHighlights, Serializable, Cloneable, Observer, net.idea.modbcum.i.processors.IProcessor<UserDefinedTree,List<ambit2.base.data.Property>>, org.openscience.cdk.qsar.IDescriptor, org.openscience.cdk.qsar.IMolecularDescriptor, IDecisionInteractive, IDecisionMethod, IDecisionMethodPrority, XMLSerializable

Direct Known Subclasses:

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

public class UserDefinedTree
extends AbstractTree
implements IDecisionInteractive, org.openscience.cdk.qsar.IMolecularDescriptor, ambit2.core.data.IObject2Properties<UserDefinedTree>

A default decision tree class, implementing IDecisionMethod interface. It stores categories in a IDecisionCategories and the tree itself in a DecisionNodesList. The tree is editable, i.e. rules can be added , removed and modified.

Author:

Nina Jeliazkova Modified 2005-11-10

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface toxTree.core.IDecisionInteractive

IDecisionInteractive.UserOptions

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	editable
protected PropertyChangeListener	listener
protected IDecisionNodesFactory	nodesFactory
protected IDecisionInteractive.UserOptions	options

Fields inherited from class toxTree.tree.AbstractTree

categories, changes, explanation, falseIfRuleNotImplemented, imageSize, logger, modified, name, priority, rules, treeRoot, web

Fields inherited from interface toxTree.core.XMLSerializable

xmltag_CATEGORIES, xmltag_CATEGORY, xmltag_CATEGORYTHRESHOLD, xmltag_CLASS, xmltag_EXPLANATION, xmltag_ID, xmltag_METHOD, xmltag_METHODPARAMETER, xmltag_METHODS, xmltag_NAME, xmltag_RULE, xmltag_RULEEXAMPLE, xmltag_RULES, xmltag_TREEROOT

Constructor Summary

Constructors

Constructor and Description
UserDefinedTree()
UserDefinedTree(IDecisionCategories classes, IDecisionRuleList rules)
UserDefinedTree(IDecisionCategories classes, String[] customRules, int[][] customTransitions, IDecisionNodesFactory nodesFactory)
UserDefinedTree(IDecisionNodesFactory nodesFactory)

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.qsar.DescriptorValue	calculate(org.openscience.cdk.interfaces.IAtomContainer mol)
Object	clone()
void	close()
protected ambit2.core.data.ArrayResult	createArrayResult(int length)
IDecisionRule	getBranch(IDecisionRule rule, boolean answer)
IDecisionRule	getBranch(int ruleId, boolean answer)
IDecisionCategory	getCategory(IDecisionRule rule, boolean answer)
IDecisionCategory	getCategory(int ruleId, boolean answer)
String[]	getDescriptorNames()
org.openscience.cdk.qsar.result.IDescriptorResult	getDescriptorResultType()
long	getID()
boolean	getInteractive()
PropertyChangeListener	getListener()
IDecisionNodesFactory	getNodesFactory()
IDecisionInteractive.UserOptions	getOptions()
String[]	getParameterNames()
Object[]	getParameters()
Object	getParameterType(String arg0)
IDecisionRule	getRule(int id)
org.openscience.cdk.qsar.DescriptorSpecification	getSpecification()
IDecisionRuleList	hasUnreachableRules()
IDecisionCategories	hasUnusedCategories()
void	initialise(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
protected IDecisionRuleList	initRules() public AbstractTree( IDecisionCategories classes, String[] customRules, int[][] customTransitions) throws DecisionMethodException { this(categories,customRules,customTransitions); } public AbstractTree( String[] customRules, int[][] customTransitions) throws DecisionMethodException { this(); setRules(customRules); setTransitions(customTransitions); setChanged(); notifyObservers(); }
boolean	isEditable()
boolean	isEnabled()
void	open()
List<ambit2.base.data.Property>	process(UserDefinedTree target)
void	removeListener()
protected void	setArrayValue(ambit2.core.data.ArrayResult result, int index, org.openscience.cdk.interfaces.IAtomContainer mol, String propertyName)
void	setEditable(boolean value)
void	setEnabled(boolean value)
void	setInteractive(boolean value)
void	setListener(PropertyChangeListener listener)
void	setNodesFactory(IDecisionNodesFactory nodesFactory)
void	setOptions(IDecisionInteractive.UserOptions options)
void	setParameters(org.openscience.cdk.interfaces.IAtomContainer mol) Can be used to display some options before applying the rules.
void	setParameters(Object[] arg0)
protected void	setTransitions(int[][] customTransitions)
String	toString()
protected boolean	verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result, IDecisionRule topRule) abstract method, to be implemented in the child class
protected void	visitCategories(DecisionNode rule, IDecisionCategories usedCategories)
protected void	visitRules(DecisionNode rule)

