toxTree.tree

Class TreeResult

java.lang.Object

toxTree.tree.TreeResult

All Implemented Interfaces:

Serializable, Comparable, IDecisionMethodPrority, IDecisionResult, IProgressStatus

Direct Known Subclasses:

AmesMutagenicityTreeResult, CDTResult, CramerTreeResult, CramerTreeResult, DNABindingTreeResult, FuncTreeResult, MATreeResult, MICTreeResult, MutantTreeResult, ProteinBindingTreeResult, SkinSensitisationTreeResult, SMARTCypTreeResult, Verhaar2TreeResult, VerhaarTreeResult

public class TreeResult
extends 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

Fields

Modifier and Type	Field and Description
protected IDecisionCategories	assignedCategories
protected IDecisionCategory	category
protected PropertyChangeSupport	changes
protected IDecisionMethod	decisionMethod
protected static Logger	logger
protected boolean	notify
protected org.openscience.cdk.interfaces.IAtomContainer	originalMolecule
protected ArrayList<RuleResult>	ruleResults
protected ProgressStatus	status
protected boolean	web

Constructor Summary

Constructors

Constructor and Description
TreeResult() Constructor

Method Summary

Modifier and Type	Method and Description
protected boolean	acceptCategory(IDecisionCategory category)
protected void	addCategory(IDecisionCategory category)
void	addPropertyChangeListener(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(Object o)
boolean	equals(Object obj)
StringBuffer	explain(boolean verbose) return StringBuffer with textual explanation of the rules executed
protected void	fireChangeEvent(PropertyChangeEvent e)
protected void	firePropertyChangeEvent(String propertyName, boolean oldValue, boolean newValue)
protected void	firePropertyChangeEvent(String propertyName, int oldValue, int newValue)
protected void	firePropertyChangeEvent(String propertyName, Object oldValue, Object newValue)
IDecisionCategories	getAssignedCategories()
IDecisionCategory	getCategory()
IDecisionCategory	getCategory(int index)
IDecisionMethod	getDecisionMethod()
List<CategoryFilter>	getFilters()
org.openscience.cdk.interfaces.IAtomContainer	getMolecule(int index)
org.openscience.cdk.interfaces.IAtomContainer	getOriginalMolecule()
int	getPriority()
PropertyChangeListener[]	getPropertyChangeListeners()
protected ambit2.base.data.ILiteratureEntry	getReference()
List<ambit2.base.data.Property>	getResultProperties() Returns the properties to contain the result in Property class
String[]	getResultPropertyNames() Returns the name of the property that will contain the result
IDecisionRule	getRule(int index)
RuleResult	getRuleResult(int index)
ArrayList<RuleResult>	getRuleResults()
int	getRuleResultsCount()
void	hilightAlert(IDecisionRule rule)
void	hilightAlert(RuleResult ruleResult)
boolean	isError()
boolean	isEstimated()
boolean	isEstimating()
boolean	isNotify()
void	removePropertyChangeListener(PropertyChangeListener l)
void	setCategory(IDecisionCategory category)
void	setDecisionMethod(IDecisionMethod decisionMethod)
void	setError(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(ArrayList<RuleResult> ruleResults)
void	setSilent(boolean silent)
void	setWeb(Boolean web)
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 Logger logger

changes

protected transient 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 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(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 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 String toString()

toString

Specified by:

toString in interface IDecisionResult

Overrides:

toString in class Object

compareTo

public int compareTo(Object o)

Specified by:

compareTo in interface 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(PropertyChangeListener l)

Specified by:

addPropertyChangeListener in interface IDecisionResult

removePropertyChangeListener

public void removePropertyChangeListener(PropertyChangeListener l)

Specified by:

removePropertyChangeListener in interface IDecisionResult

getPropertyChangeListeners

public PropertyChangeListener[] getPropertyChangeListeners()

Specified by:

getPropertyChangeListeners in interface IDecisionResult

fireChangeEvent

protected void fireChangeEvent(PropertyChangeEvent e)

firePropertyChangeEvent

protected void firePropertyChangeEvent(String propertyName,
                                       int oldValue,
                                       int newValue)

firePropertyChangeEvent

protected void firePropertyChangeEvent(String propertyName,
                                       boolean oldValue,
                                       boolean newValue)

firePropertyChangeEvent

protected void firePropertyChangeEvent(String propertyName,
                                       Object oldValue,
                                       Object newValue)

equals

public boolean equals(Object obj)

Overrides:

equals in class 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 String[] getResultPropertyNames()

Description copied from interface: IDecisionResult

Returns the name of the property that will contain the result

Specified by:

getResultPropertyNames in interface IDecisionResult

getReference

protected ambit2.base.data.ILiteratureEntry getReference()

getResultProperties

public List<ambit2.base.data.Property> getResultProperties()
                                                    throws net.idea.modbcum.i.exceptions.AmbitException

Description copied from interface: IDecisionResult

Returns the properties to contain the result in Property class

Specified by:

getResultProperties in interface IDecisionResult

Returns:

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getRuleResults

public ArrayList<RuleResult> getRuleResults()

setRuleResults

public void setRuleResults(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 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(Boolean web)

Specified by:

setWeb in interface IDecisionResult