toxTree.tree
Class TreeResult

java.lang.Object
  extended by toxTree.tree.TreeResult
All Implemented Interfaces:
java.io.Serializable, java.lang.Comparable, IDecisionMethodPrority, IDecisionResult, IProgressStatus
Direct Known Subclasses:
CramerTreeResult, CramerTreeResult, DNABindingTreeResult, FuncTreeResult, MATreeResult, MICTreeResult, MutantTreeResult, ProteinBindingTreeResult, SkinSensitisationTreeResult, SMARTCypTreeResult, Verhaar2TreeResult, VerhaarTreeResult

public class TreeResult
extends java.lang.Object
implements IDecisionResult

A default class implementing IDecisionResult

Version:
0.1, 2005-4-30
Author:
Nina Jeliazkova nina@acad.bg
See Also:
Serialized Form

Field Summary
protected  IDecisionCategories assignedCategories
           
protected  IDecisionCategory category
           
protected  java.beans.PropertyChangeSupport changes
           
protected  IDecisionMethod decisionMethod
           
protected static TTLogger logger
           
protected  boolean notify
           
protected  org.openscience.cdk.interfaces.IAtomContainer originalMolecule
           
protected  java.util.ArrayList<RuleResult> ruleResults
           
protected  ProgressStatus status
           
protected  boolean web
           
 
Constructor Summary
TreeResult()
          Constructor
 
Method Summary
protected  boolean acceptCategory(IDecisionCategory category)
           
protected  void addCategory(IDecisionCategory category)
           
 void addPropertyChangeListener(java.beans.PropertyChangeListener l)
           
 void addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)
           
 void assignResult(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean classify(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 void clear()
           
protected  void clearResults()
           
 int compareTo(java.lang.Object o)
           
 boolean equals(java.lang.Object obj)
           
 java.lang.StringBuffer explain(boolean verbose)
          return StringBuffer with textual explanation of the rules executed
protected  void fireChangeEvent(java.beans.PropertyChangeEvent e)
           
protected  void firePropertyChangeEvent(java.lang.String propertyName, boolean oldValue, boolean newValue)
           
protected  void firePropertyChangeEvent(java.lang.String propertyName, int oldValue, int newValue)
           
protected  void firePropertyChangeEvent(java.lang.String propertyName, java.lang.Object oldValue, java.lang.Object newValue)
           
 IDecisionCategories getAssignedCategories()
           
 IDecisionCategory getCategory()
           
 IDecisionCategory getCategory(int index)
           
 IDecisionMethod getDecisionMethod()
           
 java.util.List<CategoryFilter> getFilters()
           
 org.openscience.cdk.interfaces.IAtomContainer getMolecule(int index)
           
 org.openscience.cdk.interfaces.IAtomContainer getOriginalMolecule()
           
 int getPriority()
           
 java.beans.PropertyChangeListener[] getPropertyChangeListeners()
           
 java.lang.String[] getResultPropertyNames()
          Returns the name of the property that will contain the result
 IDecisionRule getRule(int index)
           
 RuleResult getRuleResult(int index)
           
 java.util.ArrayList<RuleResult> getRuleResults()
           
 int getRuleResultsCount()
           
 void hilightAlert(IDecisionRule rule)
           
 void hilightAlert(RuleResult ruleResult)
           
 boolean isError()
           
 boolean isEstimated()
           
 boolean isEstimating()
           
 boolean isNotify()
           
 void removePropertyChangeListener(java.beans.PropertyChangeListener l)
           
 void setCategory(IDecisionCategory category)
           
 void setDecisionMethod(IDecisionMethod decisionMethod)
           
 void setError(java.lang.String message)
           
 void setEstimated()
           
 void setEstimated(boolean value)
           
 void setEstimating()
           
 void setMolecule(org.openscience.cdk.interfaces.IAtomContainer molecule)
           
 void setNotify(boolean notify)
           
