toxtree.plugins.smartcyp

Class SMARTCYPPlugin

java.lang.Object

java.util.Observable

toxTree.tree.AbstractTree

toxTree.tree.UserDefinedTree

toxtree.plugins.smartcyp.SMARTCYPPlugin

All Implemented Interfaces:

ambit2.core.data.IObject2Properties<UserDefinedTree>, ambit2.core.data.IStructureDiagramDepiction<BufferedImage>, ambit2.core.data.IStructureDiagramHighlights, Serializable, Cloneable, Observer, net.idea.modbcum.i.processors.IProcessor<UserDefinedTree,List<ambit2.base.data.Property>>, org.openscience.cdk.qsar.IDescriptor, org.openscience.cdk.qsar.IMolecularDescriptor, IDecisionInteractive, IDecisionMethod, IDecisionMethodPrority, IMetaboliteGenerator, XMLSerializable

public class SMARTCYPPlugin
extends UserDefinedTree
implements IDecisionInteractive, IMetaboliteGenerator

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface toxTree.core.IDecisionInteractive

IDecisionInteractive.UserOptions

Field Summary

Fields

Modifier and Type	Field and Description
static String[]	c_rules
protected boolean	residuesIDVisible

Fields inherited from class toxTree.tree.UserDefinedTree

editable, listener, nodesFactory, options

Fields inherited from class toxTree.tree.AbstractTree

categories, changes, explanation, falseIfRuleNotImplemented, imageSize, logger, modified, name, priority, rules, treeRoot, web

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
SMARTCYPPlugin()

Method Summary

Modifier and Type	Method and Description
void	addPropertyChangeListener(PropertyChangeListener l)
protected ambit2.core.data.ArrayResult	createArrayResult(int length)
IDecisionResult	createDecisionResult()
boolean	equals(Object obj)
StringBuffer	explainRules(IDecisionResult result, boolean verbose)
String	getHelp(RuleResult ruleResult)
BufferedImage	getLegend(int width, int height)
String	getName()
org.openscience.cdk.interfaces.IAtomContainerSet	getProducts(org.openscience.cdk.interfaces.IAtomContainer reactant, RuleResult ruleResult)
org.openscience.cdk.qsar.DescriptorSpecification	getSpecification()
boolean	isResiduesIDVisible()
void	removePropertyChangeListener(PropertyChangeListener l)
protected void	setArrayValue(ambit2.core.data.ArrayResult result, int index, org.openscience.cdk.interfaces.IAtomContainer mol, String propertyName)
void	setEditable(boolean value)
void	setName(String value)
void	setParameters(org.openscience.cdk.interfaces.IAtomContainer mol) Can be used to display some options before applying the rules.
void	setResiduesIDVisible(boolean residuesIDVisible)
String	toString()

Methods inherited from class toxTree.tree.UserDefinedTree

calculate, clone, close, getBranch, getBranch, getCategory, getCategory, getDescriptorNames, getDescriptorResultType, getID, getInteractive, getListener, getNodesFactory, getOptions, getParameterNames, getParameters, getParameterType, getRule, hasUnreachableRules, hasUnusedCategories, initialise, initRules, isEditable, isEnabled, open, process, removeListener, setEnabled, setInteractive, setListener, setNodesFactory, setOptions, setParameters, setTransitions, verifyRules, visitCategories, visitRules

Methods inherited from class toxTree.tree.AbstractTree

addDecisionRule, classify, clearChanged, fromXML, getCategories, getEditor, getExplanation, getImage, getImage, getImageSize, getNumberOfClasses, getNumberOfRules, getPriority, getRule, getRules, getTitle, getTopRule, isFalseIfRuleNotImplemented, isModified, isWeb, optionsPanel, printResults, printToStream, retrieveExplanation, setCategories, setChanged, setDecisionRule, setExplanation, setFalseIfRuleNotImplemented, setImageSize, setModified, setPriority, setRules, setRules, setTitle, setWeb, testRulesWithSelector, toShallowXML, toXML, update, verifyResidues, verifyRules, walkRules, walkRules

Methods inherited from class java.util.Observable

addObserver, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface toxTree.core.IDecisionInteractive

getInteractive, getListener, getOptions, removeListener, setInteractive, setListener, setOptions

Field Detail

residuesIDVisible

protected boolean residuesIDVisible

c_rules

public static final transient String[] c_rules

Constructor Detail

SMARTCYPPlugin

public SMARTCYPPlugin()
               throws DecisionMethodException

Throws:

DecisionMethodException

Method Detail

addPropertyChangeListener

public void addPropertyChangeListener(PropertyChangeListener l)

Specified by:

addPropertyChangeListener in interface IDecisionMethod

Overrides:

addPropertyChangeListener in class AbstractTree

removePropertyChangeListener

public void removePropertyChangeListener(PropertyChangeListener l)

Specified by:

removePropertyChangeListener in interface IDecisionMethod

Overrides:

removePropertyChangeListener in class AbstractTree

toString

public String toString()

Overrides:

toString in class UserDefinedTree

getName

public String getName()

setName

public void setName(String value)

explainRules

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

Specified by:

explainRules in interface IDecisionMethod

Overrides:

explainRules in class AbstractTree

Throws:

DecisionMethodException

See Also:

IDecisionMethod.explainRules(IDecisionResult,boolean)

isResiduesIDVisible

public boolean isResiduesIDVisible()

setResiduesIDVisible

public void setResiduesIDVisible(boolean residuesIDVisible)

setEditable

public void setEditable(boolean value)

Specified by:

setEditable in interface IDecisionMethod

Overrides:

setEditable in class UserDefinedTree

setParameters

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

Description copied from class: AbstractTree

Can be used to display some options before applying the rules.

Specified by:

setParameters in interface IDecisionMethod

Overrides:

setParameters in class UserDefinedTree

getSpecification

public org.openscience.cdk.qsar.DescriptorSpecification getSpecification()

Specified by:

getSpecification in interface org.openscience.cdk.qsar.IDescriptor

Overrides:

getSpecification in class UserDefinedTree

createDecisionResult

public IDecisionResult createDecisionResult()

Specified by:

createDecisionResult in interface IDecisionMethod

Overrides:

createDecisionResult in class AbstractTree

equals

public boolean equals(Object obj)

Overrides:

equals in class AbstractTree

createArrayResult

protected ambit2.core.data.ArrayResult createArrayResult(int length)

Overrides:

createArrayResult in class UserDefinedTree

setArrayValue

protected void setArrayValue(ambit2.core.data.ArrayResult result,
                             int index,
                             org.openscience.cdk.interfaces.IAtomContainer mol,
                             String propertyName)

Overrides:

setArrayValue in class UserDefinedTree

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>

Overrides:

getLegend in class AbstractTree

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getProducts

public org.openscience.cdk.interfaces.IAtomContainerSet getProducts(org.openscience.cdk.interfaces.IAtomContainer reactant,
                                                                    RuleResult ruleResult)
                                                             throws Exception

Specified by:

getProducts in interface IMetaboliteGenerator

Throws:

Exception

getHelp

public String getHelp(RuleResult ruleResult)

Specified by:

getHelp in interface IMetaboliteGenerator