Methods inherited from class toxTree.tree.AbstractTree

addDecisionRule, addPropertyChangeListener, classify, clearChanged, createDecisionResult, equals, explainRules, fromXML, getCategories, getEditor, getExplanation, getImage, getImage, getImageSize, getLegend, getNumberOfClasses, getNumberOfRules, getPriority, getRule, getRules, getTitle, getTopRule, isFalseIfRuleNotImplemented, isModified, isWeb, optionsPanel, printResults, printToStream, removePropertyChangeListener, retrieveExplanation, setCategories, setChanged, setDecisionRule, setExplanation, setFalseIfRuleNotImplemented, setImageSize, setModified, setPriority, setRules, setRules, setTitle, setWeb, testRulesWithSelector, toShallowXML, toXML, update, verifyResidues, verifyRules, walkRules, walkRules

Methods inherited from class java.util.Observable

addObserver, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers

Methods inherited from class java.lang.Object

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

Field Detail

editable

protected boolean editable

nodesFactory

protected IDecisionNodesFactory nodesFactory

options

protected IDecisionInteractive.UserOptions options

listener

protected transient PropertyChangeListener listener

Constructor Detail

UserDefinedTree

public UserDefinedTree(IDecisionNodesFactory nodesFactory)

UserDefinedTree

public UserDefinedTree()

UserDefinedTree

public UserDefinedTree(IDecisionCategories classes,
                       IDecisionRuleList rules)

UserDefinedTree

public UserDefinedTree(IDecisionCategories classes,
                       String[] customRules,
                       int[][] customTransitions,
                       IDecisionNodesFactory nodesFactory)
                throws DecisionMethodException

Parameters:

classes -

customRules -

customTransitions -

Throws:

DecisionMethodException

Method Detail

getOptions

public IDecisionInteractive.UserOptions getOptions()

Specified by:

getOptions in interface IDecisionInteractive

setOptions

public void setOptions(IDecisionInteractive.UserOptions options)

Specified by:

setOptions in interface IDecisionInteractive

getListener

public PropertyChangeListener getListener()

Specified by:

getListener in interface IDecisionInteractive

setListener

public void setListener(PropertyChangeListener listener)

Specified by:

setListener in interface IDecisionInteractive

initRules

protected IDecisionRuleList initRules()

Description copied from class: AbstractTree

public AbstractTree( IDecisionCategories classes, String[] customRules, int[][] customTransitions) throws DecisionMethodException { this(categories,customRules,customTransitions); } public AbstractTree( String[] customRules, int[][] customTransitions) throws DecisionMethodException { this(); setRules(customRules); setTransitions(customTransitions); setChanged(); notifyObservers(); }

Specified by:

initRules in class AbstractTree

setTransitions

protected void setTransitions(int[][] customTransitions)

Specified by:

setTransitions in class AbstractTree

visitRules

protected void visitRules(DecisionNode rule)

hasUnreachableRules

public IDecisionRuleList hasUnreachableRules()

Specified by:

hasUnreachableRules in interface IDecisionMethod

visitCategories

protected void visitCategories(DecisionNode rule,
                               IDecisionCategories usedCategories)

hasUnusedCategories

public IDecisionCategories hasUnusedCategories()

Specified by:

hasUnusedCategories in interface IDecisionMethod

verifyRules

protected boolean verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol,
                              IDecisionResult result,
                              IDecisionRule topRule)
                       throws DecisionMethodException

Description copied from class: AbstractTree

abstract method, to be implemented in the child class

Specified by:

verifyRules in class AbstractTree

Parameters:

mol - - org.openscience.cdk.interfaces.AtomContainer to be analyzed

result - - IDecisionResult the result from the decision tree application

topRule - - the starting rule

Returns:

Throws:

DecisionMethodException

getBranch

public IDecisionRule getBranch(IDecisionRule rule,
                               boolean answer)

Specified by:

getBranch in interface IDecisionMethod

getBranch

public IDecisionRule getBranch(int ruleId,
                               boolean answer)

getCategory

public IDecisionCategory getCategory(IDecisionRule rule,
                                     boolean answer)

