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

A

abrev() - Method in class Dtree.Create
 
abrev() - Method in class DtreeCreateEO
 
abrev() - Method in class DtreeCreateHMetis
 
abrev() - Method in class DtreeCreateHMetis1
 
abrev() - Method in class DtreeCreateHMetis1wn
 
abrev() - Method in class DtreeCreateJT
 
abrev() - Method in class DtreeCreateString
 
abrev() - Method in class DgraphCreateHMetis
 
abrev() - Method in class DgraphCreateHMetis1
 
abrev() - Method in class DgraphCreateHMetis1wn
 
ABSOLUTE_CHANGE - Static variable in class SensitivitySuggestionComparator
 
AbstractCodeGenius - Class in edu.ucla.util.code
 
AbstractCodeGenius() - Constructor for class AbstractCodeGenius
 
AbstractCodeOption - Class in edu.ucla.util.code
 
AbstractCodeOption() - Constructor for class AbstractCodeOption
 
AbstractCopier - Class in edu.ucla.belief.io
Abstract implementation of Copier with a default implementation of copyVariable().
AbstractCopier() - Constructor for class AbstractCopier
 
AbstractDirectedGraph - Class in edu.ucla.structure
Convenience class for implementing DirectedGraph.
AbstractDirectedGraph() - Constructor for class AbstractDirectedGraph
 
AbstractEliminationTreeGenerator - Class in edu.ucla.belief.tree
 
AbstractEliminationTreeGenerator(TableIndex[], List) - Constructor for class AbstractEliminationTreeGenerator
 
AbstractEnumProperty - Class in edu.ucla.util
 
AbstractEnumProperty() - Constructor for class AbstractEnumProperty
 
AbstractHuginAlgorithm - Class in il2.inf.jointree
 
AbstractHuginAlgorithm(EliminationOrders.JT, Table[]) - Constructor for class AbstractHuginAlgorithm
 
AbstractInferenceEngine - Class in edu.ucla.belief
 
AbstractInferenceEngine(Dynamator) - Constructor for class AbstractInferenceEngine
 
AbstractSaxHandler - Class in edu.ucla.belief.io
 
AbstractSaxHandler() - Constructor for class AbstractSaxHandler
 
AbstractScriptGenius - Class in edu.ucla.util.code
 
AbstractScriptGenius() - Constructor for class AbstractScriptGenius
 
AbstractSSAlgorithm - Class in il2.inf.jointree
 
AbstractSSAlgorithm(EliminationOrders.JT, Table[]) - Constructor for class AbstractSSAlgorithm
 
AbstractStringifier - Class in edu.ucla.util
 
AbstractStringifier() - Constructor for class AbstractStringifier
 
AbstractStringifier.DateFormatFilename - Class in edu.ucla.util
copied from sensitivity.TestCompleteness
AbstractZCAlgorithm - Class in il2.inf.jointree
 
AbstractZCAlgorithm(EliminationOrders.JT, Table[]) - Constructor for class AbstractZCAlgorithm
 
accept(File) - Method in class InflibFileFilter
 
accept(Object) - Method in interface Filter
 
accumulate(Stats.Stat) - Method in class Stats.Stat
 
aceMode - Static variable in class UaiMain
 
acStats() - Method in class JoinTreeAlgorithm
Counts the nodes and edges of the AC that is encoded by the jointree.
activeVars() - Method in class Binner
 
activeVars() - Method in class DynamicEliminator
 
actualMemoryAllocated() - Method in class RC2NodeInternal
 
add(Macros.Recoverable...) - Method in class Macros.RecoveryInfo
 
add(Object) - Method in class BeliefNetworkImpl
 
add(String) - Method in class EOGenerator.RC
 
add(Map) - Method in class LearningData
 
add(Map) - Method in class LearningDataOld
Adds an evidence record to the list.
add(RCGenerator.RC.RCLine) - Method in class RCGenerator.RC
 
