toxTree.tree.rules

Class RuleSubstructures

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.AbstractRuleHilightHits

toxTree.tree.rules.RuleSubstructures

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable

Direct Known Subclasses:

RuleAliphaticWithSomeFuncGroups, RuleAllSubstructures, RuleAnySubstructure, RuleCarbohydrate, RuleIonicGroups, RuleKroesFig1Q1, RuleLactoneOrCyclicDiester, RuleOnlyAllowedSubstructures, RuleRings

public abstract class RuleSubstructures
extends AbstractRuleHilightHits
implements IRuleSubstructures

An abstract class to implement substructure rules

Author:

Nina Jeliazkova Modified 2005-8-14

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected ArrayList<String>	ids
static String	MSG_HASGROUP

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
RuleSubstructures()

Method Summary

Modifier and Type	Method and Description
void	addSubstructure(org.openscience.cdk.interfaces.IAtomContainer fragment) The fragment will be added to the list of substructures to be searched for
void	clearSubstructures() removes all substructures defined for a rule
boolean	equals(Object obj)
ArrayList	getIds()
QueryAtomContainers	getQuery()
org.openscience.cdk.interfaces.IAtomContainer	getSubstructure(int index) Returns a substructure AtomContainer at a given rules
List	getSubstructures() Returns a list ArrayList of AtomContainer defined for the rule
int	getSubstructuresCount()
protected QueryAtomContainers	initQuery()
boolean	isImplemented()
org.openscience.cdk.interfaces.IAtomContainer	removeSubstructure(int index) Removes substructure at a given index
void	setIds(ArrayList ids)
void	setQuery(QueryAtomContainers query)
void	setSubstructure(int index, org.openscience.cdk.interfaces.IAtomContainer atomContainer) sets substructure at index
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)

Methods inherited from class toxTree.tree.AbstractRuleHilightHits

getSelector

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 toxTree.core.IDecisionRule

addPropertyChangeListener, clearFlags, clone, getEditor, getExampleMolecule, getExplanation, getID, getNum, getSelector, getTitle, hideResiduesID, isEditable, isResidueIDHidden, removePropertyChangeListener, setEditable, setExampleMolecule, setExplanation, setID, setNum, setTitle, toString, verifyRule

Field Detail

MSG_HASGROUP

public static transient String MSG_HASGROUP

ids

protected ArrayList<String> ids

Constructor Detail

RuleSubstructures

public RuleSubstructures()
                  throws Exception

Throws:

Exception

Method Detail

initQuery

protected QueryAtomContainers initQuery()
                                 throws Exception

Throws:

Exception

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

addSubstructure

public void addSubstructure(org.openscience.cdk.interfaces.IAtomContainer fragment)

The fragment will be added to the list of substructures to be searched for

Specified by:

addSubstructure in interface IRuleSubstructures

Parameters:

fragment - /* (non-Javadoc)

See Also:

addSubstructure(IAtomContainer)

clearSubstructures

public void clearSubstructures()

Description copied from interface: IRuleSubstructures

removes all substructures defined for a rule

Specified by:

clearSubstructures in interface IRuleSubstructures

getSubstructuresCount

public int getSubstructuresCount()

Specified by:

getSubstructuresCount in interface IRuleSubstructures

Returns:

the number of substructures defined for the rule

getSubstructure

public org.openscience.cdk.interfaces.IAtomContainer getSubstructure(int index)

Description copied from interface: IRuleSubstructures

Returns a substructure AtomContainer at a given rules

Specified by:

getSubstructure in interface IRuleSubstructures

Returns:

molecule AtomContainer

setSubstructure

public void setSubstructure(int index,
                            org.openscience.cdk.interfaces.IAtomContainer atomContainer)

Description copied from interface: IRuleSubstructures

sets substructure at index

Specified by:

setSubstructure in interface IRuleSubstructures

equals

public boolean equals(Object obj)

Overrides:

equals in class AbstractRule

removeSubstructure

public org.openscience.cdk.interfaces.IAtomContainer removeSubstructure(int index)

Description copied from interface: IRuleSubstructures

Removes substructure at a given index

Specified by:

removeSubstructure in interface IRuleSubstructures

Returns:

AtomContainer

getSubstructures

public List getSubstructures()

Description copied from interface: IRuleSubstructures

Returns a list ArrayList of AtomContainer defined for the rule

Specified by:

getSubstructures in interface IRuleSubstructures

Returns:

list List

getQuery

public QueryAtomContainers getQuery()

setQuery

public void setQuery(QueryAtomContainers query)

getIds

public ArrayList getIds()

setIds

public void setIds(ArrayList ids)

verifyRule

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

Specified by:

verifyRule in class AbstractRuleHilightHits

Throws:

DecisionMethodException