toxTree.tree

Class BatchDecisionResultsList

java.lang.Object

java.util.Observable

toxTree.tree.DecisionMethodsList

toxTree.tree.DecisionResultsList

toxTree.tree.BatchDecisionResultsList

All Implemented Interfaces:

ambit2.core.data.IStructureDiagramDepiction<BufferedImage>, ambit2.core.data.IStructureDiagramHighlights, Serializable, Cloneable, Comparable, Iterable, Collection, List, Observer, IDecisionMethod, IDecisionMethodPrority, IDecisionMethodsList, IDecisionResult, IProgressStatus, XMLSerializable

public class BatchDecisionResultsList
extends DecisionResultsList
implements IDecisionMethod, IDecisionResult

Encapsulates DecisionResultsList as IDecisionMethod.

Author:

Nina Jeliazkova nina@acad.bg Modified Dec 17, 2006

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected Dimension	imageSize
protected PropertyChangeSupport	pssupport
protected ProgressStatus	status

Fields inherited from class toxTree.tree.DecisionMethodsList

list, logger

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

Constructors

Constructor and Description
BatchDecisionResultsList()

Method Summary

Modifier and Type	Method and Description
void	addDecisionRule(IDecisionRule rule)
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)
boolean	classify(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
int	compareTo(Object o)
IDecisionResult	createDecisionResult()
StringBuffer	explain(boolean verbose)
StringBuffer	explainRules(IDecisionResult result, boolean verbose)
protected void	firePropertyChangeEvent(String propertyName, Object oldValue, Object newValue)
IDecisionCategories	getAssignedCategories()
IDecisionRule	getBranch(IDecisionRule rule, boolean answer)
IDecisionCategories	getCategories()
IDecisionCategory	getCategory()
IDecisionCategory	getCategory(IDecisionRule rule, boolean answer)
IDecisionCategory	getCategory(int index)
IDecisionMethod	getDecisionMethod()
IDecisionMethodEditor	getEditor() Each rule provides an editor, which is a class implementing IDecisionMethodEditor.
String	getExplanation()
List<CategoryFilter>	getFilters()
BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer mol)
BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer mol, String ruleID, int width, int height, boolean atomnumbers)
Dimension	getImageSize()
BufferedImage	getLegend(int width, int height)
org.openscience.cdk.interfaces.IAtomContainer	getMolecule(int index)
int	getNumberOfClasses()
int	getNumberOfRules()
int	getPriority()
PropertyChangeListener[]	getPropertyChangeListeners()
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 id)
IDecisionRule	getRule(String name)
RuleResult	getRuleResult(int index)
int	getRuleResultsCount()
IDecisionRuleList	getRules()
String	getTitle()
IDecisionRule	getTopRule()
IDecisionRuleList	hasUnreachableRules()
IDecisionCategories	hasUnusedCategories()
void	hilightAlert(IDecisionRule rule)
void	hilightAlert(RuleResult ruleresult)
boolean	isEditable()
boolean	isError()
boolean	isEstimated()
boolean	isEstimating()
boolean	isModified()
boolean	isNotify()
boolean	isWeb()
void	removePropertyChangeListener(PropertyChangeListener l)
void	setCategory(IDecisionCategory classID)
void	setDecisionMethod(IDecisionMethod method)
void	setDecisionRule(IDecisionRule rule)
void	setEditable(boolean value)
void	setError(String message)
void	setEstimated()
void	setEstimated(boolean value)
void	setEstimating()
void	setExplanation(String value)
void	setImageSize(Dimension imageSize)
void	setModified(boolean value)
void	setMolecule(org.openscience.cdk.interfaces.IAtomContainer molecule)
void	setNotify(boolean notify)
void	setParameters(org.openscience.cdk.interfaces.IAtomContainer mol)
void	setPercentEstimated(int percent)
void	setPriority(int priority)
void	setSilent(boolean silent)
void	setTitle(String value)
void	setWeb(Boolean web)
String	toString()
void	update(Observable arg0, Object arg1)
boolean	verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
void	walkRules(IDecisionRule rule, IProcessRule processor)

Methods inherited from class toxTree.tree.DecisionResultsList

addDecisionMethod, getMethod, getResult, remove, remove

Methods inherited from class toxTree.tree.DecisionMethodsList

add, add, addAll, addAll, clear, contains, containsAll, fromXML, get, getList, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, loadAllFromPlugins, loadFromPlugins, loadPluginsByConfiguration, removeAll, retainAll, set, setList, setMethods, size, subList, toArray, toArray, toShallowXML, toXML

Methods inherited from class java.util.Observable

addObserver, clearChanged, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers, setChanged