add(Table) - Method in class Table
Could return a Table or TableScaled.
add(Object) - Method in class AbstractDirectedGraph
 
add(Object) - Method in interface Graph
Adds vertex to the graph(Optional operation).
add(Object) - Method in class HashGraph
Adds vertex to the graph(Optional operation).
add(int, Object) - Method in class MappedList
Not supported.
add(Object) - Method in class MappedList
Appends the specified element to the end of this list.
add(double[], double[]) - Static method in class DblArrays
 
add(LinearFunction) - Method in class LinearFunction
 
add(Object) - Method in class WeakLinkedList
Appends the specified element to the end of this list.
add(int, Object) - Method in class WeakLinkedList
Inserts the specified element at the specified position in this list.
add(SubDomain) - Method in class Binner
 
add(IntSet) - Method in class ConnectivityOrderer
 
add(SubDomain) - Method in class DynamicEliminator
 
add(int, double) - Method in class IntPriorityQueue
Inserts the given element into the queue.
add(IntSet) - Method in interface Orderer
 
add(double) - Method in class DoubleList
 
add(int) - Method in class Graph
 
add(int) - Method in class IntList
 
add(int) - Method in class IntSet
 
add(Object, Object) - Method in class MappedHeap
 
add(Instantiation) - Method in class MPE
 
addAll(Collection) - Method in class BeliefNetworkImpl
 
addAll(Collection) - Method in class AbstractDirectedGraph
 
addAll(Collection) - Method in class HashGraph
 
addAll(Collection) - Method in class MappedList
Appends all of the elements in the specified collection to the end of this list, in the order that they are returned by the specified collection's iterator.
addAll(int, Collection) - Method in class MappedList
Not supported.
addAll(Collection) - Method in class WeakLinkedList
Appends all of the elements in the specified collection to the end of this list, in the order that they are returned by the specified collection's iterator.
addAll(int, Collection) - Method in class WeakLinkedList
Inserts all of the elements in the specified collection into this list, starting at the specified position.
addAll(Collection) - Method in class Binner
 
addAll(Collection) - Method in class ConnectivityOrderer
 
addAll(Collection) - Method in class DynamicEliminator
 
addAll(Collection) - Method in interface Orderer
 
addAll(double[]) - Method in class DoubleList
 
addAll(int[]) - Method in class IntList
 
addAll(MPE) - Method in class MPE
 
addAllNodes(RC2Node, Collection) - Static method in class RC2Utils
Add rt and all descendants to ret (stops descending when any node is already in ret.
addAuditor(BeliefNetwork.Auditor) - Method in interface BeliefNetwork
 
addAuditor(BeliefNetwork.Auditor) - Method in class BeliefNetworkImpl
 
addChangeListener(ChangeListener) - Method in class BeliefPropagationSettings
interface ChangeBroadcaster
addChangeListener(ChangeListener) - Method in class JoinTreeSettings
interface ChangeBroadcaster
addChangeListener(ChangeListener) - Method in class RCSettings
interface ChangeBroadcaster
addChangeListener(ChangeListener) - Method in class Settings
interface ChangeBroadcaster
addChangeListener(ChangeListener) - Method in interface ChangeBroadcaster
 
addChangeListener(ChangeListener) - Method in class AbstractCodeGenius
interface ChangeBroadcaster
addChangeListener(ChangeListener) - Method in class SettingsImpl
interface ChangeBroadcaster
addChild(NeticaObject) - Method in class NeticaObject
 
addChildOfLastNode(Object) - Method in interface Tree
 
addChildOfRootNode(Object) - Method in interface Tree
 
addChildSubmodel(DSLSubmodel) - Method in class DSLSubmodel
 
addCond(EOGenerator.Vertex) - Method in class EOGenerator.EO
 
addConstant(double, FiniteVariable) - Method in class Pedigree.GeneticNetwork
 
addConstant(Pedigree.NumberedConstant, FiniteVariable) - Method in class Pedigree.GeneticNetwork
 
