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java.lang.Objectjava.util.Observable
toxTree.tree.AbstractRule
public abstract class AbstractRule
An abstract class implementing IDecisionRule
interface.
Used as a base class for all rules in ToxTreeApp
application.
Field Summary | |
---|---|
protected java.beans.PropertyChangeSupport |
changes
|
protected boolean |
editable
|
static java.lang.String |
ERR_STRUCTURENOTPREPROCESSED
|
protected java.lang.String[] |
examples
|
protected java.lang.StringBuffer |
explanation
|
protected java.lang.String |
id
|
protected static TTLogger |
logger
|
static java.lang.String |
MSG_NO
|
static java.lang.String |
MSG_YES
|
protected int |
no
|
protected boolean |
residueIDHidden
|
protected java.lang.String |
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 | |
---|---|
AbstractRule()
Constructor |
Method Summary | |
---|---|
void |
addPropertyChangeListener(java.beans.PropertyChangeListener l)
|
void |
clearFlags(org.openscience.cdk.interfaces.IAtomContainer mol)
When rules analyze a molecule, a set of properties are set. |
java.lang.Object |
clone()
|
static IDecisionRule |
createRule(java.lang.String className)
|
boolean |
equals(java.lang.Object obj)
|
void |
fromXML(org.w3c.dom.Element xml)
|
IDecisionRuleEditor |
getEditor()
See IDecisionRule.getEditor() |
org.openscience.cdk.interfaces.IMolecule |
getExampleMolecule(boolean ruleResult)
if ruleResult is TRUE, returns the example molecule if the rule is answered YES if ruleResult is FALSE, returns the example molecule if the rule is answered NO |
java.lang.String[] |
getExamples()
|
java.lang.String |
getExplanation()
Rule explanation is an arbitrary text, could be multiline and may contain html tags. |
java.lang.String |
getID()
Rule identifier is an arbitrary string, preferably short one |
int |
getNum()
|
ambit2.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> |
getSelector()
|
java.lang.String |
getTitle()
Rule name is an arbitrary string, preferably one line, reflecting the essence of the rule (e.g. |
void |
hideResiduesID(boolean hide)
|
boolean |
isEditable()
|
boolean |
isImplemented()
|
boolean |
isResidueIDHidden()
|
protected void |
log(java.util.logging.Level level,
java.lang.String message)
|
protected void |
log(java.util.logging.Level level,
java.lang.String message,
java.lang.Object param)
|
protected void |
log(java.util.logging.Level level,
java.lang.String message,
java.lang.Object[] params)
|
static org.openscience.cdk.interfaces.IMolecule |
makeMolecule(boolean yes)
This is to ensure each derived class will provide an example of a molecule which resolves to the yes and no rule outcome |
void |
removePropertyChangeListener(java.beans.PropertyChangeListener l)
|
void |
setEditable(boolean value)
|
void |
setExampleMolecule(org.openscience.cdk.interfaces.IAtomContainer mol,
boolean ruleResult)
Sets example molecule for the YES or NO answer of the rule |
void |
setExamples(java.lang.String[] examples)
|
void |
setExplanation(java.lang.String message)
Sets rule explanation |
void |
setID(java.lang.String id)
Sets rule identifier |
void |
setNum(int no)
|
void |
setTitle(java.lang.String name)
Sets rule name |
org.w3c.dom.Element |
toShallowXML(org.w3c.dom.Document document)
|
java.lang.String |
toString()
|
org.w3c.dom.Element |
toXML(org.w3c.dom.Document document)
|
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 |
---|
verifyRule |
Field Detail |
---|
public static transient java.lang.String ERR_STRUCTURENOTPREPROCESSED
public static transient java.lang.String MSG_YES
public static transient java.lang.String MSG_NO
protected static transient TTLogger logger
protected transient java.beans.PropertyChangeSupport changes
protected java.lang.String title
protected java.lang.StringBuffer explanation
protected java.lang.String id
protected int no
protected java.lang.String[] examples
protected boolean residueIDHidden
protected boolean editable
Constructor Detail |
---|