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface toxTree.core.IDecisionResult

clear

Methods inherited from interface java.util.List

equals, hashCode, replaceAll, sort, spliterator

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Field Detail

pssupport

protected PropertyChangeSupport pssupport

status

protected ProgressStatus status

imageSize

protected Dimension imageSize

Constructor Detail

BatchDecisionResultsList

public BatchDecisionResultsList()

Method Detail

getImageSize

public Dimension getImageSize()

Specified by:

getImageSize in interface ambit2.core.data.IStructureDiagramDepiction<BufferedImage>

setImageSize

public void setImageSize(Dimension imageSize)

Specified by:

setImageSize in interface ambit2.core.data.IStructureDiagramDepiction<BufferedImage>

addDecisionRule

public void addDecisionRule(IDecisionRule rule)
                     throws DecisionMethodException

Specified by:

addDecisionRule in interface IDecisionMethod

Throws:

DecisionMethodException

addPropertyChangeListener

public void addPropertyChangeListener(PropertyChangeListener l)

Specified by:

addPropertyChangeListener in interface IDecisionMethod

Specified by:

addPropertyChangeListener in interface IDecisionResult

firePropertyChangeEvent

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

setParameters

public void setParameters(org.openscience.cdk.interfaces.IAtomContainer mol)

Specified by:

setParameters in interface IDecisionMethod

classify

public boolean classify(org.openscience.cdk.interfaces.IAtomContainer mol,
                        IDecisionResult result)
                 throws DecisionMethodException

Specified by:

classify in interface IDecisionMethod

Throws:

DecisionMethodException

assignResult

public void assignResult(org.openscience.cdk.interfaces.IAtomContainer mol)
                  throws DecisionResultException

Specified by:

assignResult in interface IDecisionResult

Throws:

DecisionResultException

createDecisionResult

public IDecisionResult createDecisionResult()

Specified by:

createDecisionResult in interface IDecisionMethod

explainRules

public StringBuffer explainRules(IDecisionResult result,
                                 boolean verbose)
                          throws DecisionMethodException

Specified by:

explainRules in interface IDecisionMethod

Throws:

DecisionMethodException

getBranch

public IDecisionRule getBranch(IDecisionRule rule,
                               boolean answer)

Specified by:

getBranch in interface IDecisionMethod

getCategories

public IDecisionCategories getCategories()

Specified by:

getCategories in interface IDecisionMethod

getCategory

public IDecisionCategory getCategory(IDecisionRule rule,
                                     boolean answer)

Specified by:

getCategory in interface IDecisionMethod

getAssignedCategories

public IDecisionCategories getAssignedCategories()

Specified by:

getAssignedCategories in interface IDecisionResult

getEditor

public IDecisionMethodEditor getEditor()

Description copied from interface: IDecisionMethod

Each rule provides an editor, which is a class implementing IDecisionMethodEditor. The editor shall provide user interface for visualization and modification of various method settings.

Specified by:

getEditor in interface IDecisionMethod

Returns:

IDecisionMethodEditor

getExplanation

public String getExplanation()

Specified by:

getExplanation in interface IDecisionMethod

getNumberOfClasses

public int getNumberOfClasses()

Specified by:

getNumberOfClasses in interface IDecisionMethod

getNumberOfRules

public int getNumberOfRules()

Specified by:

getNumberOfRules in interface IDecisionMethod

getRule

public IDecisionRule getRule(int id)

Specified by:

getRule in interface IDecisionMethod

Specified by:

getRule in interface IDecisionResult

getRule

public IDecisionRule getRule(String name)

Specified by:

getRule in interface IDecisionMethod

getRules

public IDecisionRuleList getRules()

Specified by:

getRules in interface IDecisionMethod

getTitle

public String getTitle()

Specified by:

getTitle in interface IDecisionMethod

getTopRule

public IDecisionRule getTopRule()

Specified by:

getTopRule in interface IDecisionMethod

hasUnreachableRules

public IDecisionRuleList hasUnreachableRules()

Specified by:

hasUnreachableRules in interface IDecisionMethod

isEditable

public boolean isEditable()

Specified by:

isEditable in interface IDecisionMethod

isModified

public boolean isModified()

Specified by:

isModified in interface IDecisionMethod

removePropertyChangeListener

public void removePropertyChangeListener(PropertyChangeListener l)

Specified by:

removePropertyChangeListener in interface IDecisionMethod

Specified by:

removePropertyChangeListener in interface IDecisionResult

getPropertyChangeListeners

public PropertyChangeListener[] getPropertyChangeListeners()

Specified by:

getPropertyChangeListeners in interface IDecisionResult

setDecisionRule

public void setDecisionRule(IDecisionRule rule)
                     throws DecisionMethodException

Specified by:

setDecisionRule in interface IDecisionMethod

Throws:

DecisionMethodException

setEditable

public void setEditable(boolean value)

Specified by:

setEditable in interface IDecisionMethod

setExplanation

public void setExplanation(String value)