 void setOriginalMolecule(org.openscience.cdk.interfaces.IAtomContainer originalMolecule)
           
 void setPercentEstimated(int percent)
           
 void setPriority(int priority)
           
 void setRuleResults(java.util.ArrayList<RuleResult> ruleResults)
           
 void setSilent(boolean silent)
           
 void setWeb(java.lang.Boolean web)
           
 java.lang.String toString()
          toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

logger

protected static transient TTLogger logger

changes

protected transient java.beans.PropertyChangeSupport changes

decisionMethod

protected IDecisionMethod decisionMethod

category

protected IDecisionCategory category

assignedCategories

protected IDecisionCategories assignedCategories

originalMolecule

protected transient org.openscience.cdk.interfaces.IAtomContainer originalMolecule

ruleResults

protected java.util.ArrayList<RuleResult> ruleResults

status

protected ProgressStatus status

notify

protected boolean notify

web

protected boolean web
Constructor Detail

TreeResult

public TreeResult()
Constructor

Parameters:
method -
Method Detail

isNotify

public boolean isNotify()

setNotify

public void setNotify(boolean notify)
Specified by:
setNotify in interface IDecisionResult

clear

public void clear()
Specified by:
clear in interface IDecisionResult

clearResults

protected void clearResults()

isError

public boolean isError()
Specified by:
isError in interface IProgressStatus

setError

public void setError(java.lang.String message)
Specified by:
setError in interface IProgressStatus

isEstimated

public boolean isEstimated()
Specified by:
isEstimated in interface IProgressStatus

isEstimating

public boolean isEstimating()
Specified by:
isEstimating in interface IProgressStatus

setEstimating

public void setEstimating()
Specified by:
setEstimating in interface IProgressStatus

setPercentEstimated

public void setPercentEstimated(int percent)
Specified by:
setPercentEstimated in interface IProgressStatus

setEstimated

public void setEstimated()
Specified by:
setEstimated in interface IProgressStatus

setEstimated

public void setEstimated(boolean value)
Specified by:
setEstimated in interface IProgressStatus

getCategory

public IDecisionCategory getCategory()
Specified by:
getCategory in interface IDecisionResult

getAssignedCategories

public IDecisionCategories getAssignedCategories()
Specified by:
getAssignedCategories in interface IDecisionResult

setCategory

public void setCategory(IDecisionCategory category)
Specified by:
setCategory in interface IDecisionResult

acceptCategory

protected boolean acceptCategory(IDecisionCategory category)

addCategory

protected void addCategory(IDecisionCategory category)

setMolecule

public void setMolecule(org.openscience.cdk.interfaces.IAtomContainer molecule)
Specified by:
setMolecule in interface IDecisionResult

setSilent

public void setSilent(boolean silent)
               throws DecisionResultException
Specified by:
setSilent in interface IDecisionResult
Throws:
DecisionResultException

addRuleResult

public void addRuleResult(IDecisionRule rule,
                          boolean value,
                          org.openscience.cdk.interfaces.IAtomContainer molecule)
                   throws DecisionResultException
Specified by:
addRuleResult in interface IDecisionResult
Throws:
DecisionResultException

explain

public java.lang.StringBuffer explain(boolean verbose)
                               throws DecisionResultException
return StringBuffer with textual explanation of the rules executed

Specified by:
explain in interface IDecisionResult
Throws:
DecisionResultException

toString

public java.lang.String toString()
toString

Specified by:
toString in interface IDecisionResult
Overrides:
toString in class java.lang.Object

compareTo

public int compareTo(java.lang.Object o)
Specified by:
compareTo in interface java.lang.Comparable
See Also:
Comparable.compareTo(java.lang.Object)

getDecisionMethod

public IDecisionMethod getDecisionMethod()
Specified by:
getDecisionMethod in interface IDecisionResult

setDecisionMethod

public void setDecisionMethod(IDecisionMethod decisionMethod)
Specified by:
setDecisionMethod in interface IDecisionResult