public AbstractRule()
Method Detail |
---|
public java.lang.String getID()
IDecisionRule
getID
in interface IDecisionRule
IDecisionRule.getID()
public void setID(java.lang.String id)
IDecisionRule
setID
in interface IDecisionRule
IDecisionRule.setID(String)
public int getNum()
getNum
in interface IDecisionRule
public void setNum(int no)
setNum
in interface IDecisionRule
public java.lang.String getTitle()
IDecisionRule
getTitle
in interface IDecisionRule
IDecisionRule.getTitle()
public void setTitle(java.lang.String name)
IDecisionRule
setTitle
in interface IDecisionRule
IDecisionRule.setTitle(java.lang.String)
public java.lang.String getExplanation()
IDecisionRule
getExplanation
in interface IDecisionRule
IDecisionRule.getExplanation()
public void setExplanation(java.lang.String message)
IDecisionRule
setExplanation
in interface IDecisionRule
IDecisionRule.setExplanation(java.lang.String)
public boolean isImplemented()
isImplemented
in interface IDecisionRule
public java.lang.String toString()
toString
in interface IDecisionRule
toString
in class java.lang.Object
public static IDecisionRule createRule(java.lang.String className) throws DecisionMethodException
DecisionMethodException
public static org.openscience.cdk.interfaces.IMolecule makeMolecule(boolean yes) throws DecisionMethodException
yes
-
org.openscience.cdk.interfaces.Molecule
DecisionMethodException
public void setExampleMolecule(org.openscience.cdk.interfaces.IAtomContainer mol, boolean ruleResult)
IDecisionRule
setExampleMolecule
in interface IDecisionRule
mol
- org.openscience.cdk.interfaces.Molecule
public org.openscience.cdk.interfaces.IMolecule getExampleMolecule(boolean ruleResult) throws DecisionMethodException
IDecisionRule
getExampleMolecule
in interface IDecisionRule
org.openscience.cdk.interfaces.Molecule
DecisionMethodException
public void addPropertyChangeListener(java.beans.PropertyChangeListener l)
addPropertyChangeListener
in interface IDecisionRule
public void removePropertyChangeListener(java.beans.PropertyChangeListener l)
removePropertyChangeListener
in interface IDecisionRule
public boolean equals(java.lang.Object obj)
equals
in class java.lang.Object
public void clearFlags(org.openscience.cdk.interfaces.IAtomContainer mol)
IDecisionRule
clearFlags
in interface IDecisionRule
mol
- org.openscience.cdk.interfaces.Molecule
public void hideResiduesID(boolean hide)
hideResiduesID
in interface IDecisionRule
public boolean isResidueIDHidden()
isResidueIDHidden
in interface IDecisionRule
public IDecisionRuleEditor getEditor()
IDecisionRule.getEditor()
getEditor
in interface IDecisionRule
IDecisionRuleEditor
public java.lang.Object clone() throws java.lang.CloneNotSupportedException
clone
in interface IDecisionRule
clone
in class java.lang.Object
java.lang.CloneNotSupportedException
public boolean isEditable()
isEditable
in interface IDecisionRule
public void setEditable(boolean value)
setEditable
in interface IDecisionRule
public void fromXML(org.w3c.dom.Element xml) throws XMLDecisionMethodException
fromXML
in interface XMLSerializable
XMLDecisionMethodException
public org.w3c.dom.Element toShallowXML(org.w3c.dom.Document document) throws XMLDecisionMethodException
toShallowXML
in interface XMLSerializable
XMLDecisionMethodException
public org.w3c.dom.Element toXML(org.w3c.dom.Document document) throws XMLDecisionMethodException
toXML
in interface XMLSerializable
XMLDecisionMethodException
public java.lang.String[] getExamples()
public void setExamples(java.lang.String[] examples)
public ambit2.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> getSelector()
getSelector
in interface IDecisionRule
protected void log(java.util.logging.Level level, java.lang.String message)
protected void log(java.util.logging.Level level, java.lang.String message, java.lang.Object param)
protected void log(java.util.logging.Level level, java.lang.String message, java.lang.Object[] params)
|
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