toxTree.tree.rules
Class RuleStructuresList

java.lang.Object
  extended by java.util.Observable
      extended by toxTree.tree.AbstractRule
          extended by toxTree.tree.rules.RuleStructuresList
All Implemented Interfaces:
java.io.Serializable, java.lang.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
protected  java.lang.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
RuleStructuresList()
           
RuleStructuresList(java.io.File file)
           
RuleStructuresList(java.lang.String resource)
           
 
Method Summary
 java.io.File getFile()
           
 java.lang.String getFilename()
           
 ambit2.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> getSelector()
           
 boolean isImplemented()
           
 void setFile(java.io.File file)
           
 void setFilename(java.lang.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 java.lang.String filename
Constructor Detail

RuleStructuresList

public RuleStructuresList()

RuleStructuresList

public RuleStructuresList(java.lang.String resource)

RuleStructuresList

public RuleStructuresList(java.io.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 java.io.File getFile()
Returns:
Returns the file.

setFile

public void setFile(java.io.File file)
             throws org.openscience.cdk.exception.CDKException,
                    java.io.IOException
Parameters:
file - The file to set.
Throws:
org.openscience.cdk.exception.CDKException
java.io.IOException

getFilename

public java.lang.String getFilename()

setFilename

public void setFilename(java.lang.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.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> getSelector()
Specified by:
getSelector in interface IDecisionRule
Overrides:
getSelector in class AbstractRule


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