classify

public boolean classify(org.openscience.cdk.interfaces.IAtomContainer mol)
                 throws DecisionResultException
Specified by:
classify in interface IDecisionResult
Throws:
DecisionResultException

addPropertyChangeListener

public void addPropertyChangeListener(java.beans.PropertyChangeListener l)
Specified by:
addPropertyChangeListener in interface IDecisionResult

removePropertyChangeListener

public void removePropertyChangeListener(java.beans.PropertyChangeListener l)
Specified by:
removePropertyChangeListener in interface IDecisionResult

getPropertyChangeListeners

public java.beans.PropertyChangeListener[] getPropertyChangeListeners()
Specified by:
getPropertyChangeListeners in interface IDecisionResult

fireChangeEvent

protected void fireChangeEvent(java.beans.PropertyChangeEvent e)

firePropertyChangeEvent

protected void firePropertyChangeEvent(java.lang.String propertyName,
                                       int oldValue,
                                       int newValue)

firePropertyChangeEvent

protected void firePropertyChangeEvent(java.lang.String propertyName,
                                       boolean oldValue,
                                       boolean newValue)

firePropertyChangeEvent

protected void firePropertyChangeEvent(java.lang.String propertyName,
                                       java.lang.Object oldValue,
                                       java.lang.Object newValue)

equals

public boolean equals(java.lang.Object obj)
Overrides:
equals in class java.lang.Object

getRuleResultsCount

public int getRuleResultsCount()
Specified by:
getRuleResultsCount in interface IDecisionResult

getMolecule

public org.openscience.cdk.interfaces.IAtomContainer getMolecule(int index)
                                                          throws DecisionResultException
Specified by:
getMolecule in interface IDecisionResult
Throws:
DecisionResultException

getCategory

public IDecisionCategory getCategory(int index)
                              throws DecisionResultException
Specified by:
getCategory in interface IDecisionResult
Throws:
DecisionResultException

getRuleResult

public RuleResult getRuleResult(int index)
                         throws DecisionResultException
Specified by:
getRuleResult in interface IDecisionResult
Throws:
DecisionResultException

getRule

public IDecisionRule getRule(int index)
                      throws DecisionResultException
Specified by:
getRule in interface IDecisionResult
Throws:
DecisionResultException

assignResult

public void assignResult(org.openscience.cdk.interfaces.IAtomContainer mol)
                  throws DecisionResultException
Specified by:
assignResult in interface IDecisionResult
Throws:
DecisionResultException

getResultPropertyNames

public java.lang.String[] getResultPropertyNames()
Description copied from interface: IDecisionResult
Returns the name of the property that will contain the result

Specified by:
getResultPropertyNames in interface IDecisionResult

getRuleResults

public java.util.ArrayList<RuleResult> getRuleResults()

setRuleResults

public void setRuleResults(java.util.ArrayList<RuleResult> ruleResults)

getPriority

public int getPriority()
Specified by:
getPriority in interface IDecisionMethodPrority

setPriority

public void setPriority(int priority)
Specified by:
setPriority in interface IDecisionMethodPrority

getFilters

public java.util.List<CategoryFilter> getFilters()
Specified by:
getFilters in interface IDecisionResult

getOriginalMolecule

public org.openscience.cdk.interfaces.IAtomContainer getOriginalMolecule()

setOriginalMolecule

public void setOriginalMolecule(org.openscience.cdk.interfaces.IAtomContainer originalMolecule)

hilightAlert

public void hilightAlert(RuleResult ruleResult)
                  throws DecisionResultException
Specified by:
hilightAlert in interface IDecisionResult
Throws:
DecisionResultException

hilightAlert

public void hilightAlert(IDecisionRule rule)
                  throws DecisionResultException
Specified by:
hilightAlert in interface IDecisionResult
Throws:
DecisionResultException

setWeb

public void setWeb(java.lang.Boolean web)
Specified by:
setWeb in interface IDecisionResult


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