toxTree.tree.rules

Class RuleStructuresList

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.rules.RuleStructuresList

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, XMLSerializable

Direct Known Subclasses:

RuleCommonComponentOfFood, RuleNormalBodyConstituent, RuleNormalBodyConstituent

public class RuleStructuresList
extends AbstractRule

A rule, which returns true if the query is isomorphic to one of the structures read from a preconfigured file of a type SDF, SMI, CSV

Author:

Nina Jeliazkova Modified 2005-9-6

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected String	filename
protected ILookupFile	lookupFile

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
RuleStructuresList()
RuleStructuresList(File file)
RuleStructuresList(String resource)

Method Summary

Modifier and Type	Method and Description
File	getFile()
String	getFilename()
ambit2.rendering.IAtomContainerHighlights	getSelector()
boolean	isImplemented()
void	setFile(File file)
void	setFilename(String filename)
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
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, equals, 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

Field Detail

lookupFile

protected transient ILookupFile lookupFile

filename

protected String filename

Constructor Detail

RuleStructuresList

public RuleStructuresList()

RuleStructuresList

public RuleStructuresList(String resource)

RuleStructuresList

public RuleStructuresList(File file)

Method Detail

verifyRule

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

IDecisionRule.verifyRule(IAtomContainer)

Parameters:

mol - org.openscience.cdk.interfaces.AtomContainer

Returns:

rule result, boolean

Throws:

DecisionMethodException

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

getFile

public File getFile()

Returns:

Returns the file.

setFile

public void setFile(File file)
             throws org.openscience.cdk.exception.CDKException,
                    IOException

Parameters:

file - The file to set.

Throws:

org.openscience.cdk.exception.CDKException

IOException

getFilename

public String getFilename()

setFilename

public void setFilename(String filename)

verifyRule

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

Throws:

DecisionMethodException

getSelector

public ambit2.rendering.IAtomContainerHighlights getSelector()

Specified by:

getSelector in interface IDecisionRule

Overrides:

getSelector in class AbstractRule