toxTree.tree.rules
Class RuleElements
java.lang.Object
java.util.Observable
toxTree.tree.AbstractRule
toxTree.tree.rules.RuleElements
- All Implemented Interfaces:
- java.io.Serializable, java.lang.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
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 |
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 |
comparison
public static java.lang.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
RuleElements
public RuleElements()
setHalogens
public void setHalogens(java.lang.String[] halogens)
setHalogens
public void setHalogens(java.util.HashSet halogens)
gethalogens
public java.util.HashSet 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 java.lang.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(java.lang.String element)
removeElement
public void removeElement(java.lang.String element)
contains
public boolean contains(java.lang.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(java.lang.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.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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