toxTree.tree

Class AbstractTree

java.lang.Object

java.util.Observable

toxTree.tree.AbstractTree

All Implemented Interfaces:

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

Direct Known Subclasses:

UserDefinedTree

public abstract class AbstractTree
extends Observable
implements IDecisionMethod, Observer, XMLSerializable

An astract class, implementing IDecisionMethod interface. Used as a base class for the decision trees in ToxTreeApp. The default editor is TreeEditorPanel.

Author:

Nina Jeliazkova
Modified 2005-4-30

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected IDecisionCategories	categories
protected PropertyChangeSupport	changes
protected String	explanation
protected boolean	falseIfRuleNotImplemented
protected Dimension	imageSize
protected static Logger	logger
protected boolean	modified
protected String	name
protected int	priority
protected IDecisionRuleList	rules
protected int	treeRoot
protected boolean	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
AbstractTree() Constructor
AbstractTree(IDecisionCategories categories)
AbstractTree(IDecisionCategories categories, IDecisionRuleList rules)

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)
protected void	clearChanged()
IDecisionResult	createDecisionResult()
boolean	equals(Object obj)
StringBuffer	explainRules(IDecisionResult result, boolean verbose)
void	fromXML(Element xml)
IDecisionCategories	getCategories()
IDecisionMethodEditor	getEditor() Each rule provides an editor, which is a class implementing IDecisionMethodEditor.
String	getExplanation()
BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer mol)
BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer mol, String ruleID, int width, int height, boolean atomnumbers)
Dimension	getImageSize()
BufferedImage	getLegend(int width, int height)
int	getNumberOfClasses()
int	getNumberOfRules()
int	getPriority()
IDecisionRule	getRule(int id)
IDecisionRule	getRule(String name)
IDecisionRuleList	getRules()
String	getTitle() returns the decision tree title (e.g.
IDecisionRule	getTopRule()
protected abstract 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	isFalseIfRuleNotImplemented()
boolean	isModified()
boolean	isWeb()
JComponent	optionsPanel(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
void	printResults(String filename)
void	printToStream(OutputStream os)
void	removePropertyChangeListener(PropertyChangeListener l)
protected String	retrieveExplanation(String resourceBundle)
void	setCategories(IDecisionCategories categories)
protected void	setChanged()
void	setDecisionRule(IDecisionRule rule)
void	setExplanation(String explanation)
void	setFalseIfRuleNotImplemented(boolean falseIfRuleNotImplemented)
void	setImageSize(Dimension imageSize)
void	setModified(boolean value)
abstract void	setParameters(org.openscience.cdk.interfaces.IAtomContainer mol) Can be used to display some options before applying the rules.
void	setPriority(int priority)
void	setRules(IDecisionRuleList rules)
protected void	setRules(String[] customRules)
void	setTitle(String value) sets decision tree title (e.g.
protected abstract void	setTransitions(int[][] customTransitions)
void	setWeb(Boolean web)
int	testRulesWithSelector()
Element	toShallowXML(Document document)
String	toString()
Element	toXML(Document document)
void	update(Observable o, Object arg)
protected boolean	verifyResidues(org.openscience.cdk.interfaces.IAtomContainerSet mols, IDecisionResult result, IDecisionRule rule)
boolean	verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result) IDecisionRule.verifyRule(IAtomContainer)
protected abstract boolean	verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result, IDecisionRule rule) abstract method, to be implemented in the child class
protected void	walkRules(IDecisionRule rule, ArrayList<Integer> visited, IProcessRule processor)
void	walkRules(IDecisionRule rule, IProcessRule processor)

Methods inherited from class java.util.Observable

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface toxTree.core.IDecisionMethod

getBranch, getCategory, hasUnreachableRules, hasUnusedCategories, isEditable, setEditable

Field Detail

logger

protected static transient Logger logger

imageSize

protected Dimension imageSize

web

protected boolean web

changes

protected transient PropertyChangeSupport changes

rules

protected IDecisionRuleList rules

categories

protected IDecisionCategories categories

falseIfRuleNotImplemented

protected boolean falseIfRuleNotImplemented

treeRoot

protected int treeRoot

name

protected String name

explanation

protected String explanation

modified

protected transient boolean modified

priority

protected int priority

Constructor Detail

AbstractTree

public AbstractTree()

Constructor

AbstractTree

public AbstractTree(IDecisionCategories categories)

AbstractTree

public AbstractTree(IDecisionCategories categories,
                    IDecisionRuleList rules)

Method Detail

getImageSize

public Dimension getImageSize()

Specified by:

getImageSize in interface ambit2.core.data.IStructureDiagramDepiction<BufferedImage>

setImageSize

public void setImageSize(Dimension imageSize)

Specified by:

setImageSize in interface ambit2.core.data.IStructureDiagramDepiction<BufferedImage>

initRules

protected abstract 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(); }

setRules

protected void setRules(String[] customRules)
                 throws DecisionMethodException

Throws:

DecisionMethodException

setTransitions

protected abstract void setTransitions(int[][] customTransitions)

getTitle

public String getTitle()

returns the decision tree title (e.g. "Cramer rules")

Specified by:

getTitle in interface IDecisionMethod

setTitle

public void setTitle(String value)

sets decision tree title (e.g. "Cramer rules")

Specified by:

setTitle in interface IDecisionMethod

addDecisionRule

public void addDecisionRule(IDecisionRule rule)
                     throws DecisionMethodException

Specified by:

addDecisionRule in interface IDecisionMethod

Throws:

DecisionMethodException

See Also:

IDecisionMethod.addDecisionRule(toxTree.core.IDecisionRule)

setDecisionRule

public void setDecisionRule(IDecisionRule rule)
                     throws DecisionMethodException

Specified by:

setDecisionRule in interface IDecisionMethod

Throws:

DecisionMethodException

See Also:

IDecisionMethod.setDecisionRule(toxTree.core.IDecisionRule)

explainRules

public StringBuffer explainRules(IDecisionResult result,
                                 boolean verbose)
                          throws DecisionMethodException

Specified by:

explainRules in interface IDecisionMethod

Throws:

DecisionMethodException

See Also:

IDecisionMethod.explainRules(IDecisionResult,boolean)

verifyResidues

protected boolean verifyResidues(org.openscience.cdk.interfaces.IAtomContainerSet mols,
                                 IDecisionResult result,
                                 IDecisionRule rule)
                          throws DecisionMethodException

Throws:

DecisionMethodException

verifyRules

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

IDecisionRule.verifyRule(IAtomContainer)

Specified by:

verifyRules in interface IDecisionMethod

Throws:

DecisionMethodException

verifyRules

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

abstract method, to be implemented in the child class

Parameters:

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

result - - IDecisionResult the result from the decision tree application

rule - - the starting rule

Returns:

Throws:

DecisionMethodException

classify

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

Specified by:

classify in interface IDecisionMethod

Throws:

DecisionMethodException

setParameters

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

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

Specified by:

setParameters in interface IDecisionMethod

Parameters:

mol -

optionsPanel

public JComponent optionsPanel(org.openscience.cdk.interfaces.IAtomContainer atomContainer)

getNumberOfRules

public int getNumberOfRules()

Specified by:

getNumberOfRules in interface IDecisionMethod

getRule

public IDecisionRule getRule(int id)

Specified by:

getRule in interface IDecisionMethod

See Also:

IDecisionMethod.getRule(int)

getRule

public IDecisionRule getRule(String name)

Specified by:

getRule in interface IDecisionMethod

See Also:

IDecisionMethod.getRule(java.lang.String)

printToStream

public void printToStream(OutputStream os)
                   throws IOException

Parameters:

os -

Throws:

IOException

printResults

public void printResults(String filename)
                  throws IOException

Parameters:

filename -

Throws:

