toxtree.plugins.dnabinding
Class DNABindingPlugin

java.lang.Object
  extended by java.util.Observable
      extended by toxTree.tree.AbstractTree
          extended by toxTree.tree.UserDefinedTree
              extended by toxtree.plugins.dnabinding.DNABindingPlugin
All Implemented Interfaces:
ambit2.core.data.IStructureDiagramHighlights, java.io.Serializable, java.lang.Cloneable, java.util.Observer, org.openscience.cdk.qsar.IDescriptor, org.openscience.cdk.qsar.IMolecularDescriptor, IDecisionInteractive, IDecisionMethod, IDecisionMethodPrority, XMLSerializable

public class DNABindingPlugin
extends UserDefinedTree
implements IDecisionInteractive

Protein binding

Author:
nina
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface toxTree.core.IDecisionInteractive
IDecisionInteractive.UserOptions
 
Field Summary
static java.lang.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
DNABindingPlugin()
           
 
Method Summary
 void addPropertyChangeListener(java.beans.PropertyChangeListener l)
           
 IDecisionResult createDecisionResult()
           
 java.lang.StringBuffer explainRules(IDecisionResult result, boolean verbose)
           
 java.lang.String getName()
           
 org.openscience.cdk.qsar.DescriptorSpecification getSpecification()
           
 boolean isResiduesIDVisible()
           
 void removePropertyChangeListener(java.beans.PropertyChangeListener l)
           
 void setEditable(boolean value)
           
 void setName(java.lang.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)
           
 java.lang.String toString()
           
 
Methods inherited from class toxTree.tree.UserDefinedTree
calculate, clone, createArrayResult, getBranch, getBranch, getCategory, getCategory, getDescriptorNames, getDescriptorResultType, getInteractive, getListener, getNodesFactory, getOptions, getParameterNames, getParameters, getParameterType, getRule, hasUnreachableRules, hasUnusedCategories, initRules, isEditable, removeListener, setArrayValue, setInteractive, setListener, setNodesFactory, setOptions, setParameters, setTransitions, verifyRules, visitCategories, visitRules
 
Methods inherited from class toxTree.tree.AbstractTree
addDecisionRule, classify, clearChanged, equals, fromXML, getCategories, getEditor, getExplanation, getImage, getImage, getImageSize, getLegend, 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 java.lang.String[] c_rules
Constructor Detail

DNABindingPlugin

public DNABindingPlugin()
                 throws DecisionMethodException
Throws:
DecisionMethodException
Method Detail

addPropertyChangeListener

public void addPropertyChangeListener(java.beans.PropertyChangeListener l)
Specified by:
addPropertyChangeListener in interface IDecisionMethod
Overrides:
addPropertyChangeListener in class AbstractTree

removePropertyChangeListener

public void removePropertyChangeListener(java.beans.PropertyChangeListener l)
Specified by:
removePropertyChangeListener in interface IDecisionMethod
Overrides:
removePropertyChangeListener in class AbstractTree

toString

public java.lang.String toString()
Overrides:
toString in class UserDefinedTree

getName

public java.lang.String getName()

setName

public void setName(java.lang.String value)

explainRules

public java.lang.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


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