Specified by:

getCategory in interface IDecisionMethod

getCategory

public IDecisionCategory getCategory(int ruleId,
                                     boolean answer)

isEditable

public boolean isEditable()

Specified by:

isEditable in interface IDecisionMethod

setEditable

public void setEditable(boolean value)

Specified by:

setEditable in interface IDecisionMethod

getRule

public IDecisionRule getRule(int id)

Specified by:

getRule in interface IDecisionMethod

Overrides:

getRule in class AbstractTree

See Also:

IDecisionMethod.getRule(int)

clone

public Object clone()
             throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

toString

public String toString()

Overrides:

toString in class AbstractTree

setParameters

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

Description copied from class: AbstractTree

Can be used to display some options before applying the rules.

Specified by:

setParameters in interface IDecisionMethod

Specified by:

setParameters in class AbstractTree

getNodesFactory

public IDecisionNodesFactory getNodesFactory()

setNodesFactory

public void setNodesFactory(IDecisionNodesFactory nodesFactory)

getInteractive

public boolean getInteractive()

Specified by:

getInteractive in interface IDecisionInteractive

setInteractive

public void setInteractive(boolean value)

Specified by:

setInteractive in interface IDecisionInteractive

createArrayResult

protected ambit2.core.data.ArrayResult createArrayResult(int length)

setArrayValue

protected void setArrayValue(ambit2.core.data.ArrayResult result,
                             int index,
                             org.openscience.cdk.interfaces.IAtomContainer mol,
                             String propertyName)

calculate

public org.openscience.cdk.qsar.DescriptorValue calculate(org.openscience.cdk.interfaces.IAtomContainer mol)

Specified by:

calculate in interface org.openscience.cdk.qsar.IMolecularDescriptor

getDescriptorNames

public String[] getDescriptorNames()

Specified by:

getDescriptorNames in interface org.openscience.cdk.qsar.IDescriptor

getDescriptorResultType

public org.openscience.cdk.qsar.result.IDescriptorResult getDescriptorResultType()

Specified by:

getDescriptorResultType in interface org.openscience.cdk.qsar.IMolecularDescriptor

getParameterNames

public String[] getParameterNames()

Specified by:

getParameterNames in interface org.openscience.cdk.qsar.IDescriptor

getParameters

public Object[] getParameters()

Specified by:

getParameters in interface org.openscience.cdk.qsar.IDescriptor

getParameterType

public Object getParameterType(String arg0)

Specified by:

getParameterType in interface org.openscience.cdk.qsar.IDescriptor

setParameters

public void setParameters(Object[] arg0)
                   throws org.openscience.cdk.exception.CDKException

Specified by:

setParameters in interface org.openscience.cdk.qsar.IDescriptor

Throws:

org.openscience.cdk.exception.CDKException

getSpecification

public org.openscience.cdk.qsar.DescriptorSpecification getSpecification()

Specified by:

getSpecification in interface org.openscience.cdk.qsar.IDescriptor

removeListener

public void removeListener()

Specified by:

removeListener in interface IDecisionInteractive

process

public List<ambit2.base.data.Property> process(UserDefinedTree target)
                                        throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

process in interface ambit2.core.data.IObject2Properties<UserDefinedTree>

Specified by:

process in interface net.idea.modbcum.i.processors.IProcessor<UserDefinedTree,List<ambit2.base.data.Property>>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

setEnabled

public void setEnabled(boolean value)

Specified by:

setEnabled in interface net.idea.modbcum.i.processors.IProcessor<UserDefinedTree,List<ambit2.base.data.Property>>

isEnabled

public boolean isEnabled()

Specified by:

isEnabled in interface net.idea.modbcum.i.processors.IProcessor<UserDefinedTree,List<ambit2.base.data.Property>>

getID

public long getID()

Specified by:

getID in interface net.idea.modbcum.i.processors.IProcessor<UserDefinedTree,List<ambit2.base.data.Property>>

close

public void close()
           throws Exception

Specified by:

close in interface net.idea.modbcum.i.processors.IProcessor<UserDefinedTree,List<ambit2.base.data.Property>>

Throws:

Exception

open

public void open()
          throws Exception

Specified by:

open in interface net.idea.modbcum.i.processors.IProcessor<UserDefinedTree,List<ambit2.base.data.Property>>

Throws:

Exception

initialise

public void initialise(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Specified by:

initialise in interface org.openscience.cdk.qsar.IDescriptor