A B C D E F G H I J L M N O P Q R S T U V W X

A

AbstractBnetFormat - class com.cra.bnet.io.AbstractBnetFormat.
Skeletal implementation of the BnetFormat interface.
AbstractBnetFormat() - Constructor for class com.cra.bnet.io.AbstractBnetFormat
Empty constructor.
AbstractNode - class com.cra.bnet.engine.AbstractNode.
Skeletal implementation of the Node interface.
AbstractNode() - Constructor for class com.cra.bnet.engine.AbstractNode
 
AbstractQueueNode - class com.cra.bnet.engine.AbstractQueueNode.
Skeletal implementation of the QueueNode interface.
AbstractQueueNode() - Constructor for class com.cra.bnet.engine.AbstractQueueNode
 
accept(BeliefEvent) - Method in class com.cra.bnet.engine.ThresholdBeliefCondition
 
accept(BeliefEvent) - Method in interface com.cra.bnet.engine.BeliefCondition
Returns true if the specified belief event meets this condition.
ad - Variable in class com.cra.bnet.engine.GeneratedEngineBase
these five arrays store partial results of belief calculations
add(Potential) - Method in class com.cra.bnet.engine.Potential
Adds this potential to the specified potential and returns the result.
addBeliefListener(BeliefListener) - Method in class com.cra.bnet.engine.Node
Registers the specified belief listener to receive belief events when this node's beliefs change.
addBeliefListener(BeliefListener) - Method in class com.cra.bnet.engine.BeliefAlert
Registers the specified belief listener so it will receive notification when belief events pass this alert's condition.
addBeliefListener(BeliefListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Registers the specified listener to receive belief events when beliefs of any node in this Bayesian network change.
addChangeListener(ChangeListener) - Method in class com.cra.bnet.engine.StructuralModificationSupport
Registers the specified change listener to receive events whenever structural modifications are made to the Bayesian network.
addChangeListener(ChangeListener) - Method in class com.cra.bnet.engine.BeliefUpdater
Registers the specified listener with this belief updater so it will receive change events whenever this belief updater is notified of any modifications to the Bayesian network.
addChild(AddNode) - Method in class com.cra.bnet.engine.MultiplyNode
Adds the specified addition node to this node's child list.
addChild(AmgNode) - Method in class com.cra.bnet.engine.AbstractNode
Adds the specified node to this node's child list.
addChild(CptEntryNode) - Method in class com.cra.bnet.engine.MultiplyNode
Adds the specified cpt entry node to this node's child list.
addChild(EvidenceNode) - Method in class com.cra.bnet.engine.MultiplyNode
Adds the specified evidence node to this node's child list.
addChild(MultiplyNode) - Method in class com.cra.bnet.engine.AddNode
Adds the specified multiply node to this node's child list.
addCptListener(CptListener) - Method in class com.cra.bnet.engine.Node
Registers the specified CPT listener to receive CPT events when this node's CPT changes.
addCptListener(CptListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Registers the specified listener to receive cpt events when the cpt of any node in this Bayesian network changes.
addDiscreteNode(String) - Method in class com.cra.bnet.engine.BayesianNetwork
Adds a new discrete node to this Bayesian network that has the specified name and two states: true and false.
addDiscreteNode(String, List) - Method in class com.cra.bnet.engine.BayesianNetwork
Adds a new discrete node to this Bayesian network that has the specified name and states.
addEdge(Node, Node) - Method in class com.cra.bnet.engine.BayesianNetwork
Adds an edge from the specified parent to the specified child to this Bayesian network.
addEdit(UndoableEdit) - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveNodeEdit
 
addEdit(UndoableEdit) - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundPostEvidenceEdit
 
addEdit(UndoableEdit) - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundChangeLocationEdit
 
addEdit(UndoableEdit) - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundChangeCptEntryEdit
 
addEmEtaListener(EmEtaListener) - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Registers the specified listener so that it will receive events from this learning algorithm.
addErrorListener(ErrorListener) - Method in class com.cra.bnet.error.ErrorNotifier
Registers the specified error listener so it will receive errors.
addEvidenceListener(EvidenceListener) - Method in class com.cra.bnet.engine.Node
Registers the specified listener to receive evidence events when evidence is posted to or retracted from this node.
addEvidenceListener(EvidenceListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Registers the specified listener to receive evidence events when evidence is posted to or retracted from any node in this Bayesian network.
AddMultiplyGraph - class com.cra.bnet.engine.AddMultiplyGraph.
An Add-Multiply Graph used to calculate beliefs in a Bayesian network.
AddMultiplyGraph() - Constructor for class com.cra.bnet.engine.AddMultiplyGraph
Creates a new empty AddMultiplyGraph.
AddMultiplyGraph(AddNode[]) - Constructor for class com.cra.bnet.engine.AddMultiplyGraph
Creates a new AddMultiplyGraph using the specified root node.
AddMultiplyGraphFactory - class com.cra.bnet.engine.AddMultiplyGraphFactory.
Factory for creating AddMultiplyGraph objects.
AddNode - class com.cra.bnet.engine.AddNode.
Represents an addition node in the AMG.
AddNode(Set[], int, int) - Constructor for class com.cra.bnet.engine.AddNode
Creates a new AddNode using the specified separator index and instantiation index.
addNodeLengths() - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
addNodeListener(NodeListener) - Method in class com.cra.bnet.engine.Node
Registers the specified node listener to receive node events when aspects of this node change.
addNodeListener(NodeListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Registers the specified listener to receive node events when aspects of any node in this Bayesian network change.
addNodePropertyChangeListener(PropertyChangeListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Registers the specified property change listener to receive events when the user properties of any node in this Bayesian network change.
addParent(AddNode) - Method in class com.cra.bnet.engine.MultiplyNode
Adds the specified addition node to this node's parent list.
addParent(AmgNode) - Method in class com.cra.bnet.engine.AbstractNode
Adds the specified node to this node's parent list.
addParent(MultiplyNode) - Method in class com.cra.bnet.engine.EvidenceNode
Adds the specified multiply node to this node's parent list.
addParent(MultiplyNode) - Method in class com.cra.bnet.engine.CptEntryNode
Adds the specified multiply node to this node's parent list.
addParent(MultiplyNode) - Method in class com.cra.bnet.engine.AddNode
Adds the specified multiply node to this nodes parent list.
addPropertyChangeListener(PropertyChangeListener) - Method in class com.cra.bnet.engine.Node
Registers the specified property change listener to receive events when the user properties of this node change.
addPropertyChangeListener(PropertyChangeListener) - Method in class com.cra.bnet.engine.BeliefUpdater
Registers the specified listener so it will receive property change events.
addPropertyChangeListener(PropertyChangeListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Registers the specified property change listener to receive events when the user properties of this Bayesian network change.
addPropertyChangeListener(PropertyChangeListener, String) - Method in class com.cra.bnet.engine.BeliefUpdater
Registers the specified listener so it will receive property change events for the specified property.
addStateListener(StateListener) - Method in class com.cra.bnet.engine.DiscreteNode
Registers the specified state listener to receive events when this discrete node's states change.
addStateListener(StateListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Registers the specified listener to receive state events when states of any node in this Bayesian network change.
addTopologyListener(TopologyListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Registers the specified topology listener to receive topology events from this Bayesian network.
addUndoableEditListener(UndoableEditListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Registers the specified listener to receive undoable edit events from this Bayesian network.
ALGORITHM_FINISHED - Static variable in class com.cra.bnet.learn.EmEtaEvent
The algorithm finished event type.
ALGORITHM_PAUSED - Static variable in class com.cra.bnet.learn.EmEtaEvent
The algorithm paused event type.
ALGORITHM_RESUMED - Static variable in class com.cra.bnet.learn.EmEtaEvent
The algorithm resumed event type.
ALGORITHM_STARTED - Static variable in class com.cra.bnet.learn.EmEtaEvent
The algorithm started event type.
ALGORITHM_STOPPED - Static variable in class com.cra.bnet.learn.EmEtaEvent
The algorithm stopped event type.
algorithmFinished(EmEtaEvent) - Method in interface com.cra.bnet.learn.EmEtaListener
Invoked when the algorithm is finished.
algorithmFinished(EmEtaEvent) - Method in class com.cra.bnet.learn.EmEtaAdapter
Invoked when the algorithm is finished.
algorithmPaused(EmEtaEvent) - Method in interface com.cra.bnet.learn.EmEtaListener
Invoked when the algorithm has been paused.
algorithmPaused(EmEtaEvent) - Method in class com.cra.bnet.learn.EmEtaAdapter
Invoked when the algorithm has been paused.
algorithmResumed(EmEtaEvent) - Method in interface com.cra.bnet.learn.EmEtaListener
Invoked when the algorithm has been resumed.
algorithmResumed(EmEtaEvent) - Method in class com.cra.bnet.learn.EmEtaAdapter
Invoked when the algorithm has been resumed.
algorithmStarted(EmEtaEvent) - Method in interface com.cra.bnet.learn.EmEtaListener
Invoked when the algorithm has started.
algorithmStarted(EmEtaEvent) - Method in class com.cra.bnet.learn.EmEtaAdapter
Invoked when the algorithm has started.
algorithmStopped(EmEtaEvent) - Method in interface com.cra.bnet.learn.EmEtaListener
Invoked when the algorithm has been stopped.
algorithmStopped(EmEtaEvent) - Method in class com.cra.bnet.learn.EmEtaAdapter
Invoked when the algorithm has been stopped.
ALL_EVIDENCE_RETRACTED - Static variable in class com.cra.bnet.engine.EvidenceEvent
The all evidence retracted event type.
ALL_EVIDENCE_RETRACTED - Static variable in class com.cra.bnet.engine.BeliefUpdater
The integer mask for all evidence retracted.
allEntriesChanged(CptEvent) - Method in interface com.cra.bnet.engine.CptListener
Invoked when all entries of a cpt have changed.
allEntriesChanged(CptEvent) - Method in class com.cra.bnet.engine.CptAdapter
 
allEvidenceRetracted(EvidenceEvent) - Method in interface com.cra.bnet.engine.EvidenceListener
Invoked when all evidence was retracted from a Bayesian network.
allEvidenceRetracted(EvidenceEvent) - Method in class com.cra.bnet.engine.EvidenceAdapter
 
AmgInferenceEngine - class com.cra.bnet.engine.AmgInferenceEngine.
Inference engine based on an add-multiply graph.
AmgInferenceEngine(BayesianNetwork) - Constructor for class com.cra.bnet.engine.AmgInferenceEngine
Creates a new AMG inference engine using the specified Bayesian network.
AmgInferenceEngine(BayesianNetwork, boolean) - Constructor for class com.cra.bnet.engine.AmgInferenceEngine
Creates a new AMG inference engine using the specified Bayesian network.
AmgNode - interface com.cra.bnet.engine.AmgNode.
Represents a node in the AMG.
AmgUtilities - class com.cra.bnet.engine.AmgUtilities.
Add-multiply graph utilities.
AmgUtilities() - Constructor for class com.cra.bnet.engine.AmgUtilities
 
assertDebug(boolean, RuntimeException) - Static method in class com.cra.bnet.debug.DebugUtils
 
assertTrue(boolean, RuntimeException) - Static method in class com.cra.bnet.debug.DebugUtils
This method was changed from assert to assertTrue since assert is a keywork in Java 1.4.
av - Variable in class com.cra.bnet.engine.GeneratedEngineBase
these five arrays store partial results of belief calculations

B

b - Variable in class com.cra.bnet.engine.GeneratedEngineBase
b[i][j] = belief for state j of node i
BayesianNetwork - class com.cra.bnet.engine.BayesianNetwork.
A Bayesian network (also known as a belief network or Bayesian belief network).
BayesianNetwork.AddEdgeEdit - class com.cra.bnet.engine.BayesianNetwork.AddEdgeEdit.
Undoable edit for adding an edge.
BayesianNetwork.AddNodeEdit - class com.cra.bnet.engine.BayesianNetwork.AddNodeEdit.
Undoable edit for adding a node.
BayesianNetwork.AddStateEdit - class com.cra.bnet.engine.BayesianNetwork.AddStateEdit.
Undoable edit for adding a state.
BayesianNetwork.ChangeCptEntryEdit - class com.cra.bnet.engine.BayesianNetwork.ChangeCptEntryEdit.
Undoable edit for changing a cpt entry.
BayesianNetwork.ChangeLocationEdit - class com.cra.bnet.engine.BayesianNetwork.ChangeLocationEdit.
Undoable edit for changing a node's location.
BayesianNetwork.ChangeNodeDescriptionEdit - class com.cra.bnet.engine.BayesianNetwork.ChangeNodeDescriptionEdit.
Undoable edit for changing a node's description.
BayesianNetwork.ClearEvidenceEdit - class com.cra.bnet.engine.BayesianNetwork.ClearEvidenceEdit.
Undoable edit for removing all evidence.
BayesianNetwork.CompoundChangeCptEntryEdit - class com.cra.bnet.engine.BayesianNetwork.CompoundChangeCptEntryEdit.
Undoable edit for changing multiple cpt entries.
BayesianNetwork.CompoundChangeCptEntryEdit() - Constructor for class com.cra.bnet.engine.BayesianNetwork.CompoundChangeCptEntryEdit
 
BayesianNetwork.CompoundChangeCptEntryEdit(String) - Constructor for class com.cra.bnet.engine.BayesianNetwork.CompoundChangeCptEntryEdit
 
BayesianNetwork.CompoundChangeLocationEdit - class com.cra.bnet.engine.BayesianNetwork.CompoundChangeLocationEdit.
Undoable edit for grouping multiple moves together.
BayesianNetwork.CompoundChangeLocationEdit() - Constructor for class com.cra.bnet.engine.BayesianNetwork.CompoundChangeLocationEdit
 
BayesianNetwork.CompoundChangeLocationEdit(String) - Constructor for class com.cra.bnet.engine.BayesianNetwork.CompoundChangeLocationEdit
 
BayesianNetwork.CompoundPostEvidenceEdit - class com.cra.bnet.engine.BayesianNetwork.CompoundPostEvidenceEdit.
Undoable edit for posting multiple pieces of evidence.
BayesianNetwork.CompoundPostEvidenceEdit() - Constructor for class com.cra.bnet.engine.BayesianNetwork.CompoundPostEvidenceEdit
 
BayesianNetwork.CompoundPostEvidenceEdit(String) - Constructor for class com.cra.bnet.engine.BayesianNetwork.CompoundPostEvidenceEdit
 
BayesianNetwork.PostEvidenceEdit - class com.cra.bnet.engine.BayesianNetwork.PostEvidenceEdit.
Undoable edit for posting evidence.
BayesianNetwork.RemoveEdgeEdit - class com.cra.bnet.engine.BayesianNetwork.RemoveEdgeEdit.
Undoable edit for removing an edge.
BayesianNetwork.RemoveEvidenceEdit - class com.cra.bnet.engine.BayesianNetwork.RemoveEvidenceEdit.
Undoable edit for removing evidence.
BayesianNetwork.RemoveNodeEdit - class com.cra.bnet.engine.BayesianNetwork.RemoveNodeEdit.
Undoable edit for removing a node.
BayesianNetwork.RemoveStateEdit - class com.cra.bnet.engine.BayesianNetwork.RemoveStateEdit.
Undoable edit for removing a state.
BayesianNetwork.RenameNetworkEdit - class com.cra.bnet.engine.BayesianNetwork.RenameNetworkEdit.
Undoable edit for renaming the network.
BayesianNetwork.RenameNodeEdit - class com.cra.bnet.engine.BayesianNetwork.RenameNodeEdit.
Undoable edit for renaming a node.
BayesianNetwork.RenameStateEdit - class com.cra.bnet.engine.BayesianNetwork.RenameStateEdit.
Undoable edit for renaming a state.
BayesianNetwork.ReorderParentEdit - class com.cra.bnet.engine.BayesianNetwork.ReorderParentEdit.
Undoable edit for reordering a parent.
BayesianNetwork.ReorderStateEdit - class com.cra.bnet.engine.BayesianNetwork.ReorderStateEdit.
Undoable edit for reordering a state.
BayesianNetwork() - Constructor for class com.cra.bnet.engine.BayesianNetwork
Creates a new, empty BayesianNetwork.
BayesianNetwork(BayesianNetwork) - Constructor for class com.cra.bnet.engine.BayesianNetwork
Creates a new BayesianNetwork that is a copy of the specified Bayesian network.
BayesianNetworks - class com.cra.bnet.engine.BayesianNetworks.
Utility methods for Bayesian networks.
BeliefAdapter - class com.cra.bnet.engine.BeliefAdapter.
An abstract adapter class for receiving belief events.
BeliefAdapter() - Constructor for class com.cra.bnet.engine.BeliefAdapter
 
BeliefAlert - class com.cra.bnet.engine.BeliefAlert.
Alerts belief listeners when a belief event meets a certain condition.
BeliefAlert(BeliefCondition) - Constructor for class com.cra.bnet.engine.BeliefAlert
Creates a new BeliefAlert using the specified condition.
BeliefAlert(BeliefCondition, BeliefListener) - Constructor for class com.cra.bnet.engine.BeliefAlert
Creates a new BeliefAlert using the specified condition and belief listener.
BeliefCondition - interface com.cra.bnet.engine.BeliefCondition.
Tests a belief event using some condition.
BeliefEvent - class com.cra.bnet.engine.BeliefEvent.
An event representing a change in beliefs for a node in a Bayesian network.
BeliefEvent(Node, double[], boolean) - Constructor for class com.cra.bnet.engine.BeliefEvent
Creates a new BeliefEvent.
BeliefListener - interface com.cra.bnet.engine.BeliefListener.
A listener for receiving events when beliefs change.
beliefsChanged(BeliefEvent) - Method in interface com.cra.bnet.engine.BeliefListener
Invoked when beliefs have changed.
beliefsChanged(BeliefEvent) - Method in class com.cra.bnet.engine.BeliefAdapter
 
beliefsInvalid(BeliefEvent) - Method in interface com.cra.bnet.engine.BeliefListener
Invoked when a modification was made to the Bayesian network that caused beliefs to become invalid.
beliefsInvalid(BeliefEvent) - Method in class com.cra.bnet.engine.BeliefAdapter
 
BeliefUpdater - class com.cra.bnet.engine.BeliefUpdater.
Controls automatic updating of beliefs for a Bayesian network.
BnetError - exception com.cra.bnet.error.BnetError.
A BNet-related error.
BnetError(BayesianNetwork) - Constructor for class com.cra.bnet.error.BnetError
Creates a new BnetError.
BnetError(BayesianNetwork, String) - Constructor for class com.cra.bnet.error.BnetError
Creates a new BnetError using the specified message.
BnetFormat - interface com.cra.bnet.io.BnetFormat.
A utility for reading and writing Bayesian networks in some format.
BnetFormatFactory - class com.cra.bnet.io.BnetFormatFactory.
A factory that provides BnetFormat implementations for clients to use.
BufferedRegExpReader - class com.cra.bnet.io.BufferedRegExpReader.
Reader implementation that buffers characters read from a regular expression matcher.
BufferedRegExpReader(Reader) - Constructor for class com.cra.bnet.io.BufferedRegExpReader
Creates a new BufferedRegExpReader that wraps the specified reader.

C

c - Variable in class com.cra.bnet.engine.GeneratedEngineBase
c[i][j] = conditional probability for configuration j of node i
calculateBeliefs(DiscreteNode) - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Calculates the current beliefs for the specified variable given the current evidence.
calculateBeliefs(DiscreteNode) - Method in class com.cra.bnet.engine.HuginInferenceEngine
Calculates the current beliefs for the specified variable given the current evidence.
calculateBeliefs0() - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
Case - interface com.cra.bnet.learn.Case.
A single case in a data set used for learning Bayesian networks.
charAt(int) - Method in class com.cra.bnet.io.BufferedRegExpReader
Returns the character at the specified index.
clear() - Method in class com.cra.bnet.engine.PotentialMappings
Removes all mappings from this potential mappings object.
clearAllEvidence() - Method in interface com.cra.bnet.engine.LightweightBayesianNetwork
 
clearAllEvidence() - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
clearEvidence() - Method in class com.cra.bnet.engine.ScgInferenceEngine
 
clearEvidence() - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Removes (or equivalently, retracts) evidence from all nodes in the network.
clearEvidence() - Method in interface com.cra.bnet.engine.InferenceEngine
Removes (or equivalently, retracts) evidence from all nodes in the network.
clearEvidence() - Method in class com.cra.bnet.engine.BayesianNetwork
Retracts evidence from all nodes in this Bayesian network.
clearEvidence() - Method in class com.cra.bnet.engine.AmgInferenceEngine
 
clearEvidence(int) - Method in interface com.cra.bnet.engine.LightweightBayesianNetwork
 
clearEvidence(int) - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
close() - Method in class com.cra.bnet.io.CraPushbackReader
Closes the stream.
close() - Method in class com.cra.bnet.io.BufferedRegExpReader
Closes this reader.
com.cra.bnet.debug - package com.cra.bnet.debug
Debugging utilities.
com.cra.bnet.engine - package com.cra.bnet.engine
Core Bayesian network data structures and algorithms.
com.cra.bnet.error - package com.cra.bnet.error
Error classes.
com.cra.bnet.io - package com.cra.bnet.io
Classes for reading Bayesian networks from files and writing Bayesian networks to files.
com.cra.bnet.learn - package com.cra.bnet.learn
Classes for learning Bayesian networks from data.
compare(double, double) - Method in class com.cra.bnet.engine.ThresholdBeliefCondition.ComparisonOperator
Compares the first specified number to the second specified number.
ComplexDataSet - class com.cra.bnet.learn.ComplexDataSet.
A more complex implementation of the DataSet interface.
ComplexDataSet(File, BayesianNetwork) - Constructor for class com.cra.bnet.learn.ComplexDataSet
Creates a new ComplexDataSet using the data in the specified file and the specified Bayesian network.
computDerivative() - Method in class com.cra.bnet.engine.ConstantNode
 
computeDerivative() - Method in class com.cra.bnet.engine.AddNode
 
computeDerivative() - Method in class com.cra.bnet.engine.AbstractNode
Computes the derivative for this node.
computeValue() - Method in class com.cra.bnet.engine.MultiplyNode
 
computeValue() - Method in class com.cra.bnet.engine.EvidenceNode
 
computeValue() - Method in class com.cra.bnet.engine.CptEntryNode
 
computeValue() - Method in class com.cra.bnet.engine.ConstantNode
 
computeValue() - Method in class com.cra.bnet.engine.AddNode
 
computeValue() - Method in class com.cra.bnet.engine.AbstractNode
Computes the value for this node.
condProbs() - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
ConstantNode - class com.cra.bnet.engine.ConstantNode.
Represents a constant node in the AMG.
ConstantNode(double) - Constructor for class com.cra.bnet.engine.ConstantNode
 
convertToIndex(int, int[]) - Method in class com.cra.bnet.engine.Cpt
Converts the specific node index and parent indices into a single index that can be used with the get(int) and set(int, double) methods.
convertToNodeAndParentIndices(int, int[]) - Method in class com.cra.bnet.engine.Cpt
Converts the specified single CPT array index into the corresponding node index and parent indices.
copy(double[]) - Static method in class com.cra.bnet.engine.BayesianNetworks
Returns a new array that is a copy of the specified array.
Cpd - interface com.cra.bnet.engine.Cpd.
A conditional probability distribution for a node in a Bayesian network.
Cpt - class com.cra.bnet.engine.Cpt.
A conditional probability table (CPT) for a discrete node in a Bayesian network.
CPT_ENTRY_CHANGED - Static variable in class com.cra.bnet.engine.BeliefUpdater
The integer mask for cpt entry changed.
CptAdapter - class com.cra.bnet.engine.CptAdapter.
An abstract adapter class for receiving CPT events.
CptAdapter() - Constructor for class com.cra.bnet.engine.CptAdapter
 
CptEntryNode - class com.cra.bnet.engine.CptEntryNode.
Represents a cpt entry node in the AMG.
CptEntryNode(DiscreteNode, int, int, double) - Constructor for class com.cra.bnet.engine.CptEntryNode
Creates a new CptEntryNode using the specified variable index, instantiation index, and probability.
CptEvent - class com.cra.bnet.engine.CptEvent.
An event representing a change in a cpt entry.
CptEvent(DiscreteNode) - Constructor for class com.cra.bnet.engine.CptEvent
Creates a new CptEvent that represents a change to all entries in the specified node's conditional probability table.
CptEvent(DiscreteNode, int, int[], double, double) - Constructor for class com.cra.bnet.engine.CptEvent
Creates a new CptEvent.
CptListener - interface com.cra.bnet.engine.CptListener.
A listener for receiving events when cpt entries change.
CraPushbackReader - class com.cra.bnet.io.CraPushbackReader.
A reader that allows characters to be pushed back into the stream.
CraPushbackReader(Reader) - Constructor for class com.cra.bnet.io.CraPushbackReader
Creates a new CraPushbackReader that wraps the specified reader.
createAddMultiplyGraph(BayesianNetwork) - Static method in class com.cra.bnet.engine.AddMultiplyGraphFactory
Creates a new Add-Multiply Graph using the specified Bayesian network.
createFormat(BufferedRegExpReader) - Method in class com.cra.bnet.io.BnetFormatFactory
Returns a BnetFormat implementation that is capable of reading a Bayesian network from the specified reader.
createHardEvidence(int, int) - Static method in class com.cra.bnet.engine.AmgUtilities
Returns an array of the specified length that represents hard evidence for the specified state.
createName() - Method in class com.cra.bnet.engine.MultiplyNode
 
createName() - Method in class com.cra.bnet.engine.EvidenceNode
 
createName() - Method in class com.cra.bnet.engine.CptEntryNode
 
createName() - Method in class com.cra.bnet.engine.ConstantNode
 
createName() - Method in class com.cra.bnet.engine.AddNode
 
createName() - Method in class com.cra.bnet.engine.AbstractNode
 
CycleError - exception com.cra.bnet.error.CycleError.
An error that occurs when a cycle-creating edge was added to a Bayesian network.
CycleError(BayesianNetwork, Node, Node) - Constructor for class com.cra.bnet.error.CycleError
Creates a new CycleError using the specified network model, source node, and target node.

D

DataSet - interface com.cra.bnet.learn.DataSet.
A data set used for learning Bayesian networks.
DataSetUtil - class com.cra.bnet.learn.DataSetUtil.
Utility class for data files used for learning.
DEBUG - Static variable in class com.cra.bnet.debug.DebugUtils
Set the system property "com.cra.util.debug.DebugUtils.RELEASE" to the value "RELEASE" to set this field false.
DebugUtils - class com.cra.bnet.debug.DebugUtils.
Debugging utilities.
DecisionAnalysisTools - class com.cra.bnet.engine.DecisionAnalysisTools.
Decision analysis utility class.
DEFAULT_PARAMETERS - Static variable in class com.cra.bnet.learn.EmEtaParameters
Default parameters.
derivativeName - Variable in class com.cra.bnet.engine.AbstractNode
 
DESCRIPTION_CHANGED - Static variable in class com.cra.bnet.engine.NodeEvent
The description changed event type.
DESCRIPTION_PROPERTY - Static variable in class com.cra.bnet.engine.BayesianNetwork
The Bayesian network description property.
descriptionChanged(NodeEvent) - Method in interface com.cra.bnet.engine.NodeListener
Invoked when the node's description has been changed.
descriptionChanged(NodeEvent) - Method in class com.cra.bnet.engine.NodeAdapter
 
DisconnectedNetworkError - exception com.cra.bnet.error.DisconnectedNetworkError.
An error that occurs when inference is attempted on a disconnected Bayesian network.
DisconnectedNetworkError(BayesianNetwork) - Constructor for class com.cra.bnet.error.DisconnectedNetworkError
Creates a new DisconnectedNetworkError.
DiscreteNode - class com.cra.bnet.engine.DiscreteNode.
A discrete node in a Bayesian network.
discreteNodeSet() - Method in class com.cra.bnet.engine.BayesianNetwork
Returns a set view of the discrete nodes contained in this Bayesian network.
Discretizer - class com.cra.bnet.engine.Discretizer.
Discretizes a value of a continuous variable to a state of a discrete variable.
Discretizer(double[]) - Constructor for class com.cra.bnet.engine.Discretizer
Creates a new Discretizer using the specified boundaries.
divideBy(Potential) - Method in class com.cra.bnet.engine.Potential
Divides this potential by the specified potential and returns the result.
dump(PrintWriter) - Method in class com.cra.bnet.engine.Potential
Prints this potential to the specified print writer.
DuplicateEdgeError - exception com.cra.bnet.error.DuplicateEdgeError.
An error that occurs when a duplicate edge was added to a Bayesian network.
DuplicateEdgeError(BayesianNetwork, Node, Node) - Constructor for class com.cra.bnet.error.DuplicateEdgeError
Creates a new DuplicateEdgeError using the specified network model, source node, and target node.
DuplicateNodeError - exception com.cra.bnet.error.DuplicateNodeError.
An error that occurs when a duplicate node was added to a Bayesian network.
DuplicateNodeError(BayesianNetwork, String) - Constructor for class com.cra.bnet.error.DuplicateNodeError
Creates a new DuplicateNodeError using the specified name.

E

e - Variable in class com.cra.bnet.engine.GeneratedEngineBase
e[i][j] = evidence for state j of node i
ed - Variable in class com.cra.bnet.engine.GeneratedEngineBase
these five arrays store partial results of belief calculations
EDGE_ADDED - Static variable in class com.cra.bnet.engine.TopologyEvent
The edge added event type.
EDGE_ADDED - Static variable in class com.cra.bnet.engine.BeliefUpdater
The integer mask for edge added.
EDGE_REMOVED - Static variable in class com.cra.bnet.engine.TopologyEvent
The edge removed event type.
EDGE_REMOVED - Static variable in class com.cra.bnet.engine.BeliefUpdater
The integer mask for edge removed.
edgeAdded(TopologyEvent) - Method in interface com.cra.bnet.engine.TopologyListener
Invoked when an edge has been added to a Bayesian network.
edgeAdded(TopologyEvent) - Method in class com.cra.bnet.engine.TopologyAdapter
 
edgeRemoved(TopologyEvent) - Method in interface com.cra.bnet.engine.TopologyListener
Invoked when an edge has been removed from a Bayesian network.
edgeRemoved(TopologyEvent) - Method in class com.cra.bnet.engine.TopologyAdapter
 
EmEtaAdapter - class com.cra.bnet.learn.EmEtaAdapter.
Adapter class for the EmEtaListener interface.
EmEtaAdapter() - Constructor for class com.cra.bnet.learn.EmEtaAdapter
Empty constructor.
EmEtaEvent - class com.cra.bnet.learn.EmEtaEvent.
An event fired by the EmEta learning algorithm.
EmEtaEvent.EmEtaEventType - class com.cra.bnet.learn.EmEtaEvent.EmEtaEventType.
 
EmEtaEvent(EmEtaLearningAlgorithm, double, int, EmEtaEvent.EmEtaEventType) - Constructor for class com.cra.bnet.learn.EmEtaEvent
Creates a new EmEtaEvent using the specified parameters.
EmEtaLearningAlgorithm - class com.cra.bnet.learn.EmEtaLearningAlgorithm.
The parameterized EM algorithm for learning cpt entries in a Bayesian network.
EmEtaLearningAlgorithm() - Constructor for class com.cra.bnet.learn.EmEtaLearningAlgorithm
Creates a new EmEtaLearningAlgorithm object.
EmEtaLearningAlgorithm(EmEtaParameters) - Constructor for class com.cra.bnet.learn.EmEtaLearningAlgorithm
Creates a new EmEtaLearningAlgorithm that uses the specified parameters.
EmEtaListener - interface com.cra.bnet.learn.EmEtaListener.
A listener for receiving notifications about the status of the EmEta learning algorithm.
EmEtaParameters - class com.cra.bnet.learn.EmEtaParameters.
Parameters for the EmEta learning algorithm.
EmEtaParameters(double, int, double) - Constructor for class com.cra.bnet.learn.EmEtaParameters
Creates a new EmEtaParameters object using the specified values.
EMPTY_PARENT_INDICES - Static variable in class com.cra.bnet.engine.Cpt
A zero-length array for use when getting or setting the CPT entries of a root node.
end() - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveNodeEdit
 
end() - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundPostEvidenceEdit
 
end() - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundChangeLocationEdit
 
end() - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundChangeCptEntryEdit
 
EngineUtilities - class com.cra.bnet.engine.EngineUtilities.
BNet engine utility methods.
ensureSum(double[], int, BigDecimal) - Static method in class com.cra.bnet.engine.EngineUtilities
Returns a big decimal array containing the elements of the specified double array rounded off to the specified number of significant digits that add up exactly to the specified target.
entryChanged(CptEvent) - Method in interface com.cra.bnet.engine.CptListener
Invoked when a cpt entry has changed.
entryChanged(CptEvent) - Method in class com.cra.bnet.engine.CptAdapter
 
EQUAL_TO - Static variable in class com.cra.bnet.engine.ThresholdBeliefCondition
The equal-to operator.
equals(Object) - Method in class com.cra.bnet.engine.Potential
Compares the specified object with this potential for equality.
equals(Object) - Method in class com.cra.bnet.engine.Node
Returns true if the specified object is equal to this node.
error(BnetError) - Method in interface com.cra.bnet.error.ErrorListener
Invoked when an error occurs.
ErrorListener - interface com.cra.bnet.error.ErrorListener.
A listener for receiving error events.
ErrorNotifier - class com.cra.bnet.error.ErrorNotifier.
A class used to notify error listeners that an error occurred.
EVIDENCE_POSTED - Static variable in class com.cra.bnet.engine.EvidenceEvent
The evidence posted event type.
EVIDENCE_POSTED - Static variable in class com.cra.bnet.engine.BeliefUpdater
The integer mask for evidence posted.
EVIDENCE_RETRACTED - Static variable in class com.cra.bnet.engine.EvidenceEvent
The evidence retracted event type.
EVIDENCE_RETRACTED - Static variable in class com.cra.bnet.engine.BeliefUpdater
The integer mask for evidence retracted.
EvidenceAdapter - class com.cra.bnet.engine.EvidenceAdapter.
An abstract adapter class for receiving evidence events.
EvidenceAdapter() - Constructor for class com.cra.bnet.engine.EvidenceAdapter
 
EvidenceEvent - class com.cra.bnet.engine.EvidenceEvent.
An event representing either evidence posted to or retracted from a Bayesian network.
EvidenceEvent(BayesianNetwork) - Constructor for class com.cra.bnet.engine.EvidenceEvent
Creates a new EvidenceEvent representing a retraction of all evidence from a Bayesian network.
EvidenceEvent(Node, double[]) - Constructor for class com.cra.bnet.engine.EvidenceEvent
Creates a new EvidenceEvent representing a posting of new evidence.
EvidenceEvent(Node, double[], boolean) - Constructor for class com.cra.bnet.engine.EvidenceEvent
Creates a new EvidenceEvent representing a retraction of evidence.
EvidenceListener - interface com.cra.bnet.engine.EvidenceListener.
A listener for receiving events when evidence is posted to or retracted from a Bayesian network.
EvidenceNode - class com.cra.bnet.engine.EvidenceNode.
Represents an evidence node in the AMG.
EvidenceNode(DiscreteNode, int, int) - Constructor for class com.cra.bnet.engine.EvidenceNode
Creates a new EvidenceNode using the specified variable index and instantiation index.
evidencePosted(EvidenceEvent) - Method in interface com.cra.bnet.engine.EvidenceListener
Invoked when evidence was posted to a node in a Bayesian network.
evidencePosted(EvidenceEvent) - Method in class com.cra.bnet.engine.EvidenceAdapter
 
evidenceRetracted(EvidenceEvent) - Method in interface com.cra.bnet.engine.EvidenceListener
Invoked when evidence was retracted from a node in a Bayesian network.
evidenceRetracted(EvidenceEvent) - Method in class com.cra.bnet.engine.EvidenceAdapter
 

F

fireAlgorithmFinished(double, int) - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Fires an algorithmFinished event to all listeners.
fireAlgorithmPaused(double, int) - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Fires an algorithmPaused event to all listeners.
fireAlgorithmResumed(double, int) - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Fires an algorithmResumed event to all listeners.
fireAlgorithmStarted(double, int) - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Fires an algorithmStarted event to all listeners.
fireAlgorithmStopped(double, int) - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Fires an algorithmStopped event to all listeners.
fireAllEntriesChanged(CptEvent) - Method in class com.cra.bnet.engine.DiscreteNode
Notifies cpt listeners and the belief updater that this node's entire cpt changed.
fireAllEvidenceRetracted() - Method in class com.cra.bnet.engine.BayesianNetwork
Notifies evidence listeners and the belief updater that all evidence was retracted from this Bayesian network.
fireBeliefEvent(double[], boolean) - Method in class com.cra.bnet.engine.DiscreteNode
Notifies belief listeners that this node's beliefs changed.
fireBeliefsChanged(BeliefEvent) - Method in class com.cra.bnet.engine.BeliefAlert
Fires the specified belief event to all registered belief listeners.
fireChangeEvent() - Method in class com.cra.bnet.engine.StructuralModificationSupport
Fires a change event to all registered change listeners.
fireDescriptionChanged(String, String) - Method in class com.cra.bnet.engine.Node
Notifies node listeners that this node's description was changed.
fireEdgeAdded(Edge) - Method in class com.cra.bnet.engine.BayesianNetwork
Notifies topology listeners and the belief updater that an edge was added to this Bayesian network.
fireEdgeRemoved(Edge) - Method in class com.cra.bnet.engine.BayesianNetwork
Notifies topology listeners and the belief updater that an edge was removed from this Bayesian network.
fireEntryChanged(CptEvent) - Method in class com.cra.bnet.engine.DiscreteNode
Notifies cpt listeners that this node's cpt changed.
fireEvidencePosted(double[]) - Method in class com.cra.bnet.engine.DiscreteNode
Notifies evidence listeners and the belief updater that evidence was posted to this node.
fireEvidenceRetracted(double[]) - Method in class com.cra.bnet.engine.DiscreteNode
Notifies evidence listeners and the belief updater that evidence was retracted from this node.
fireInconsistentEvidenceRetracted(double[]) - Method in class com.cra.bnet.engine.DiscreteNode
Notifies evidence listeners that inconsistent evidence was retracted from this node.
fireInvalidBeliefs() - Method in class com.cra.bnet.engine.BayesianNetwork
Notifies belief listeners that all nodes have invalid beliefs.
fireIterationFinished(double, int) - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Fires an algorithmFinished event to all listeners.
fireLocationChanged(Point, Point) - Method in class com.cra.bnet.engine.Node
Notifies node listeners that this node's location was changed.
fireNameChanged(String, String) - Method in class com.cra.bnet.engine.Node
Notifies node listeners that this node's name was changed.
fireNodeAdded(Node) - Method in class com.cra.bnet.engine.BayesianNetwork
Notifies topology listeners and the belief updater that a node was added to this Bayesian network.
fireNodeRemoved(Node) - Method in class com.cra.bnet.engine.BayesianNetwork
Notifies topology listeners and the belief updater that a node was removed from this Bayesian network.
fireParentReordered(Node, int) - Method in class com.cra.bnet.engine.Node
Notifies node listeners and the belief updater that one of this node's parents was reordered.
fireStateAdded(String, int) - Method in class com.cra.bnet.engine.DiscreteNode
Notifies node listeners and the belief updater that a new state was added to this node.
fireStateChanged() - Method in class com.cra.bnet.engine.BeliefUpdater
Fires a change event to all registered change listeners.
fireStateNameChanged(String, String, int) - Method in class com.cra.bnet.engine.DiscreteNode
Notifies node listeners and the belief updater that the name of one of this node's states was changed.
fireStateRemoved(String, int) - Method in class com.cra.bnet.engine.DiscreteNode
Notifies node listeners and the belief updater that a state was removed from this node.
fireStateReordered(String, int) - Method in class com.cra.bnet.engine.DiscreteNode
Notifies node listeners that one of this node's states was reordered.
fromDecimal(int) - Method in class com.cra.bnet.engine.VbnConverter
 
FullyObservableLearningAlgorithm - class com.cra.bnet.learn.FullyObservableLearningAlgorithm.
A learning algorithm for networks whose nodes are fully observed.
FullyObservableLearningAlgorithm() - Constructor for class com.cra.bnet.learn.FullyObservableLearningAlgorithm
 
Fuzzifier - class com.cra.bnet.engine.Fuzzifier.
Fuzzifies a value of a continuous variable to soft evidence for a discrete variable.
Fuzzifier(double[]) - Constructor for class com.cra.bnet.engine.Fuzzifier
Creates a new Fuzzifier using the specified centers.

G

generateCases(BayesianNetwork, Collection, int, Writer) - Static method in class com.cra.bnet.engine.BayesianNetworks
Generates data from the specified Bayesian network for the specified nodes and writes it to the specified writer.
GeneratedEngineBase - class com.cra.bnet.engine.GeneratedEngineBase.
Base class for generated inference engines.
GeneratedEngineBase() - Constructor for class com.cra.bnet.engine.GeneratedEngineBase
 
get(int) - Method in class com.cra.bnet.engine.Potential
Returns the value of this potential indexed by the specified DECIMAL index.
get(int[]) - Method in class com.cra.bnet.engine.Potential
Returns the value of this potential indexed by the specified index.
get(int, int[]) - Method in class com.cra.bnet.engine.Cpt
Returns the conditional probability that this cpt's node being is the specified state, given that its parents are in the specified states.
getAlgorithm() - Method in class com.cra.bnet.learn.EmEtaEvent
Returns the algorithm that fired this event.
getAllFormats() - Method in class com.cra.bnet.io.BnetFormatFactory
Returns an unmodifiable list of all registered formats.
getBases() - Method in class com.cra.bnet.engine.VbnConverter
 
getBayesianNetwork() - Method in class com.cra.bnet.engine.Node
Returns the Bayesian network that this node belongs to.
getBayesianNetwork() - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Returns this inference engine's Bayesian network.
getBayesianNetwork() - Method in class com.cra.bnet.engine.EvidenceEvent
Returns the Bayesian network that evidence was posted to or retracted from.
getBayesianNetwork() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns the Bayesian network that this belief updater controls.
getBelief(String) - Method in class com.cra.bnet.engine.DiscreteNode
Returns the belief that this discrete node is in the specified state.
getBelief(String) - Method in class com.cra.bnet.engine.BeliefEvent
Returns the new belief for the specified state.
getBeliefCondition() - Method in class com.cra.bnet.engine.BeliefAlert
Returns this alert's condition.
getBeliefs() - Method in class com.cra.bnet.engine.DiscreteNode
Returns all of this discrete node's updated beliefs.
getBeliefs() - Method in class com.cra.bnet.engine.BeliefEvent
Returns the new beliefs.
getBeliefs(DiscreteNode) - Method in class com.cra.bnet.engine.ScgInferenceEngine
 
getBeliefs(DiscreteNode) - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Returns the current beliefs for the specified variable.
getBeliefs(DiscreteNode) - Method in interface com.cra.bnet.engine.InferenceEngine
Returns the current beliefs for the specified variable.
getBeliefs(DiscreteNode) - Method in class com.cra.bnet.engine.AmgInferenceEngine
 
getBeliefs(DiscreteNode) - Method in class com.cra.bnet.engine.AddMultiplyGraph
Returns the beliefs for the specified variable in the Bayesian network.
getBeliefs(int) - Method in interface com.cra.bnet.engine.LightweightBayesianNetwork
 
getBeliefs(int) - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
getBeliefUpdater() - Method in class com.cra.bnet.engine.BayesianNetwork
Returns this Bayesian network's belief updater.
getBeliefUpdateSettings() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns this belief updater's belief update settings.
getBfsIterator() - Method in class com.cra.bnet.engine.AddMultiplyGraph
Returns an iterator over the nodes in this AMG in breadth-first order, starting at the root node.
getBoundaries() - Method in class com.cra.bnet.engine.Discretizer
Returns the boundaries that this discretizer uses.
getBuffer() - Method in class com.cra.bnet.io.BufferedRegExpReader
Returns the buffer used to store characters read from the underlying reader.
getCaseCount() - Method in class com.cra.bnet.learn.SimpleDataSet
Returns the number of cases in this data set.
getCaseCount() - Method in interface com.cra.bnet.learn.DataSet
Returns the number of cases in this data set.
getCaseCount() - Method in class com.cra.bnet.learn.ComplexDataSet
Returns the number of cases in this data set.
getCases() - Method in class com.cra.bnet.learn.SimpleDataSet
Returns an iterator over the cases in this data set.
getCases() - Method in interface com.cra.bnet.learn.DataSet
Returns an iterator over the cases in this data set.
getCases() - Method in class com.cra.bnet.learn.ComplexDataSet
Returns an iterator over the cases in this data set.
getCenters() - Method in class com.cra.bnet.engine.Fuzzifier
Returns the centers that this fuzzifier uses.
getChildren() - Method in interface com.cra.bnet.engine.AmgNode
Returns a list of this node's children.
getChildren() - Method in class com.cra.bnet.engine.AbstractNode
 
getCliquePotential(Set) - Method in class com.cra.bnet.engine.HuginInferenceEngine
 
getCluster() - Method in class com.cra.bnet.engine.MultiplyNode
Returns this node's cluster.
getClusterIndex() - Method in class com.cra.bnet.engine.MultiplyNode
Returns this node's cluster index.
getComparisonOperator() - Method in class com.cra.bnet.engine.ThresholdBeliefCondition
Returns this condition's comparison operator.
getConditionalProbability(int, int) - Method in interface com.cra.bnet.engine.LightweightBayesianNetwork
 
getConditionalProbability(int, int) - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
getCpd() - Method in class com.cra.bnet.engine.Node
Returns this node's conditional probability distribution.
getCpt() - Method in class com.cra.bnet.engine.DiscreteNode
Returns this node's conditional probability table.
getCptEntryNode(DiscreteNode, int) - Method in class com.cra.bnet.engine.AddMultiplyGraph
 
getCurrentVersion() - Method in class com.cra.bnet.io.XbnFormat
Returns the current version number.
getDebugOutput() - Static method in class com.cra.bnet.debug.DebugUtils
 
getDelta() - Method in class com.cra.bnet.learn.EmEtaEvent
Returns the current value of delta.
getDerivative() - Method in interface com.cra.bnet.engine.AmgNode
Returns this node's derivative.
getDerivative() - Method in class com.cra.bnet.engine.AbstractNode
 
getDerivativeName() - Method in class com.cra.bnet.engine.MultiplyNode
 
getDerivativeName() - Method in class com.cra.bnet.engine.EvidenceNode
 
getDerivativeName() - Method in interface com.cra.bnet.engine.AmgNode
Returns this node's derivative name.
getDerivativeName() - Method in class com.cra.bnet.engine.AddNode
 
getDerivativeName() - Method in class com.cra.bnet.engine.AbstractNode
 
getDescription() - Method in class com.cra.bnet.engine.Node
Returns this node's description.
getDescription() - Method in class com.cra.bnet.engine.BayesianNetwork
Returns this Bayesian network's description.
getDescription() - Method in class com.cra.bnet.io.XbnFormat
Returns a short description of the XBN format.
getDescription() - Method in class com.cra.bnet.io.NeticaFormat
Returns a short description of the Netica format.
getDescription() - Method in class com.cra.bnet.io.HuginFormat
Returns a short description of the Hugin format.
getDescription() - Method in interface com.cra.bnet.io.BnetFormat
Returns a short description of the format that this BnetFormat supports.
getDiscreteNode(String) - Method in class com.cra.bnet.engine.BayesianNetwork
Returns the discrete node in this Bayesian network that has the specified name.
getDocument(BayesianNetwork) - Method in class com.cra.bnet.io.XbnFormat
Returns a DOM document that contains the specified Bayesian network in XBN format.
getEdge() - Method in class com.cra.bnet.engine.TopologyEvent
Returns the edge that was added to or removed from the Bayesian network.
getError() - Method in interface com.cra.bnet.io.BnetFormat
Returns a description of the last error that occurred while reading or writing a Bayesian network.
getError() - Method in class com.cra.bnet.io.AbstractBnetFormat
Returns a description of the last error that occurred while reading or writing a Bayesian network.
getEvidence() - Method in class com.cra.bnet.engine.EvidenceNode
Returns this node's evidence.
getEvidence() - Method in class com.cra.bnet.engine.EvidenceEvent
Returns the evidence posted to or retracted from the node.
getEvidence() - Method in class com.cra.bnet.engine.DiscreteNode
Returns the evidence posted to this discrete node.
getEvidence() - Method in interface com.cra.bnet.learn.Observation
Returns the evidence which represents this observation.
getEvidence(DiscreteNode) - Method in class com.cra.bnet.engine.ScgInferenceEngine
 
getEvidence(DiscreteNode) - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Returns the current evidence associated with the specified variable.
getEvidence(DiscreteNode) - Method in interface com.cra.bnet.engine.InferenceEngine
Returns the current evidence associated with the specified variable.
getEvidence(DiscreteNode) - Method in class com.cra.bnet.engine.AmgInferenceEngine
 
getEvidence(DiscreteNode) - Method in class com.cra.bnet.engine.AddMultiplyGraph
Returns the evidence for the specified variable in the Bayesian network.
getEvidence(DiscreteNode, String) - Static method in class com.cra.bnet.engine.BayesianNetworks
Returns the current evidence for the specified state of the specified node.
getEvidence(double) - Method in class com.cra.bnet.engine.Fuzzifier
Fuzzifies the specified value and creates soft evidence that can be posted to a discrete node.
getEvidence(double) - Method in class com.cra.bnet.engine.Discretizer
Discretizes the specified value and creates evidence that can be posted to a discrete node.
getEvidence(int) - Method in interface com.cra.bnet.engine.LightweightBayesianNetwork
 
getEvidence(int) - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
getEvidence(String) - Method in class com.cra.bnet.engine.DiscreteNode
Returns the evidence posted to the specified state of this discrete node.
getEvidenceNode(DiscreteNode, int) - Method in class com.cra.bnet.engine.AddMultiplyGraph
 
getExtension() - Method in class com.cra.bnet.io.XbnFormat
Returns the XBN file extension, ie the string "xbn".
getExtension() - Method in class com.cra.bnet.io.NeticaFormat
Returns the Netica file extension, ie the string "dne".
getExtension() - Method in class com.cra.bnet.io.HuginFormat
Returns the Hugin file extension, ie the string "net".
getExtension() - Method in interface com.cra.bnet.io.BnetFormat
Returns the file extension that this BnetFormat supports.
getHardEvidence(DiscreteNode, String) - Static method in class com.cra.bnet.engine.BayesianNetworks
Returns an array representing hard evidence for the specified state of the specified node.
getIndex() - Method in class com.cra.bnet.engine.StateEvent
Returns the index of the state.
getIndex() - Method in class com.cra.bnet.engine.NodeEvent
Returns the index of parent.
getIndex(DiscreteNode) - Method in class com.cra.bnet.engine.AddMultiplyGraph
 
getIndex(double) - Method in class com.cra.bnet.engine.Discretizer
Returns the index of the discrete state that the specified value is discretized to.
getIndices() - Method in class com.cra.bnet.engine.ParentIndices
Returns the array of parent indices.
getInferenceEngine() - Method in class com.cra.bnet.engine.BayesianNetwork
Returns the inference engine being used by this Bayesian network.
getInstance() - Static method in class com.cra.bnet.error.ErrorNotifier
Returns the single instance of this class.
getInstance() - Static method in class com.cra.bnet.io.BnetFormatFactory
Returns the single instance of this factory.
getInstantiationIndex() - Method in class com.cra.bnet.engine.MultiplyNode
Returns this node's instantiation index.
getInstantiationIndex() - Method in class com.cra.bnet.engine.EvidenceNode
Returns this node's instantiation index.
getInstantiationIndex() - Method in class com.cra.bnet.engine.CptEntryNode
Returns this node's instantiation index.
getInstantiationIndex() - Method in class com.cra.bnet.engine.AddNode
Returns this node's instantiation index.
getIterationNumber() - Method in class com.cra.bnet.learn.EmEtaEvent
Returns the current iteration number.
getJunctionTree() - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Returns this inference engine's current junction tree.
getLastBelief(String) - Method in class com.cra.bnet.engine.DiscreteNode
Returns this discrete node's last belief for the specified state - the one most recently sent to all belief listeners registered with this node.
getLastBeliefs() - Method in class com.cra.bnet.engine.DiscreteNode
Returns this discrete node's last beliefs, those that were most recently sent to all belief listeners registered with this node.
getLearningRate() - Method in class com.cra.bnet.learn.EmEtaParameters
Returns the learning rate (also known as eta).
getLocation() - Method in class com.cra.bnet.engine.Node
Returns this node's location.
getMapping(List, List) - Method in class com.cra.bnet.engine.PotentialMappings
Returns the mapping from a potential over the first list of nodes to a potential over the second list of nodes.
getMappings() - Method in class com.cra.bnet.engine.Potential
Returns the mappings for this potential.
getMaxDecimal() - Method in class com.cra.bnet.engine.VbnConverter
This returns the largest decimal number expressible in this format, NOT the total number of expressible values (which of course includes 0).
getMaximumIterations() - Method in class com.cra.bnet.learn.EmEtaParameters
Returns the maximum number of iterations.
getMinimumDelta() - Method in class com.cra.bnet.learn.EmEtaParameters
Returns the minimum value for delta.
getMissingDataString() - Method in class com.cra.bnet.learn.SimpleDataSet
Retuns the string that represents a missing value in the data file.
getMutualInformation(BayesianNetwork, DiscreteNode) - Static method in class com.cra.bnet.engine.DecisionAnalysisTools
Returns an unmodifiable map containing the mutual information between the specified query variable and every variable in the specified Bayesian network (including the query variable itself).
getMutualInformation(BayesianNetwork, DiscreteNode, double) - Static method in class com.cra.bnet.engine.DecisionAnalysisTools
Returns an unmodifiable map containing the mutual information between the specified query variable and every variable in the specified Bayesian network (including the query variable itself).
getName() - Method in class com.cra.bnet.engine.Node
Returns this node's name.
getName() - Method in class com.cra.bnet.engine.BayesianNetwork
Returns this Bayesian network's name.
getName() - Method in interface com.cra.bnet.engine.AmgNode
Returns this node's name.
getName() - Method in class com.cra.bnet.engine.AbstractNode
 
getName() - Method in class com.cra.bnet.error.DuplicateNodeError
Returns the name of the node that could not be added to the Bayesian network.
getNetwork() - Method in class com.cra.bnet.engine.TopologyEvent
Returns the Bayesian network that this event occured upon.
getNetwork() - Method in class com.cra.bnet.engine.StructuralModificationSupport
Returns the Bayesian network this listener is observing for structural modifications.
getNetwork() - Method in class com.cra.bnet.error.BnetError
 
getNewEvidence() - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Returns the evidence that has not been multiplied into the junction tree potentials yet.
getNewLocation() - Method in class com.cra.bnet.engine.NodeEvent
Returns the new location.
getNewName() - Method in class com.cra.bnet.engine.StateEvent
Returns the new state name.
getNewName() - Method in class com.cra.bnet.engine.NodeEvent
Returns the new node name.
getNewQuotients() - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Returns the evidence quotients that have not been multiplied into the junction tree potentials yet.
getNewValue() - Method in class com.cra.bnet.engine.CptEvent
Returns the new cpt entry.
getNode() - Method in class com.cra.bnet.engine.TopologyEvent
Returns the node that added to or removed from the Bayesian network.
getNode() - Method in class com.cra.bnet.engine.ThresholdBeliefCondition
 
getNode() - Method in class com.cra.bnet.engine.StateEvent
Returns the node this event occurred on.
getNode() - Method in class com.cra.bnet.engine.NodeEvent
Returns the node this event occurred on.
getNode() - Method in class com.cra.bnet.engine.EvidenceNode
 
getNode() - Method in class com.cra.bnet.engine.EvidenceEvent
Returns the node that evidence was posted to or retracted from.
getNode() - Method in class com.cra.bnet.engine.CptEvent
Returns the node whose cpt changed.
getNode() - Method in class com.cra.bnet.engine.CptEntryNode
 
getNode() - Method in class com.cra.bnet.engine.Cpt
Returns this cpt's node.
getNode() - Method in class com.cra.bnet.engine.BeliefEvent
Returns the node whose beliefs changed.
getNode() - Method in interface com.cra.bnet.engine.BeliefCondition
Returns the node that this condition operates on.
getNode() - Method in class com.cra.bnet.error.SelfLoopError
Returns the node that was both the source and target of the self-loop edge.
getNode(String) - Method in class com.cra.bnet.engine.BayesianNetwork
Returns the node in this Bayesian network that has the specified name.
getNodeIndex() - Method in class com.cra.bnet.engine.CptEvent
Returns the index of the node corresponding to the conditional probability that changed.
getNodeName() - Method in interface com.cra.bnet.learn.Observation
Returns the name of this observation's node.
getNodes() - Method in class com.cra.bnet.engine.Potential
Returns the domain list of this potential.
getNumBases() - Method in class com.cra.bnet.engine.VbnConverter
 
getObservations() - Method in interface com.cra.bnet.learn.Case
Returns an iterator over the observations of this case.
getOldLocation() - Method in class com.cra.bnet.engine.NodeEvent
Returns the old location.
getOldName() - Method in class com.cra.bnet.engine.StateEvent
Returns the old state name.
getOldName() - Method in class com.cra.bnet.engine.NodeEvent
Returns the old node name.
getOldValue() - Method in class com.cra.bnet.engine.CptEvent
Returns the old cpt entry.
getOrders() - Method in class com.cra.bnet.engine.VbnConverter
 
getParameters() - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Returns the parameters that this learning algorithm is using.
getParent() - Method in class com.cra.bnet.engine.NodeEvent
Returns the parent that was reordered or null if the type of this event is not PARENT_REORDERED.
getParentIndices() - Method in class com.cra.bnet.engine.CptEvent
Returns the indices of the parents corresponding to the conditional probability that changed.
getParentIndices() - Method in class com.cra.bnet.engine.Cpt
Returns an iterator over all possible configurations of this cpt's node's parents.
getParents() - Method in class com.cra.bnet.engine.Node
Returns an unmodifiable list of this node's parents.
getParents() - Method in interface com.cra.bnet.engine.AmgNode
Returns a list of this node's parents.
getParents() - Method in class com.cra.bnet.engine.AbstractNode
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.AddNodeEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveNodeEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.AddEdgeEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveEdgeEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.RenameNetworkEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.RenameNodeEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.ChangeNodeDescriptionEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.ReorderParentEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.AddStateEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveStateEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.ReorderStateEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.RenameStateEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.PostEvidenceEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundPostEvidenceEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveEvidenceEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.ClearEvidenceEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.ChangeLocationEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundChangeLocationEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.ChangeCptEntryEdit
 
getPresentationName() - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundChangeCptEntryEdit
 
getProbability() - Method in class com.cra.bnet.engine.CptEntryNode
Returns this node's probability.
getProperties() - Method in class com.cra.bnet.engine.Node
Returns this node's user properties.
getProperties() - Method in class com.cra.bnet.engine.BayesianNetwork
Returns this Bayesian network's user properties.
getRandomIndex(double[]) - Static method in class com.cra.bnet.engine.BayesianNetworks
Returns an index chosen randomly using the specified distribution.
getRandomStateUsingBeliefs(DiscreteNode) - Static method in class com.cra.bnet.engine.BayesianNetworks
Returns a state of the specified node chosen randomly basedon the probabilities of the node's current beliefs.
getRandomStateUsingCpt(DiscreteNode, int[]) - Static method in class com.cra.bnet.engine.BayesianNetworks
Returns a state of the specified node chosen randomly based on the probabilities in the row in the CPT corresponding to the specified parent states.
getRoots() - Method in class com.cra.bnet.engine.AddMultiplyGraph
Returns this AMG's root node.
getSaturated() - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Returns the nodes saturated in this junction tree inference engine.
getSeparator() - Method in class com.cra.bnet.engine.AddNode
Returns this node's separator.
getSeparatorIndex() - Method in class com.cra.bnet.engine.AddNode
Returns this node's separator index.
getSize(List) - Static method in class com.cra.bnet.engine.VbnConverter
Returns the size of a vbn over the specified list of nodes without actually creating one.
getSource() - Method in class com.cra.bnet.error.DuplicateEdgeError
Returns the source node of the duplicate edge.
getSource() - Method in class com.cra.bnet.error.CycleError
Returns the source node of the cycle-creating edge.
getState() - Method in class com.cra.bnet.engine.ThresholdBeliefCondition
Returns this condition's state.
getState(DiscreteNode, double[]) - Static method in class com.cra.bnet.engine.BayesianNetworks
Returns the state of the specified node that corresponds to the specified hard evidence.
getStateCount(int) - Method in interface com.cra.bnet.engine.LightweightBayesianNetwork
 
getStateCount(int) - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
getStates() - Method in class com.cra.bnet.engine.DiscreteNode
Returns a fully modifiable list of this discrete node's states.
getStates(int) - Method in interface com.cra.bnet.engine.LightweightBayesianNetwork
 
getStates(int) - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
getTarget() - Method in class com.cra.bnet.error.DuplicateEdgeError
Returns the target node of the duplicate edge.
getTarget() - Method in class com.cra.bnet.error.CycleError
Returns the target node of the cycle-creating edge.
getThreshold() - Method in class com.cra.bnet.engine.ThresholdBeliefCondition
Returns this condition's threshold.
getTopology() - Method in class com.cra.bnet.engine.BayesianNetwork
Returns the topology of this Bayesian network.
getType() - Method in class com.cra.bnet.engine.TopologyEvent
Returns the type of this event.
getType() - Method in class com.cra.bnet.engine.StateEvent
Returns the type of this state event.
getType() - Method in class com.cra.bnet.engine.NodeEvent
Returns the type of this node event.
getType() - Method in class com.cra.bnet.engine.EvidenceEvent
Returns the type of this evidence event.
getUndoableEditSupport() - Method in class com.cra.bnet.engine.BayesianNetwork
Returns this Bayesian network's undoable edit support.
getUniqueNodeName(BayesianNetwork, String) - Static method in class com.cra.bnet.engine.BayesianNetworks
Returns a unique node name for the specified Bayesian network based on the specified base name.
getUniqueNodeName(BayesianNetwork, String, int, boolean) - Static method in class com.cra.bnet.engine.BayesianNetworks
Returns a unique node name for the specified Bayesian network based on the specified base name.
getValue() - Method in interface com.cra.bnet.engine.AmgNode
Returns this node's value.
getValue() - Method in class com.cra.bnet.engine.AbstractNode
 
getValueName() - Method in class com.cra.bnet.engine.MultiplyNode
 
getValueName() - Method in interface com.cra.bnet.engine.AmgNode
Returns this node's value name.
getValueName() - Method in class com.cra.bnet.engine.AddNode
 
getValueName() - Method in class com.cra.bnet.engine.AbstractNode
 
getValuesParsed() - Method in class com.cra.bnet.learn.SimpleDataSet
Checks if any value was parsed in this object, in which case this parser is compatible with the selected data file.
getValuesParsed() - Method in interface com.cra.bnet.learn.DataSet
Checks if any value was parsed in this object, in which case this parser is compatible with the selected data file.
getValuesParsed() - Method in class com.cra.bnet.learn.ComplexDataSet
Checks if any value was parsed in this object, in which case this parser is compatible with the selected data file.
getVariable(String) - Method in interface com.cra.bnet.engine.LightweightBayesianNetwork
 
getVariable(String) - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
getVariableCount() - Method in interface com.cra.bnet.engine.LightweightBayesianNetwork
 
getVariableCount() - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
getVariableIndex() - Method in class com.cra.bnet.engine.EvidenceNode
Returns this node's variable index.
getVariableIndex() - Method in class com.cra.bnet.engine.CptEntryNode
Returns this node's variable index.
getVariableIndex(int) - Method in class com.cra.bnet.engine.AddMultiplyGraph
Returns the discrete node at the specified index.
getVariableName(int) - Method in interface com.cra.bnet.engine.LightweightBayesianNetwork
 
getVariableName(int) - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
GREATER_THAN - Static variable in class com.cra.bnet.engine.ThresholdBeliefCondition
The greater-than operator.
GREATER_THAN_OR_EQUAL_TO - Static variable in class com.cra.bnet.engine.ThresholdBeliefCondition
The greater-than-or-equal-to operator.

H

hashCode() - Method in class com.cra.bnet.engine.Potential
Returns the hash code value for this potential.
hashCode() - Method in class com.cra.bnet.engine.Node
Returns this node's hash code.
HuginFormat - class com.cra.bnet.io.HuginFormat.
Reads and writes Bayesian networks in Hugin format.
HuginFormat() - Constructor for class com.cra.bnet.io.HuginFormat
 
HuginInferenceEngine - class com.cra.bnet.engine.HuginInferenceEngine.
Implementation of the Hugin inference algorithm.
HuginInferenceEngine(BayesianNetwork) - Constructor for class com.cra.bnet.engine.HuginInferenceEngine
Creates a new Hugin inference engine using the specified Bayesian network.
HuginInferenceEngine(BayesianNetwork, boolean) - Constructor for class com.cra.bnet.engine.HuginInferenceEngine
Creates a new Hugin inference engine using the specified Bayesian network.

I

InconsistentEvidenceError - exception com.cra.bnet.error.InconsistentEvidenceError.
An error that occurs when inconsistent evidence is posted to a Bayesian network.
InconsistentEvidenceError(BayesianNetwork) - Constructor for class com.cra.bnet.error.InconsistentEvidenceError
Creates a new InconsistentEvidenceError.
InferenceEngine - interface com.cra.bnet.engine.InferenceEngine.
An engine that performs probabilistic inference on a Bayesian network.
initialize() - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Initializes the junction tree potentials.
initialize() - Method in class com.cra.bnet.engine.HuginInferenceEngine
Initializes the junction tree potentials.
isAllOnes(double[]) - Static method in class com.cra.bnet.engine.BayesianNetworks
Returns true if all evidence values in the specified array are equal to 1.0.
isAllZeros(double[]) - Static method in class com.cra.bnet.engine.BayesianNetworks
Returns true if all evidence values in the specified evidnce array are equal to 0.0.
isCaching() - Method in class com.cra.bnet.engine.PotentialMappings
Returns true if mappings are to be cached and false otherwise.
isEnd(int) - Method in class com.cra.bnet.io.BufferedRegExpReader
Returns true if the specified index is greater than the last valid index and false if it is a valid index.
isInconsistentEvidence() - Method in class com.cra.bnet.engine.EvidenceEvent
Returns true if this event represents a retraction of inconsistent evidence and false if it represents a normal retraction of evidence.
isNetworkCompatible(BayesianNetwork) - Method in class com.cra.bnet.learn.ComplexDataSet
Whenever a new BayesianNetwork is to be used with this data set, check to see if the nodes are compatible.
isNetworkCompatible(BayesianNetwork, File) - Static method in class com.cra.bnet.learn.DataSetUtil
Whenever a data file is to be used with a BayesianNetwork, check to see if the data nodes exist in the network.
isNormalized(int) - Method in class com.cra.bnet.engine.Cpt
Returns true if all rows in this CPT are normalized using the specified number of significant digits.
isNormalized(int[], int) - Method in class com.cra.bnet.engine.Cpt
Returns true if the row specified by the parent indices is normalized using the specified number of significant digits.
isOnQueue() - Method in interface com.cra.bnet.engine.QueueNode
Returns true if this node is on the queue and false if it is not.
isOnQueue() - Method in class com.cra.bnet.engine.AbstractQueueNode
 
isResetNeeded() - Method in class com.cra.bnet.engine.AddMultiplyGraph
 
isRunning() - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Returns true if this learning algorithm is currently running and false otherwise.
isUpdatingOnAllEvidenceRetracted() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns true if beliefs are updated after all evidence is retracted.
isUpdatingOnCptEntryChanged() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns true if beliefs are updated after a cpt entry changes.
isUpdatingOnEdgeAdded() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns true if beliefs are updated after an edge is added.
isUpdatingOnEdgeRemoved() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns true if beliefs are updated after an edge is removed.
isUpdatingOnEvidencePosted() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns true if beliefs are updated after evidence is posted.
isUpdatingOnEvidenceRetracted() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns true if beliefs are updated after evidence is retracted.
isUpdatingOnNodeAdded() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns true if beliefs are updated after a node is added.
isUpdatingOnNodeRemoved() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns true if beliefs are updated after a node is removed.
isUpdatingOnParentReordered() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns true if beliefs are updated after a parent is reordered.
isUpdatingOnStateAdded() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns true if beliefs are updated after a state is added.
isUpdatingOnStateRemoved() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns true if beliefs are updated after a state is removed.
isUpdatingOnStateReordered() - Method in class com.cra.bnet.engine.BeliefUpdater
Returns true if beliefs are updated after a state is reordered.
isValid() - Method in class com.cra.bnet.engine.BeliefEvent
Returns true if the new beliefs are valid and false if they are invalid.
isValid(BufferedRegExpReader) - Method in class com.cra.bnet.io.XbnFormat
Returns true if the specified reader contains XBN data.
isValid(BufferedRegExpReader) - Method in class com.cra.bnet.io.NeticaFormat
Returns false because this method has not yet been implemented.
isValid(BufferedRegExpReader) - Method in class com.cra.bnet.io.HuginFormat
Returns false because this method has not yet been implemented.
isValid(BufferedRegExpReader) - Method in interface com.cra.bnet.io.BnetFormat
Returns true if the specified reader contains data understood by this BnetFormat and false if it is not supported.
isValid(int[]) - Method in class com.cra.bnet.engine.VbnConverter
 
isValidating() - Method in class com.cra.bnet.io.XbnFormat
Returns true if the XML parsers should validate or false if they should not.
isValidBeliefs(double[]) - Static method in class com.cra.bnet.engine.BayesianNetworks
Returns true if the specified beliefs are valid.
ITERATION_FINISHED - Static variable in class com.cra.bnet.learn.EmEtaEvent
The iteration finished event type.
iterationFinished(EmEtaEvent) - Method in interface com.cra.bnet.learn.EmEtaListener
Invoked when an iteration of the algorithm has finished.
iterationFinished(EmEtaEvent) - Method in class com.cra.bnet.learn.EmEtaAdapter
Invoked when an iteration of the algorithm has finished.

J

JunctionTree - class com.cra.bnet.engine.JunctionTree.
Constructs a junction tree from a given directed graph.
JunctionTree(Graph) - Constructor for class com.cra.bnet.engine.JunctionTree
Creates a new junction tree from the specified directed graph.
JunctionTree(Graph, Map) - Constructor for class com.cra.bnet.engine.JunctionTree
Creates a new junction tree from the specified directed graph using the specified vertex weights.
JunctionTreeInferenceEngine - class com.cra.bnet.engine.JunctionTreeInferenceEngine.
Skeletal implementation of the InferenceEngine interface for junction tree based inference algorithms.
JunctionTreeInferenceEngine(BayesianNetwork) - Constructor for class com.cra.bnet.engine.JunctionTreeInferenceEngine
Creates a new junction tree inference engine using the specified Bayesian network.
JunctionTreeInferenceEngine(BayesianNetwork, boolean) - Constructor for class com.cra.bnet.engine.JunctionTreeInferenceEngine
Creates a new junction tree inference engine using the specified Bayesian network.

L

learn(DataSet, BayesianNetwork) - Method in class com.cra.bnet.learn.FullyObservableLearningAlgorithm
Learns the CPT entries in the specified Bayesian network from the specified data set.
learn(DataSet, BayesianNetwork, boolean) - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Updates the conditional probability tables of the specified Bayesian network using the specified data set.
length() - Method in class com.cra.bnet.io.BufferedRegExpReader
Returns the length of this character sequence.
LESS_THAN - Static variable in class com.cra.bnet.engine.ThresholdBeliefCondition
The less-than operator.
LESS_THAN_OR_EQUAL_TO - Static variable in class com.cra.bnet.engine.ThresholdBeliefCondition
The less-than-or-equal-to operator.
LightweightBayesianNetwork - interface com.cra.bnet.engine.LightweightBayesianNetwork.
A lightweight Bayesian network data structure.
LOCATION_CHANGED - Static variable in class com.cra.bnet.engine.NodeEvent
The location changed event type.
locationChanged(NodeEvent) - Method in interface com.cra.bnet.engine.NodeListener
Invoked when the node's location has been changed.
locationChanged(NodeEvent) - Method in class com.cra.bnet.engine.NodeAdapter
 

M

makeConsistent() - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Makes the junction tree consistent so beliefs can be calculated from it.
marginalize(List) - Method in class com.cra.bnet.engine.Potential
Marginalizes the specified nodes out of this potential and returns the resulting potential.
mark(int) - Method in class com.cra.bnet.io.CraPushbackReader
This method always throws an UnsupportedOperationException.
mark(int) - Method in class com.cra.bnet.io.BufferedRegExpReader
Throws an UnsupportedOperationException since the mark method is not supported by this class.
markSupported() - Method in class com.cra.bnet.io.CraPushbackReader
This method always returns false since the mark method is not supported.
markSupported() - Method in class com.cra.bnet.io.BufferedRegExpReader
Returns false sine the mark method is not supported by this class.
md - Variable in class com.cra.bnet.engine.GeneratedEngineBase
these five arrays store partial results of belief calculations
modified - Variable in class com.cra.bnet.engine.GeneratedEngineBase
true when something changed and beliefs need to be recalculated
multiply(Potential) - Method in class com.cra.bnet.engine.Potential
Multiplies this potential by the specified potential and returns the product.
multiplyEvidence() - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Multiplies the new evidence into the junction tree potentials.
multiplyEvidence() - Method in class com.cra.bnet.engine.HuginInferenceEngine
Multiplies the new evidence into the junction tree potentials.
MultiplyNode - class com.cra.bnet.engine.MultiplyNode.
Represents a multiplication node in the AMG.
MultiplyNode(Set, int, int) - Constructor for class com.cra.bnet.engine.MultiplyNode
Creates a new MultiplyNode using the specified cluster index and instantiation index.
multiplyNodeLengths() - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
mv - Variable in class com.cra.bnet.engine.GeneratedEngineBase
these five arrays store partial results of belief calculations

N

n - Variable in class com.cra.bnet.engine.GeneratedEngineBase
n[i] = name of node i
name - Variable in class com.cra.bnet.engine.AbstractNode
 
NAME_CHANGED - Static variable in class com.cra.bnet.engine.NodeEvent
The name changed event type.
NAME_PROPERTY - Static variable in class com.cra.bnet.engine.BayesianNetwork
The Bayesian network name property.
nameChanged(NodeEvent) - Method in interface com.cra.bnet.engine.NodeListener
Invoked when the node's name has been changed.
nameChanged(NodeEvent) - Method in class com.cra.bnet.engine.NodeAdapter
 
NeticaFormat - class com.cra.bnet.io.NeticaFormat.
Reads and writes Bayesian networks in Netica format.
NeticaFormat() - Constructor for class com.cra.bnet.io.NeticaFormat
 
Node - class com.cra.bnet.engine.Node.
A node in a Bayesian network.
NODE_ADDED - Static variable in class com.cra.bnet.engine.TopologyEvent
The node added event type.
NODE_ADDED - Static variable in class com.cra.bnet.engine.BeliefUpdater
The integer mask for node added.
NODE_REMOVED - Static variable in class com.cra.bnet.engine.TopologyEvent
The node removed event type.
NODE_REMOVED - Static variable in class com.cra.bnet.engine.BeliefUpdater
The integer mask for node removed.
NodeAdapter - class com.cra.bnet.engine.NodeAdapter.
An abstract adapter class for receiving node events.
NodeAdapter() - Constructor for class com.cra.bnet.engine.NodeAdapter
 
nodeAdded(TopologyEvent) - Method in interface com.cra.bnet.engine.TopologyListener
Invoked when a node has been added to a Bayesian network.
nodeAdded(TopologyEvent) - Method in class com.cra.bnet.engine.TopologyAdapter
 
NodeEvent - class com.cra.bnet.engine.NodeEvent.
A node-related event.
NodeEvent(Node, Node, int) - Constructor for class com.cra.bnet.engine.NodeEvent
Creates a new parent reordered NodeEvent using the specified node, parent, and index.
NodeEvent(Node, Point, Point) - Constructor for class com.cra.bnet.engine.NodeEvent
Creates a new location changed NodeEvent using the specified node, old and new locations.
NodeEvent(Node, String, String, NodeEvent.NodeEventType) - Constructor for class com.cra.bnet.engine.NodeEvent
Creates a new name or description changed NodeEvent using the specified node, old name, and new name.
NodeListener - interface com.cra.bnet.engine.NodeListener.
A listener that receives node events from a node in a Bayesian network.
nodeNames() - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
nodeRemoved(TopologyEvent) - Method in interface com.cra.bnet.engine.TopologyListener
Invoked when a node has been removed from a Bayesian network.
nodeRemoved(TopologyEvent) - Method in class com.cra.bnet.engine.TopologyAdapter
 
nodes - Variable in class com.cra.bnet.engine.Potential
 
nodeSet() - Method in class com.cra.bnet.engine.BayesianNetwork
Returns a set view of the nodes contained in this Bayesian network.
normalize() - Method in class com.cra.bnet.engine.Potential
Normalizes the values of this potential so that they sum to unity and returns the result.
normalize(int[]) - Method in class com.cra.bnet.engine.Cpt
Normalizes the row specified by the parent indices so it will sum to one.
normalize(int[], int) - Method in class com.cra.bnet.engine.Cpt
Normalizes the row specified by the parent indices so it will sum to one using the specified number of significant digits.
normalizeAll() - Method in class com.cra.bnet.engine.Cpt
Normalizes each row in the entire conditional probability table so that each row will sum to one.
normalizeAll(int) - Method in class com.cra.bnet.engine.Cpt
Normalizes each row in the entire conditional probability table so each row will sum to one using the specified number of significant digits.
normalizeAllHelper() - Method in class com.cra.bnet.engine.Cpt
Helper method that actually normalizes the entire conditional probability table without posting an undoable edit.
NOT_EQUAL_TO - Static variable in class com.cra.bnet.engine.ThresholdBeliefCondition
The not-equal-to operator.

O

Observation - interface com.cra.bnet.learn.Observation.
An observation of a single node for learning Bayesian networks.

P

PARENT_REORDERED - Static variable in class com.cra.bnet.engine.NodeEvent
The parent reordered event type.
PARENT_REORDERED - Static variable in class com.cra.bnet.engine.BeliefUpdater
The integer mask for parent reordered.
ParentIndices - class com.cra.bnet.engine.ParentIndices.
Utility class for generating an array of parent indices for use with Cpt using parent and state names.
ParentIndices(Node) - Constructor for class com.cra.bnet.engine.ParentIndices
Creates a new ParentIndices for the specified node.
parentReordered(NodeEvent) - Method in interface com.cra.bnet.engine.NodeListener
Invoked when one of the node's parents has been reordered.
parentReordered(NodeEvent) - Method in class com.cra.bnet.engine.NodeAdapter
 
pause() - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Requests this learning algorithm to pause execution.
post(BnetError) - Method in class com.cra.bnet.error.ErrorNotifier
Notifies all error listeners of the specified error.
postEvidence(DiscreteNode, double[]) - Method in class com.cra.bnet.engine.AddMultiplyGraph
Posts the specified evidence to the specified variable.
Potential - class com.cra.bnet.engine.Potential.
Basic implementation of a potential.
Potential() - Constructor for class com.cra.bnet.engine.Potential
We need a default constructor so that the implicit call to super from a subclass can succeed.
Potential(DiscreteNode, double[]) - Constructor for class com.cra.bnet.engine.Potential
Creates a new potential over the specified node that has the specified values.
Potential(List) - Constructor for class com.cra.bnet.engine.Potential
Creates a new potential over the specified nodes.
Potential(List, PotentialMappings) - Constructor for class com.cra.bnet.engine.Potential
Creates a new potential over the specified nodes that uses the specified potential mappings.
Potential(Potential) - Constructor for class com.cra.bnet.engine.Potential
Creates a new potential that is a copy of the specified potential.
PotentialMappings - class com.cra.bnet.engine.PotentialMappings.
A cache of mappings between potentials.
PotentialMappings() - Constructor for class com.cra.bnet.engine.PotentialMappings
Creates a new empty PotentialMappings object.
printException(Exception, String) - Static method in class com.cra.bnet.debug.DebugUtils
 

Q

QueueNode - interface com.cra.bnet.engine.QueueNode.
Adds boolean OnQueue property to the Node interface.

R

randomizeAll() - Method in class com.cra.bnet.engine.Cpt
Sets each row in this CPT to normalized, random values that sum to one.
randomizeCpts(BayesianNetwork) - Static method in class com.cra.bnet.engine.BayesianNetworks
Randomizes the CPT of every node in the specified network.
read() - Method in class com.cra.bnet.io.CraPushbackReader
Reads a single character and returns it.
read() - Method in class com.cra.bnet.io.BufferedRegExpReader
Reads a single character and returns it.
read(char[], int, int) - Method in class com.cra.bnet.io.CraPushbackReader
Reads the specified number of characters into the specified array, starting at the specified index.
read(char[], int, int) - Method in class com.cra.bnet.io.BufferedRegExpReader
Reads the specified number of characters into the specified character array, starting at the specified index and returns the number of characters actually read.
read(File) - Static method in class com.cra.bnet.io.XbnFormat
Returns the Bayesian network read from the specified file.
read(File) - Static method in class com.cra.bnet.io.NeticaFormat
Returns the Bayesian network read from the specified file.
read(File) - Static method in class com.cra.bnet.io.HuginFormat
Returns the Bayesian network read from the specified file.
read(Reader) - Method in class com.cra.bnet.io.XbnFormat
Returns the Bayesian network obtained from the specified reader.
read(Reader) - Method in class com.cra.bnet.io.NeticaFormat
Returns the Bayesian network obtained from the specified reader.
read(Reader) - Method in class com.cra.bnet.io.HuginFormat
Returns the Bayesian network obtained from the specified reader.
read(Reader) - Method in class com.cra.bnet.io.BnetFormatFactory
Returns the Bayesian network obtained from the specified reader or null if it could not be read.
read(Reader) - Method in interface com.cra.bnet.io.BnetFormat
Returns the Bayesian network obtained from the specified reader.
ready() - Method in class com.cra.bnet.io.CraPushbackReader
Returns true if this reader is ready to be read from and false if it is not.
ready() - Method in class com.cra.bnet.io.BufferedRegExpReader
Returns true if this reader is ready to supply characters and false if it is not.
reconstruct() - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Notifies this engine that it must reconstruct its junction tree before doing anything else.
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.AddNodeEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveNodeEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.AddEdgeEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveEdgeEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.RenameNetworkEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.RenameNodeEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.ChangeNodeDescriptionEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.ReorderParentEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.AddStateEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveStateEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.ReorderStateEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.RenameStateEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.PostEvidenceEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundPostEvidenceEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveEvidenceEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.ClearEvidenceEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.ChangeLocationEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundChangeLocationEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.ChangeCptEntryEdit
 
redo() - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundChangeCptEntryEdit
 
registerFormat(BnetFormat) - Method in class com.cra.bnet.io.BnetFormatFactory
Registers the specified format with this factory.
removeBeliefListener(BeliefListener) - Method in class com.cra.bnet.engine.Node
Unregisters the specified listener so it will no longer receive belief events from this node.
removeBeliefListener(BeliefListener) - Method in class com.cra.bnet.engine.BeliefAlert
Unregisters the specified belief listener so it will no longer receive events from this alert.
removeBeliefListener(BeliefListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Unregisters the specified listener so it will no longer receive belief events from this Bayesian network.
removeChangeListener(ChangeListener) - Method in class com.cra.bnet.engine.StructuralModificationSupport
Unregisters the specified change listener so it will no longer receive change events when structural modifications are made to the Bayesian network.
removeChangeListener(ChangeListener) - Method in class com.cra.bnet.engine.BeliefUpdater
Unregisters the specified listener with this belief updater so it will no longer receive change events whenever this belief updater is notified of any modifications to the Bayesian network.
removeCptListener(CptListener) - Method in class com.cra.bnet.engine.Node
Unregisters the specified listener so it will no longer receive CPT events from this node.
removeCptListener(CptListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Unregisters the specified listener so it will no longer receive cpt events from this Bayesian network.
removed() - Method in class com.cra.bnet.engine.ScgInferenceEngine
 
removed() - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
 
removed() - Method in interface com.cra.bnet.engine.InferenceEngine
Called by BayesianNetwork to notify this inference engine that it has been replaced by another inference engine and will not be used anymore.
removed() - Method in class com.cra.bnet.engine.AmgInferenceEngine
 
removeEdge(Node, Node) - Method in class com.cra.bnet.engine.BayesianNetwork
Removes the edge from the specified parent to the specified child from this Bayesian network.
removeEmEtaListener(EmEtaListener) - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Unregisters the specified listener so that it will no longer receive events from this learning algorithm.
removeErrorListener(ErrorListener) - Method in class com.cra.bnet.error.ErrorNotifier
Unregisters the specified error listener so it will no longer receive error events.
removeEvidence() - Method in class com.cra.bnet.engine.DiscreteNode
Retracts all the evidence posted to this discrete node.
removeEvidence(DiscreteNode) - Method in class com.cra.bnet.engine.ScgInferenceEngine
 
removeEvidence(DiscreteNode) - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Removes (or equivalently, retracts) evidence from the specified variable.
removeEvidence(DiscreteNode) - Method in interface com.cra.bnet.engine.InferenceEngine
Removes (or equivalently, retracts) evidence from the specified variable.
removeEvidence(DiscreteNode) - Method in class com.cra.bnet.engine.AmgInferenceEngine
 
removeEvidenceListener(EvidenceListener) - Method in class com.cra.bnet.engine.Node
Unregisters the specified listener so it will no longer receive evidence events from this node.
removeEvidenceListener(EvidenceListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Unregisters the specified listener so it will no longer receive evidence events from this Bayesian network.
removeNode(Node) - Method in class com.cra.bnet.engine.BayesianNetwork
Removes the specified node and all connected edges from this Bayesian network.
removeNodeListener(NodeListener) - Method in class com.cra.bnet.engine.Node
Unregisters the specified listener so it will no longer receive node events from this node.
removeNodeListener(NodeListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Unregisters the specified listener so it will no longer receive node events from this Bayesian network.
removeNodePropertyChangeListener(PropertyChangeListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Unregisters the specified property change listener so it will no longer receive events when the user properties of nodes change.
removePropertyChangeListener(PropertyChangeListener) - Method in class com.cra.bnet.engine.Node
Unregisters the specified property change listener so it will no longer receive events when the user properties of this node change.
removePropertyChangeListener(PropertyChangeListener) - Method in class com.cra.bnet.engine.BeliefUpdater
Unregisters the specified listener so it will not receive property change events.
removePropertyChangeListener(PropertyChangeListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Unregisters the specified property change listener so that it will not receive property change events from this Bayesian network.
removePropertyChangeListener(PropertyChangeListener, String) - Method in class com.cra.bnet.engine.BeliefUpdater
Unregisters the specified listener so it will not receive property change events for the specified property.
removeStateListener(StateListener) - Method in class com.cra.bnet.engine.DiscreteNode
Unregisters the specified state listener so it will no longer receive events when this discrete node's states change.
removeStateListener(StateListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Unregisters the specified listener so it will no longer receive state events from this Bayesian network.
removeTopologyListener(TopologyListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Unregisters the specified topology listener so that it will not receive topology events from this Bayesian network.
removeUndoableEditListener(UndoableEditListener) - Method in class com.cra.bnet.engine.BayesianNetwork
Unregisters the specified listener so it will no longer receive undoable edit events from this Bayesian network.
reorder(Object, int) - Method in interface com.cra.bnet.engine.StateList
Moves the specfied object to the specified index.
reorderParent(DiscreteNode, int) - Method in class com.cra.bnet.engine.Cpt
Called by BN.Node.reorderParent to notify its cpt that a parent has been reordered.
reorderParent(DiscreteNode, int) - Method in interface com.cra.bnet.engine.Cpd
Called by Node.reorderParent to notify its cpd that a parent has been reordered.
reorderParent(Node, int) - Method in class com.cra.bnet.engine.Node
Moves the specified parent to the specified index.
reset() - Method in interface com.cra.bnet.engine.AmgNode
Resets this node.
reset() - Method in class com.cra.bnet.engine.AddMultiplyGraph
Resets/initializes this AMG.
reset() - Method in class com.cra.bnet.engine.AbstractNode
 
reset() - Method in class com.cra.bnet.io.CraPushbackReader
This method always throws an UnsupportedOperationException.
reset() - Method in class com.cra.bnet.io.BufferedRegExpReader
Resets this reader so it will start returning the buffered characters before reading more characters from the underlying reader.
restorePotentials() - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Restores the junction tree potentials to their initialized state.
restorePotentials() - Method in class com.cra.bnet.engine.HuginInferenceEngine
Restores the junction tree potentials to their initialized state.
resume() - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Requests this learning algorithm to resume execution.
retractAllEvidence() - Method in class com.cra.bnet.engine.AddMultiplyGraph
Retracts the evidence from all variables.
retractEvidence(DiscreteNode) - Method in class com.cra.bnet.engine.AddMultiplyGraph
Retracts the evidence from the specified variable.

S

s - Variable in class com.cra.bnet.engine.GeneratedEngineBase
s[i][j] = name of state j of node i
ScgInferenceEngine - class com.cra.bnet.engine.ScgInferenceEngine.
Inference engine based on generated source code.
ScgInferenceEngine(BayesianNetwork) - Constructor for class com.cra.bnet.engine.ScgInferenceEngine
Creates a new SCG inference engine using the specified Bayesian network.
ScgInferenceEngine(BayesianNetwork, boolean) - Constructor for class com.cra.bnet.engine.ScgInferenceEngine
Creates a new SCG inference engine using the specified Bayesian network.
SelfLoopError - exception com.cra.bnet.error.SelfLoopError.
An error that occurs when a self-loop edge was added to a Bayesian network.
SelfLoopError(BayesianNetwork, Node) - Constructor for class com.cra.bnet.error.SelfLoopError
Creates a new SelfLoopError using the specified network model and node.
sendMessage(Set, Set) - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Sends a message from the first clique to the second clique.
sendMessage(Set, Set) - Method in class com.cra.bnet.engine.HuginInferenceEngine
Sends a message from the first clique to the second clique.
set(int[], double) - Method in class com.cra.bnet.engine.Potential
Sets the value of this potential indexed by the specified index to the specified value.
set(int, double) - Method in class com.cra.bnet.engine.Potential
Sets the value of this potential indexed by the specified integer index to the specified value.
set(int, int[], double) - Method in class com.cra.bnet.engine.Cpt
Sets the conditional probability that this cpt's node is in the specified state (given that its parents are in the specified states) to the specified value.
set(String, String) - Method in class com.cra.bnet.engine.ParentIndices
Sets the element of the parent array that corresponds to the specified parent to the index of that parent's specified state.
setBeliefUpdateSettings(int) - Method in class com.cra.bnet.engine.BeliefUpdater
Sets this belief updater's belief update settings to the specified settings.
setCache(boolean) - Method in class com.cra.bnet.engine.PotentialMappings
If the specified boolean argument is true, this object will cache its mappings.
setConditionalProbability(int, int, double) - Method in interface com.cra.bnet.engine.LightweightBayesianNetwork
 
setConditionalProbability(int, int, double) - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
setCpd(Cpd) - Method in class com.cra.bnet.engine.Node
Sets this node's conditional probability distribution.
setDebugOutput(PrintWriter) - Static method in class com.cra.bnet.debug.DebugUtils
Default output is System.out.
setDescription(String) - Method in class com.cra.bnet.engine.Node
Sets this node's description to the specified description.
setDescription(String) - Method in class com.cra.bnet.engine.BayesianNetwork
Sets this Bayesian network's description to the specified description.
setError(String) - Method in class com.cra.bnet.io.AbstractBnetFormat
Sets the error to the specified error.
setEvidence(DiscreteNode, double[]) - Method in class com.cra.bnet.engine.ScgInferenceEngine
 
setEvidence(DiscreteNode, double[]) - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Posts the specified evidence to the specified variable.
setEvidence(DiscreteNode, double[]) - Method in interface com.cra.bnet.engine.InferenceEngine
Posts the specified evidence to the specified variable.
setEvidence(DiscreteNode, double[]) - Method in class com.cra.bnet.engine.AmgInferenceEngine
 
setEvidence(double) - Method in class com.cra.bnet.engine.EvidenceNode
Sets this node's evidence to the specified value.
setEvidence(double[]) - Method in class com.cra.bnet.engine.DiscreteNode
Posts the specified evidence to this discrete node.
setEvidence(int, double[]) - Method in interface com.cra.bnet.engine.LightweightBayesianNetwork
 
setEvidence(int, double[]) - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
setEvidence(String, double) - Method in class com.cra.bnet.engine.DiscreteNode
Posts the specified evidence to the specified state.
setInferenceEngine(InferenceEngine) - Method in class com.cra.bnet.engine.BayesianNetwork
Sets this Bayesian network's inference engine to the specified inference engine.
setLocation(Point) - Method in class com.cra.bnet.engine.Node
Sets this node's location to the specified point.
setLocation(Point) - Method in class com.cra.bnet.engine.BayesianNetwork.AddNodeEdit
 
setLocationHelper(Point) - Method in class com.cra.bnet.engine.Node
Use this method instead of setLocation if you don't want a ChangeLocationEdit to be posted.
setMappings(PotentialMappings) - Method in class com.cra.bnet.engine.Potential
Sets the mappings that this potential uses to the specified mappings.
setName(String) - Method in class com.cra.bnet.engine.Node
Sets this node's name to the specified name.
setName(String) - Method in class com.cra.bnet.engine.BayesianNetwork
Sets the name of this Bayesian network to the specified name.
setNetwork(BayesianNetwork) - Method in class com.cra.bnet.engine.StructuralModificationSupport
Sets the Bayesian network to observe for structural modifications to the specified network.
setOnQueue(boolean) - Method in interface com.cra.bnet.engine.QueueNode
Sets this node's OnQueue property to the specified value.
setOnQueue(boolean) - Method in class com.cra.bnet.engine.AbstractQueueNode
 
setParameters(EmEtaParameters) - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Sets the parameters used by this learning algorithm to the specified parameters.
setPriors(BayesianNetwork, double) - Method in class com.cra.bnet.learn.FullyObservableLearningAlgorithm
Sets all CPT entries in the specified Bayesian network to the specified prior value.
setProbability(double) - Method in class com.cra.bnet.engine.CptEntryNode
Sets this node's probability to the specified value.
setResetNeeded(boolean) - Method in class com.cra.bnet.engine.AddMultiplyGraph
 
setSaturated(List) - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
Sets the nodes saturated in this junction tree inference engine.
setUpdateOnAllEvidenceRetracted(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when evidence is retracted depending on the specified parameter.
setUpdateOnAnything(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when any event occurs depending on the specified parameter.
setUpdateOnCptEntryChanged(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when a cpt entry changes depending on the specified parameter.
setUpdateOnEdgeAdded(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when an edge is added depending on the specified parameter.
setUpdateOnEdgeRemoved(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when an edge is removed depending on the specified parameter.
setUpdateOnEvidence(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when evidence is posted or retracted depending on the specified parameter.
setUpdateOnEvidencePosted(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when evidence is posted depending on the specified parameter.
setUpdateOnEvidenceRetracted(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when evidence is retracted depending on the specified parameter.
setUpdateOnNodeAdded(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when a node is added depending on the specified parameter.
setUpdateOnNodeRemoved(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when a node is removed depending on the specified parameter.
setUpdateOnParentReordered(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when a parent is reordered depending on the specified parameter.
setUpdateOnStateAdded(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when a state is added depending on the specified parameter.
setUpdateOnStateRemoved(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when a state is removed depending on the specified parameter.
setUpdateOnStateReordered(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates beliefs when a state is reordered depending on the specified parameter.
setValidating(boolean) - Method in class com.cra.bnet.io.XbnFormat
Tells the XML parsers used for reading and writing to validate if the specified boolean is true or not to validate if it is false.
SimpleDataSet - class com.cra.bnet.learn.SimpleDataSet.
Simple implementation of the DataSet interface.
SimpleDataSet(File, BayesianNetwork) - Constructor for class com.cra.bnet.learn.SimpleDataSet
Creates a new SimpleDataSet using the data in the specified file and the specified Bayesian network.
SimpleDataSet(File, BayesianNetwork, String) - Constructor for class com.cra.bnet.learn.SimpleDataSet
Creates a new SimpleDataSet using the data in the specified file and the specified Bayesian network.
size() - Method in class com.cra.bnet.engine.VbnConverter
Returns the total number of values expressible in this format.
size() - Method in class com.cra.bnet.engine.Cpt
Returns the size of this conditional probability table.
skip(long) - Method in class com.cra.bnet.io.BufferedRegExpReader
Throws an UnsupportedOperationException since this class doesn't support the skip method.
STATE_ADDED - Static variable in class com.cra.bnet.engine.StateEvent
The state added event type.
STATE_ADDED - Static variable in class com.cra.bnet.engine.BeliefUpdater
The integer mask for state added.
STATE_NAME_CHANGED - Static variable in class com.cra.bnet.engine.StateEvent
The state name changed event type.
STATE_REMOVED - Static variable in class com.cra.bnet.engine.StateEvent
The state removed event type.
STATE_REMOVED - Static variable in class com.cra.bnet.engine.BeliefUpdater
The integer mask for state removed.
STATE_REORDERED - Static variable in class com.cra.bnet.engine.StateEvent
The state reordered event type.
STATE_REORDERED - Static variable in class com.cra.bnet.engine.BeliefUpdater
The integer mask for state reordered.
StateAdapter - class com.cra.bnet.engine.StateAdapter.
An abstract adapter class for receiving state events.
StateAdapter() - Constructor for class com.cra.bnet.engine.StateAdapter
 
stateAdded(StateEvent) - Method in interface com.cra.bnet.engine.StateListener
Invoked when a new state has beed added to the node.
stateAdded(StateEvent) - Method in class com.cra.bnet.engine.StateAdapter
 
StateEvent - class com.cra.bnet.engine.StateEvent.
A state-related event.
StateEvent.StateEventType - class com.cra.bnet.engine.StateEvent.StateEventType.
Type of state event.
StateEvent(DiscreteNode, String, int, StateEvent.StateEventType) - Constructor for class com.cra.bnet.engine.StateEvent
Creates a new state added, state removed, or state reordered StateEvent using the specified node, state name, state index, and event type.
StateEvent(DiscreteNode, String, String, int) - Constructor for class com.cra.bnet.engine.StateEvent
Creates a new state name changed StateEvent using the specified node, old state name, new state name, and state index.
StateList - interface com.cra.bnet.engine.StateList.
A list of states of a discrete node.
StateListener - interface com.cra.bnet.engine.StateListener.
A listener that receives state events from a discrete node in a Bayesian network.
stateNameChanged(StateEvent) - Method in interface com.cra.bnet.engine.StateListener
Invoked when the name of one of the node's states has been changed.
stateNameChanged(StateEvent) - Method in class com.cra.bnet.engine.StateAdapter
 
stateNames() - Method in class com.cra.bnet.engine.GeneratedEngineBase
 
stateRemoved(StateEvent) - Method in interface com.cra.bnet.engine.StateListener
Invoked when a state has been removed from the node.
stateRemoved(StateEvent) - Method in class com.cra.bnet.engine.StateAdapter
 
stateReordered(StateEvent) - Method in interface com.cra.bnet.engine.StateListener
Invoked when one of the node's states has been reordered.
stateReordered(StateEvent) - Method in class com.cra.bnet.engine.StateAdapter
 
stop() - Method in class com.cra.bnet.engine.BeliefAlert
Stops this alert from firing any more belief events.
stop(boolean) - Method in class com.cra.bnet.learn.EmEtaLearningAlgorithm
Requests this learning algorithm to stop execution.
StructuralModificationSupport - class com.cra.bnet.engine.StructuralModificationSupport.
A utility class used for detecting structural modifications to a Bayesian network.
StructuralModificationSupport(BayesianNetwork) - Constructor for class com.cra.bnet.engine.StructuralModificationSupport
Creates a new StructuralModificationSupport that listens for structural modifcations to the specified Bayesian network.
StructuralModificationSupport(BayesianNetwork, ChangeListener) - Constructor for class com.cra.bnet.engine.StructuralModificationSupport
Creates a new StructuralModificationSupport that listens for structural modifcations to the specified Bayesian network and registers the specified change listener.
substring(int) - Method in class com.cra.bnet.io.BufferedRegExpReader
Throws an UnsupportedOperationException since this class doesn't support the substring(int) method.
substring(int, int) - Method in class com.cra.bnet.io.BufferedRegExpReader
Returns the substring between the two specified indices.

T

table - Variable in class com.cra.bnet.engine.Potential
 
ThresholdBeliefCondition - class com.cra.bnet.engine.ThresholdBeliefCondition.
A condition of the form belief for node=state operator threshold.
ThresholdBeliefCondition.ComparisonOperator - class com.cra.bnet.engine.ThresholdBeliefCondition.ComparisonOperator.
An operator that compares two numbers.
ThresholdBeliefCondition(DiscreteNode, String, ThresholdBeliefCondition.ComparisonOperator, double) - Constructor for class com.cra.bnet.engine.ThresholdBeliefCondition
Creates a new ThresholdBeliefCondition using the specified node, state, threshold, and comparison operator.
toArray() - Method in class com.cra.bnet.engine.Potential
Returns the values of this potential in an array.
toDecimal(int[]) - Method in class com.cra.bnet.engine.VbnConverter
 
TopologyAdapter - class com.cra.bnet.engine.TopologyAdapter.
An abstract adapter class for receiving topology events.
TopologyAdapter() - Constructor for class com.cra.bnet.engine.TopologyAdapter
 
TopologyEvent - class com.cra.bnet.engine.TopologyEvent.
A topology-related event for a Bayesian network.
TopologyEvent(BayesianNetwork, TopologyEvent.TopologyEventType, Edge) - Constructor for class com.cra.bnet.engine.TopologyEvent
Creates a new edge-related TopologyEvent.
TopologyEvent(BayesianNetwork, TopologyEvent.TopologyEventType, Node) - Constructor for class com.cra.bnet.engine.TopologyEvent
Creates a new node-related TopologyEvent.
TopologyListener - interface com.cra.bnet.engine.TopologyListener.
A listener for receiving events when the topology of a Bayesian network changes.
toString() - Method in class com.cra.bnet.engine.TopologyEvent
Returns a string representation of this topology event.
toString() - Method in class com.cra.bnet.engine.ThresholdBeliefCondition.ComparisonOperator
Returns a string representation of this comparison operator.
toString() - Method in class com.cra.bnet.engine.StateEvent
Returns a string representation of this state event.
toString() - Method in class com.cra.bnet.engine.StateEvent.StateEventType
Returns a string representation of this state event type.
toString() - Method in class com.cra.bnet.engine.NodeEvent
Returns a string representation of this node event.
toString() - Method in class com.cra.bnet.engine.Node
Returns a string representation of this node.
toString() - Method in class com.cra.bnet.engine.MultiplyNode
Returns a string representation of this node.
toString() - Method in class com.cra.bnet.engine.EvidenceNode
Returns a string representation of this node.
toString() - Method in class com.cra.bnet.engine.EvidenceEvent
Returns a string representation of this evidence event.
toString() - Method in class com.cra.bnet.engine.DiscreteNode
Returns a String representation of this discrete node.
toString() - Method in class com.cra.bnet.engine.CptEvent
Returns a string representation of this cpt event.
toString() - Method in class com.cra.bnet.engine.CptEntryNode
Returns a string representation of this node.
toString() - Method in class com.cra.bnet.engine.Cpt
Returns a String representation of this conditional probability table.
toString() - Method in class com.cra.bnet.engine.BeliefEvent
Returns a string representation of this belief event.
toString() - Method in class com.cra.bnet.engine.BayesianNetwork
Returns a string representation of this Bayesian network.
toString() - Method in class com.cra.bnet.engine.AddNode
Returns a string representation of this node.
toString() - Method in class com.cra.bnet.learn.EmEtaParameters
Returns a string representation of this parameters object.
toString() - Method in class com.cra.bnet.learn.EmEtaEvent
Returns a string representation of this EmEta event.
toString() - Method in class com.cra.bnet.learn.EmEtaEvent.EmEtaEventType
 
toString() - Method in class com.cra.bnet.learn.ComplexDataSet
 
traceIf(boolean, String) - Static method in class com.cra.bnet.debug.DebugUtils
 
traceMsg(String) - Static method in class com.cra.bnet.debug.DebugUtils
 
transferEvidence() - Method in class com.cra.bnet.engine.JunctionTreeInferenceEngine
 

U

undo() - Method in class com.cra.bnet.engine.BayesianNetwork.AddNodeEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveNodeEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.AddEdgeEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveEdgeEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.RenameNetworkEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.RenameNodeEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.ChangeNodeDescriptionEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.ReorderParentEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.AddStateEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveStateEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.ReorderStateEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.RenameStateEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.PostEvidenceEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundPostEvidenceEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.RemoveEvidenceEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.ClearEvidenceEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.ChangeLocationEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundChangeLocationEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.ChangeCptEntryEdit
 
undo() - Method in class com.cra.bnet.engine.BayesianNetwork.CompoundChangeCptEntryEdit
 
uniform(int[]) - Method in class com.cra.bnet.engine.Cpt
Sets the row specified by the parent indices to a uniform probability distribution.
uniformAll() - Method in class com.cra.bnet.engine.Cpt
Sets each row in the entire conditional probability table to uniform distributions.
UnlimitedNodesError - exception com.cra.bnet.error.UnlimitedNodesError.
An error that occurs when the maximum limit of nodes is reached in an evaluation version.
UnlimitedNodesError(BayesianNetwork) - Constructor for class com.cra.bnet.error.UnlimitedNodesError
Creates a new UnlimitedNodesError.
unread(char[]) - Method in class com.cra.bnet.io.CraPushbackReader
Pushes back an array of characters.
unread(char[], int, int) - Method in class com.cra.bnet.io.CraPushbackReader
Push back a portion of an array of characters.
unread(int) - Method in class com.cra.bnet.io.CraPushbackReader
Pushes back a single character into the pushback buffer.
unregisterFormat(BnetFormat) - Method in class com.cra.bnet.io.BnetFormatFactory
Unregisters the specified format.
UPDATE_ON_ALL_EVIDENCE_RETRACTED_PROPERTY - Static variable in class com.cra.bnet.engine.BeliefUpdater
Property that represents a change in updating on all evidence retracted.
UPDATE_ON_CPT_ENTRY_CHANGED_PROPERTY - Static variable in class com.cra.bnet.engine.BeliefUpdater
Property that represents a change in updating on a cpt entry changed.
UPDATE_ON_EDGE_ADDED_PROPERTY - Static variable in class com.cra.bnet.engine.BeliefUpdater
Property that represents a change in updating on edge added.
UPDATE_ON_EDGE_REMOVED_PROPERTY - Static variable in class com.cra.bnet.engine.BeliefUpdater
Property that represents a change in updating on edge removed.
UPDATE_ON_EVIDENCE_POSTED_PROPERTY - Static variable in class com.cra.bnet.engine.BeliefUpdater
Property that represents a change in updating on evidence posted.
UPDATE_ON_EVIDENCE_RETRACTED_PROPERTY - Static variable in class com.cra.bnet.engine.BeliefUpdater
Property that represents a change in updating on evidence retracted.
UPDATE_ON_NODE_ADDED_PROPERTY - Static variable in class com.cra.bnet.engine.BeliefUpdater
Property that represents a change in updating on node added.
UPDATE_ON_NODE_REMOVED_PROPERTY - Static variable in class com.cra.bnet.engine.BeliefUpdater
Property that represents a change in updating on node removed.
UPDATE_ON_PARENT_REORDERED_PROPERTY - Static variable in class com.cra.bnet.engine.BeliefUpdater
Property that represents a change in updating on parent reordered.
UPDATE_ON_STATE_ADDED_PROPERTY - Static variable in class com.cra.bnet.engine.BeliefUpdater
Property that represents a change in updating on state added.
UPDATE_ON_STATE_REMOVED_PROPERTY - Static variable in class com.cra.bnet.engine.BeliefUpdater
Property that represents a change in updating on state removed.
UPDATE_ON_STATE_REORDERED_PROPERTY - Static variable in class com.cra.bnet.engine.BeliefUpdater
Property that represents a change in updating on state reordered.
updateBeliefs() - Method in class com.cra.bnet.engine.BeliefUpdater
Updates all beliefs in the Bayesian network.
updateBeliefs(boolean) - Method in class com.cra.bnet.engine.BeliefUpdater
Updates all beliefs in the Bayesian network and forces belief events to be fired if the specified boolean is true.

V

valueName - Variable in class com.cra.bnet.engine.AbstractNode
 
vbn - Variable in class com.cra.bnet.engine.Potential
 
VbnConverter - class com.cra.bnet.engine.VbnConverter.
This class represents the format of a number in which each digit has an arbitrary integer base.
VbnConverter(int[]) - Constructor for class com.cra.bnet.engine.VbnConverter
Creates a new vbn format with the specified bases, and caches the orders.
VbnConverter(List) - Constructor for class com.cra.bnet.engine.VbnConverter
This is a convenience constructor that takes a list of nodes.

W

write(BayesianNetwork, File) - Static method in class com.cra.bnet.io.XbnFormat
Writes the specified Bayesian network to the specified file.
write(BayesianNetwork, File) - Static method in class com.cra.bnet.io.NeticaFormat
Writes the specified Bayesian network to the specified file.
write(BayesianNetwork, File) - Static method in class com.cra.bnet.io.HuginFormat
Writes the specified Bayesian network to the specified file.
write(BayesianNetwork, Writer) - Method in class com.cra.bnet.io.XbnFormat
Writes the specified Bayesian network to the specified writer in XBN format and returns true if the Bayesian network was written successfully.
write(BayesianNetwork, Writer) - Method in class com.cra.bnet.io.NeticaFormat
Writes the specified Bayesian network to the specified writer in Netica format and returns true if the Bayesian network was written successfully.
write(BayesianNetwork, Writer) - Method in class com.cra.bnet.io.HuginFormat
Writes the specified Bayesian network to the specified writer in Hugin format and returns true if the Bayesian network was written successfully.
write(BayesianNetwork, Writer) - Method in interface com.cra.bnet.io.BnetFormat
Writes the specified Bayesian network to the specified writer and returns true if the Bayesian network was written successfully.

X

XbnFormat - class com.cra.bnet.io.XbnFormat.
Reads and writes Bayesian networks in XBN format.
XbnFormat() - Constructor for class com.cra.bnet.io.XbnFormat
Creates a new XbnFormat.

A B C D E F G H I J L M N O P Q R S T U V W X