Specified by:

setExplanation in interface IDecisionMethod

setModified

public void setModified(boolean value)

Specified by:

setModified in interface IDecisionMethod

setTitle

public void setTitle(String value)

Specified by:

setTitle in interface IDecisionMethod

verifyRules

public boolean verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol,
                           IDecisionResult result)
                    throws DecisionMethodException

Specified by:

verifyRules in interface IDecisionMethod

Throws:

DecisionMethodException

addRuleResult

public void addRuleResult(IDecisionRule rule,
                          boolean value,
                          org.openscience.cdk.interfaces.IAtomContainer molecule)
                   throws DecisionResultException

Specified by:

addRuleResult in interface IDecisionResult

Throws:

DecisionResultException

classify

public boolean classify(org.openscience.cdk.interfaces.IAtomContainer mol)
                 throws DecisionResultException

Specified by:

classify in interface IDecisionResult

Throws:

DecisionResultException

setMolecule

public void setMolecule(org.openscience.cdk.interfaces.IAtomContainer molecule)
                 throws DecisionResultException

Specified by:

setMolecule in interface IDecisionResult

Throws:

DecisionResultException

setSilent

public void setSilent(boolean silent)
               throws DecisionResultException

Specified by:

setSilent in interface IDecisionResult

Throws:

DecisionResultException

explain

public StringBuffer explain(boolean verbose)
                     throws DecisionResultException

Specified by:

explain in interface IDecisionResult

Throws:

DecisionResultException

getCategory

public IDecisionCategory getCategory()

Specified by:

getCategory in interface IDecisionResult

getCategory

public IDecisionCategory getCategory(int index)
                              throws DecisionResultException

Specified by:

getCategory in interface IDecisionResult

Throws:

DecisionResultException

getDecisionMethod

public IDecisionMethod getDecisionMethod()

Specified by:

getDecisionMethod in interface IDecisionResult

getMolecule

public org.openscience.cdk.interfaces.IAtomContainer getMolecule(int index)
                                                          throws DecisionResultException

Specified by:

getMolecule in interface IDecisionResult

Throws:

DecisionResultException

getRuleResult

public RuleResult getRuleResult(int index)
                         throws DecisionResultException

Specified by:

getRuleResult in interface IDecisionResult

Throws:

DecisionResultException

getRuleResultsCount

public int getRuleResultsCount()

Specified by:

getRuleResultsCount in interface IDecisionResult

setCategory

public void setCategory(IDecisionCategory classID)

Specified by:

setCategory in interface IDecisionResult

setDecisionMethod

public void setDecisionMethod(IDecisionMethod method)

Specified by:

setDecisionMethod in interface IDecisionResult

compareTo

public int compareTo(Object o)

Specified by:

compareTo in interface Comparable

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

hasUnusedCategories

public IDecisionCategories hasUnusedCategories()

Specified by:

hasUnusedCategories in interface IDecisionMethod

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

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

getPriority

public int getPriority()

Specified by:

getPriority in interface IDecisionMethodPrority

setPriority

public void setPriority(int priority)

Specified by:

setPriority in interface IDecisionMethodPrority

update

public void update(Observable arg0,
                   Object arg1)

Specified by:

update in interface Observer

Overrides:

update in class DecisionResultsList

walkRules

public void walkRules(IDecisionRule rule,
                      IProcessRule processor)
               throws DecisionMethodException

Specified by:

walkRules in interface IDecisionMethod

Throws:

DecisionMethodException

getFilters

public List<CategoryFilter> getFilters()

Specified by:

getFilters in interface IDecisionResult

isNotify

public boolean isNotify()

setNotify

public void setNotify(boolean notify)

Specified by:

setNotify in interface IDecisionResult

toString

public String toString()

Specified by:

toString in interface IDecisionResult

Overrides:

toString in class Object

hilightAlert

public void hilightAlert(IDecisionRule rule)
                  throws DecisionResultException

Specified by:

hilightAlert in interface IDecisionResult

Throws:

DecisionResultException

hilightAlert

public void hilightAlert(RuleResult ruleresult)
                  throws DecisionResultException

Specified by:

hilightAlert in interface IDecisionResult

Throws:

DecisionResultException

getImage

public BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer mol,
                              String ruleID,
                              int width,
                              int height,
                              boolean atomnumbers)
                       throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getImage in interface ambit2.core.data.IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getImage

public BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer mol)
                       throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getImage in interface ambit2.core.data.IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

setWeb

public void setWeb(Boolean web)

Specified by:

setWeb in interface IDecisionMethod

Specified by:

setWeb in interface IDecisionResult

isWeb

public boolean isWeb()

Specified by:

isWeb in interface IDecisionMethod

getLegend

public BufferedImage getLegend(int width,
                               int height)
                        throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getLegend in interface ambit2.core.data.IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException