toxTree.tree

Class AbstractRule

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, XMLSerializable

Direct Known Subclasses:

AbstractRuleHilightHits, AbstractRuleSmartSubstructure, Find, KroesRule8, LinearDiscriminantRule, MetaboliteGenerator, Rule13_AliphaticMonoalcohols, Rule3MemberedHeterocycle, RuleAnySubstituents, RuleDescriptor, RuleElements, RuleHeterocyclic, RuleKetoneAlcoholEtc, RuleManyAromaticRings, RuleOpenChain, RuleStructuresList, RuleSufficientSulphonateGroups, RuleTwoOrMoreRings, RuleVerifyProperty, UserInputRule

public abstract class AbstractRule
extends Observable
implements IDecisionRule, XMLSerializable

An abstract class implementing IDecisionRule interface. Used as a base class for all rules in ToxTreeApp application.

Version:

0.1, 2005-5-2

Author:

Nina Jeliazkova

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected PropertyChangeSupport	changes
protected boolean	editable
static String	ERR_STRUCTURENOTPREPROCESSED
protected String[]	examples
protected StringBuffer	explanation
protected String	id
protected static Logger	logger
static String	MSG_NO
static String	MSG_YES
protected int	no
protected boolean	residueIDHidden
protected String	title

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
AbstractRule() Constructor

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()
static IDecisionRule	createRule(String className)
boolean	equals(Object obj)
void	fromXML(Element xml)
IDecisionRuleEditor	getEditor() See IDecisionRule.getEditor()
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[]	getExamples()
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
int	getNum()
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()
protected void	log(Level level, String message)
protected void	log(Level level, String message, Object param)
protected void	log(Level level, String message, Object[] params)
static org.openscience.cdk.interfaces.IAtomContainer	makeMolecule(boolean yes) This is to ensure each derived class will provide an example of a molecule which resolves to the yes and no rule outcome
void	removePropertyChangeListener(PropertyChangeListener l)
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	setExamples(String[] examples)
void	setExplanation(String message) Sets rule explanation
void	setID(String id) Sets rule identifier
void	setNum(int no)
void	setTitle(String name) Sets rule name
Element	toShallowXML(Document document)
String	toString()
Element	toXML(Document document)

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

Methods inherited from interface toxTree.core.IDecisionRule

verifyRule

Field Detail

ERR_STRUCTURENOTPREPROCESSED

public static transient String ERR_STRUCTURENOTPREPROCESSED

MSG_YES

public static transient String MSG_YES

MSG_NO

public static transient String MSG_NO

logger

protected static transient Logger logger

changes

protected transient PropertyChangeSupport changes

title

protected String title

explanation

protected StringBuffer explanation

id

protected String id

no

protected int no

examples

protected String[] examples

residueIDHidden

protected boolean residueIDHidden

editable

protected boolean editable

Constructor Detail

AbstractRule

public AbstractRule()

Constructor

Method Detail

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

See Also:

IDecisionRule.getID()

setID

public void setID(String id)

Description copied from interface: IDecisionRule

Sets rule identifier

Specified by:

setID in interface IDecisionRule

See Also:

IDecisionRule.setID(String)

getNum

public int getNum()

Specified by:

getNum in interface IDecisionRule

setNum

public void setNum(int no)

Specified by:

setNum in interface IDecisionRule

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

See Also:

IDecisionRule.getTitle()

setTitle

public void setTitle(String name)

Description copied from interface: IDecisionRule

Sets rule name

Specified by:

setTitle in interface IDecisionRule

See Also:

IDecisionRule.setTitle(java.lang.String)

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

See Also:

IDecisionRule.getExplanation()

setExplanation

public void setExplanation(String message)

Description copied from interface: IDecisionRule

Sets rule explanation

Specified by:

setExplanation in interface IDecisionRule

See Also:

IDecisionRule.setExplanation(java.lang.String)

isImplemented

public boolean isImplemented()

Specified by:

isImplemented in interface IDecisionRule

Returns:

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

toString

public String toString()

Specified by:

toString in interface IDecisionRule

Overrides:

toString in class Object

createRule

public static IDecisionRule createRule(String className)
                                throws DecisionMethodException

Throws:

DecisionMethodException

makeMolecule

public static org.openscience.cdk.interfaces.IAtomContainer makeMolecule(boolean yes)
                                                                  throws DecisionMethodException

This is to ensure each derived class will provide an example of a molecule which resolves to the yes and no rule outcome

Parameters:

yes -

Returns:

org.openscience.cdk.interfaces.Molecule

Throws:

DecisionMethodException

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

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

addPropertyChangeListener

public void addPropertyChangeListener(PropertyChangeListener l)

Specified by:

addPropertyChangeListener in interface IDecisionRule

removePropertyChangeListener

public void removePropertyChangeListener(PropertyChangeListener l)

Specified by:

removePropertyChangeListener in interface IDecisionRule

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

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()

See IDecisionRule.getEditor()

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

isEditable

public boolean isEditable()

Specified by:

isEditable in interface IDecisionRule

setEditable

public void setEditable(boolean value)

Specified by:

setEditable in interface IDecisionRule

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

getExamples

public String[] getExamples()

setExamples

public void setExamples(String[] examples)

getSelector

public ambit2.rendering.IAtomContainerHighlights getSelector()

Specified by:

getSelector in interface IDecisionRule

log

protected void log(Level level,
                   String message)

log

protected void log(Level level,
                   String message,
                   Object param)

log

protected void log(Level level,
                   String message,
                   Object[] params)