toxTree.tree.rules

Class RuleElements

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.rules.RuleElements

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, XMLSerializable

Direct Known Subclasses:

RuleAllAllowedElements, RuleElementsCounter, RuleHasOtherThanC_H_O_N_S2

public class RuleElements
extends AbstractRule

Verifies if the molecule consists of only allowed elements

Author:

Nina Jeliazkova Modified 2005-8-14

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String[]	comparison
protected SmartElementsList	elements
protected int	mode
static int	modeAllSpecifiedElements
static int	modeAnySpecifiedElements
static int	modeOnlySpecifiedElements

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
RuleElements()

Method Summary

Modifier and Type	Method and Description
void	addElement(String element)
boolean	contains(String element) IDecisionRule.verifyRule(IAtomContainer)
boolean	equals(Object obj)
SmartElementsList	getElements()
TreeSet	gethalogens()
int	getMode()
ambit2.rendering.IAtomContainerHighlights	getSelector()
String	getTitle() Rule name is an arbitrary string, preferably one line, reflecting the essence of the rule (e.g.
boolean	hasOnlySpecifiedElements()
boolean	isImplemented()
void	removeElement(String element)
void	select(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
void	setComparisonMode(int mode)
void	setElements(SmartElementsList elements)
void	setHalogens(String[] halogens)
void	setHalogens(TreeSet halogens)
void	setMode(int mode)
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, 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

Field Detail

comparison

public static String[] comparison

modeOnlySpecifiedElements

public static final int modeOnlySpecifiedElements

See Also:

Constant Field Values

modeAllSpecifiedElements

public static final int modeAllSpecifiedElements

See Also:

Constant Field Values

modeAnySpecifiedElements

public static final int modeAnySpecifiedElements

See Also:

Constant Field Values

elements

protected SmartElementsList elements

mode

protected int mode

Constructor Detail

RuleElements

public RuleElements()

Method Detail

setHalogens

public void setHalogens(String[] halogens)

setHalogens

public void setHalogens(TreeSet halogens)

gethalogens

public TreeSet gethalogens()

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

hasOnlySpecifiedElements

public boolean hasOnlySpecifiedElements()

Returns:

Returns the hasOnlySpecifiedElements.

setComparisonMode

public void setComparisonMode(int mode)

Parameters:

hasOnlySpecifiedElements - The hasOnlySpecifiedElements to set.

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

Overrides:

getTitle in class AbstractRule

Returns:

rule name

See Also:

IDecisionRule.getTitle()

addElement

public void addElement(String element)

removeElement

public void removeElement(String element)

contains

public boolean contains(String element)

IDecisionRule.verifyRule(IAtomContainer)

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??

Parameters:

mol - org.openscience.cdk.interfaces.AtomContainer

Returns:

rule result, boolean

Throws:

DecisionMethodException

verifyRule

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

Throws:

DecisionMethodException

select

public void select(org.openscience.cdk.interfaces.IAtomContainer mol,
                   org.openscience.cdk.interfaces.IAtomContainer selected)

equals

public boolean equals(Object obj)

Overrides:

equals in class AbstractRule

getElements

public SmartElementsList getElements()

setElements

public void setElements(SmartElementsList elements)

getMode

public int getMode()

setMode

public void setMode(int mode)

getSelector

public ambit2.rendering.IAtomContainerHighlights getSelector()

Specified by:

getSelector in interface IDecisionRule

Overrides:

getSelector in class AbstractRule