IOException

isFalseIfRuleNotImplemented

public boolean isFalseIfRuleNotImplemented()

setFalseIfRuleNotImplemented

public void setFalseIfRuleNotImplemented(boolean falseIfRuleNotImplemented)

addPropertyChangeListener

public void addPropertyChangeListener(PropertyChangeListener l)

Specified by:

addPropertyChangeListener in interface IDecisionMethod

removePropertyChangeListener

public void removePropertyChangeListener(PropertyChangeListener l)

Specified by:

removePropertyChangeListener in interface IDecisionMethod

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

getCategories

public IDecisionCategories getCategories()

Specified by:

getCategories in interface IDecisionMethod

toString

public String toString()

Overrides:

toString in class Object

createDecisionResult

public IDecisionResult createDecisionResult()

Specified by:

createDecisionResult in interface IDecisionMethod

getNumberOfClasses

public int getNumberOfClasses()

Specified by:

getNumberOfClasses in interface IDecisionMethod

getRules

public IDecisionRuleList getRules()

Specified by:

getRules in interface IDecisionMethod

getExplanation

public String getExplanation()

Specified by:

getExplanation in interface IDecisionMethod

setExplanation

public void setExplanation(String explanation)

Specified by:

setExplanation in interface IDecisionMethod

update

public void update(Observable o,
                   Object arg)

Specified by:

update in interface Observer

getTopRule

public IDecisionRule getTopRule()

Specified by:

getTopRule in interface IDecisionMethod

setChanged

protected void setChanged()

Overrides:

setChanged in class Observable

clearChanged

protected void clearChanged()

Overrides:

clearChanged in class Observable

isModified

public boolean isModified()

Specified by:

isModified in interface IDecisionMethod

setModified

public void setModified(boolean value)

Specified by:

setModified in interface IDecisionMethod

getEditor

public IDecisionMethodEditor getEditor()

Description copied from interface: IDecisionMethod

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.

Specified by:

getEditor in interface IDecisionMethod

Returns:

IDecisionMethodEditor

fromXML

public void fromXML(Element xml)
             throws XMLDecisionMethodException

Specified by:

fromXML in interface XMLSerializable

Throws:

XMLDecisionMethodException

toShallowXML

public Element toShallowXML(Document document)
                     throws XMLDecisionMethodException

Specified by:

toShallowXML in interface XMLSerializable

Throws:

XMLDecisionMethodException

toXML

public Element toXML(Document document)
              throws XMLDecisionMethodException

Specified by:

toXML in interface XMLSerializable

Throws:

XMLDecisionMethodException

setRules

public void setRules(IDecisionRuleList rules)

setCategories

public void setCategories(IDecisionCategories categories)

getPriority

public int getPriority()

Specified by:

getPriority in interface IDecisionMethodPrority

setPriority

public void setPriority(int priority)

Specified by:

setPriority in interface IDecisionMethodPrority

testRulesWithSelector

public int testRulesWithSelector()
                          throws Exception

Throws:

Exception

walkRules

public void walkRules(IDecisionRule rule,
                      IProcessRule processor)
               throws DecisionMethodException

Specified by:

walkRules in interface IDecisionMethod

Throws:

DecisionMethodException

walkRules

protected void walkRules(IDecisionRule rule,
                         ArrayList<Integer> visited,
                         IProcessRule processor)
                  throws DecisionMethodException

Throws:

DecisionMethodException

getImage

public BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer mol)
                       throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getImage in interface ambit2.core.data.IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getImage

public BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer mol,
                              String ruleID,
                              int width,
                              int height,
                              boolean atomnumbers)
                       throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getImage in interface ambit2.core.data.IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

setWeb

public void setWeb(Boolean web)

Specified by:

setWeb in interface IDecisionMethod

isWeb

public boolean isWeb()

Specified by:

isWeb in interface IDecisionMethod

getLegend

public BufferedImage getLegend(int width,
                               int height)
                        throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getLegend in interface ambit2.core.data.IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

retrieveExplanation

protected String retrieveExplanation(String resourceBundle)