toxTree.tree.rules.smarts

Class AbstractRuleSmartSubstructure<T>

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure<T>

All Implemented Interfaces:

ambit2.smarts.query.ISmartsPatternFactory, Serializable, Cloneable, IDecisionRule, IImplementationDetails, XMLSerializable, IRuleSMARTSubstructures

Direct Known Subclasses:

RuleSMARTSSubstructureAmbit, RuleSMARTSubstructureCDK

public abstract class AbstractRuleSmartSubstructure<T>
extends AbstractRule
implements IRuleSMARTSubstructures, ambit2.smarts.query.ISmartsPatternFactory

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	containsAllSubstructures
protected ambit2.smarts.query.ISmartsPattern	final_and_patch
protected Map<String,ambit2.smarts.query.ISmartsPattern<T>>	smartsPatterns

Fields inherited from class toxTree.tree.AbstractRule

changes, editable, ERR_STRUCTURENOTPREPROCESSED, examples, explanation, id, logger, MSG_NO, MSG_YES, no, residueIDHidden, 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
AbstractRuleSmartSubstructure()

Method Summary

Modifier and Type	Method and Description
void	addSubstructure(String smarts)
void	addSubstructure(String title, String smarts)
void	addSubstructure(String title, String smarts, boolean negate)
void	clearSubstructures()
boolean	containsAllSubstructures()
void	deleteSubstructure(String title)
boolean	equals(Object obj)
String	getImplementationDetails()
protected abstract T	getObjectToVerify(org.openscience.cdk.interfaces.IAtomContainer mol)
ambit2.rendering.IAtomContainerHighlights	getSelector()
Map<String,ambit2.smarts.query.ISmartsPattern<T>>	getSmartsPatterns()
String	getSubstructure(String title)
void	initSingleSMARTS(Map<String,ambit2.smarts.query.ISmartsPattern<T>> table, String id, String smartPattern)
protected boolean	isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, T processedObject) Returns true always.
boolean	isImplemented()
void	removeSingleSMARTS(Hashtable table, String id)
void	setContainsAllSubstructures(boolean allSmarts)
void	setSmartsPatterns(Hashtable<String,ambit2.smarts.query.ISmartsPattern<T>> smartsPatterns)
void	setSubstructure(String title, String smarts)
void	setSubstructure(String title, String smarts, boolean negate)
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) This is the core of a IDecisionRule behaviour.
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)

Methods inherited from class toxTree.tree.AbstractRule

addPropertyChangeListener, clearFlags, clone, createRule, fromXML, getEditor, getExampleMolecule, getExamples, getExplanation, getID, getNum, getTitle, hideResiduesID, isEditable, isResidueIDHidden, log, log, log, makeMolecule, removePropertyChangeListener, setEditable, setExampleMolecule, setExamples, setExplanation, setID, setNum, setTitle, toShallowXML, toString, toXML

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 ambit2.smarts.query.ISmartsPatternFactory

createSmartsPattern

Field Detail

smartsPatterns

protected Map<String,ambit2.smarts.query.ISmartsPattern<T>> smartsPatterns

containsAllSubstructures

protected boolean containsAllSubstructures

final_and_patch

protected transient ambit2.smarts.query.ISmartsPattern final_and_patch

Constructor Detail

AbstractRuleSmartSubstructure

public AbstractRuleSmartSubstructure()

Method Detail

addSubstructure

public void addSubstructure(String title,
                            String smarts,
                            boolean negate)
                     throws ambit2.smarts.query.SMARTSException

Throws:

ambit2.smarts.query.SMARTSException

addSubstructure

public void addSubstructure(String title,
                            String smarts)
                     throws ambit2.smarts.query.SMARTSException

Specified by:

addSubstructure in interface IRuleSMARTSubstructures

Throws:

ambit2.smarts.query.SMARTSException

addSubstructure

public void addSubstructure(String smarts)
                     throws ambit2.smarts.query.SMARTSException

Specified by:

addSubstructure in interface IRuleSMARTSubstructures

Throws:

ambit2.smarts.query.SMARTSException

setSubstructure

public void setSubstructure(String title,
                            String smarts,
                            boolean negate)
                     throws ambit2.smarts.query.SMARTSException

Throws:

ambit2.smarts.query.SMARTSException

setSubstructure

public void setSubstructure(String title,
                            String smarts)
                     throws ambit2.smarts.query.SMARTSException

Specified by:

setSubstructure in interface IRuleSMARTSubstructures

Throws:

ambit2.smarts.query.SMARTSException

getSubstructure

public String getSubstructure(String title)
                       throws ambit2.smarts.query.SMARTSException

Specified by:

getSubstructure in interface IRuleSMARTSubstructures

Returns:

smarts, corresponding to title

Throws:

ambit2.smarts.query.SMARTSException

clearSubstructures

public void clearSubstructures()

Specified by:

clearSubstructures in interface IRuleSMARTSubstructures

deleteSubstructure

public void deleteSubstructure(String title)

Specified by:

deleteSubstructure in interface IRuleSMARTSubstructures

getObjectToVerify

protected abstract T getObjectToVerify(org.openscience.cdk.interfaces.IAtomContainer mol)

getSelector

public ambit2.rendering.IAtomContainerHighlights getSelector()

Specified by:

getSelector in interface IDecisionRule

Overrides:

getSelector in class AbstractRule

verifyRule

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

Throws:

DecisionMethodException

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

removeSingleSMARTS

public void removeSingleSMARTS(Hashtable table,
                               String id)
                        throws ambit2.smarts.query.SMARTSException

Throws:

ambit2.smarts.query.SMARTSException

initSingleSMARTS

public void initSingleSMARTS(Map<String,ambit2.smarts.query.ISmartsPattern<T>> table,
                             String id,
                             String smartPattern)
                      throws ambit2.smarts.query.SMARTSException

Throws:

ambit2.smarts.query.SMARTSException

isImplemented

public boolean isImplemented()

Specified by:

isImplemented in interface IDecisionRule

Overrides:

isImplemented in class AbstractRule

Returns:

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

containsAllSubstructures

public boolean containsAllSubstructures()

Specified by:

containsAllSubstructures in interface IRuleSMARTSubstructures

setContainsAllSubstructures

public void setContainsAllSubstructures(boolean allSmarts)

Specified by:

setContainsAllSubstructures in interface IRuleSMARTSubstructures

getSmartsPatterns

public Map<String,ambit2.smarts.query.ISmartsPattern<T>> getSmartsPatterns()

setSmartsPatterns

public void setSmartsPatterns(Hashtable<String,ambit2.smarts.query.ISmartsPattern<T>> smartsPatterns)

getImplementationDetails

public String getImplementationDetails()

Specified by:

getImplementationDetails in interface IImplementationDetails

isAPossibleHit

protected boolean isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol,
                                 T processedObject)
                          throws DecisionMethodException

Returns true always. Override to apply simple prescreening for the rule;

Parameters:

mol -

Returns:

Throws:

DecisionMethodException

equals

public boolean equals(Object obj)

Overrides:

equals in class AbstractRule