addDataPoint(double) - Method in class DataSetStatistic
 
addDecorator(Dynamator.Decorator) - Method in class Dynamator
 
addDeepVariables(Collection, DSLSubmodel) - Method in interface GenieNet
Recusively traverse submodel tree rooted at forModel and add all variables to ret.
addDeepVariables(Collection, DSLSubmodel) - Method in class GenieNetImpl
Recusively traverse submodel tree rooted at forModel and add all variables to ret.
addDefinition(NeticaObject) - Method in class NeticaObject
 
addDim(int) - Method in class Domain
 
addDim(String, int) - Method in class Domain
 
addDim(String, List) - Method in class Domain
 
addDim(String, String[]) - Method in class Domain
 
addEdge(Variable, Variable, boolean) - Method in interface BeliefNetwork
Adds an edge to the belief network.
addEdge(Object, Object) - Method in class BeliefNetworkImpl
 
addEdge(Variable, Variable, boolean) - Method in class BeliefNetworkImpl
Adds an edge to the belief network.
addEdge(Object, Object) - Method in class AbstractDirectedGraph
 
addEdge(Object, Object) - Method in interface DirectedGraph
Adds the directed edge to the graph(Optional operation).
addEdge(Object, Object) - Method in interface Graph
Adds edge to the graph(Optional operation).
addEdge(Object, Object) - Method in class HashDirectedGraph
Adds the directed edge to the graph(Optional operation).
addEdge(Object, Object) - Method in class HashGraph
Adds edge to the graph(Optional operation).
addEdge(int, int) - Method in class Graph
 
addElim(EOGenerator.Vertex) - Method in class EOGenerator.EO
 
addElim(Object, int, double) - Method in class EOGenerator.EO
 
addEntry(String, Object) - Method in class NeticaObject
 
addEvidence(FiniteVariable, Object) - Method in class JointWrapper
 
addEvidenceChangeListener(EvidenceChangeListener) - Method in class EvidenceController
 
addFirst(Object) - Method in class WeakLinkedList
Inserts the given element at the beginning of this list.
addHistory(DecisionLeaf) - Method in class DecisionTreeImpl
 
addHistory(DecisionInternal) - Method in class DecisionTreeImpl
 
addInto(Table) - Method in class Table
 
addIntoTrivial(Table) - Method in class Table
 
addIntoTrivialScale(Table, double) - Method in class Table
 
addIterationListener(EvidenceChangeListener) - Method in class EdgeDeletionInferenceEngine
 
ADDITION - Static variable in interface ArithmeticExpression
 
ADDITION - Static variable in class EliminationTree
 
addLast(Object) - Method in class WeakLinkedList
Appends the given element to the end of this list.
addListener(DecisionListener) - Method in interface DecisionNode
 
addListener(DecisionListener) - Method in class DecisionNodeAbstract
 
addListener(DecisionListener) - Method in interface DecisionTree
 
addListener(DecisionListener) - Method in class DecisionTreeImpl
interface DecisionTree
addNew() - Method in class Graph
 
addNewDtreeListener(ChangeListener) - Method in class Settings
 
addPriorityEvidenceChangeListener(EvidenceChangeListener) - Method in class EvidenceController
 
addValue(String) - Method in class CPTImportColumnInfo
 
addVariable(Variable, boolean) - Method in interface BeliefNetwork
Adds a new node to the graph, with no parents.
addVariable(Variable, boolean) - Method in class BeliefNetworkImpl
Adds a new node to the graph, with no parents.
addVariable(Variable, boolean) - Method in class GenieNetImpl
 
addVertex(Object) - Method in class BeliefNetworkImpl
 
addVertex(Object) - Method in class AbstractDirectedGraph
 
addVertex(Object) - Method in interface DirectedGraph
Adds vertex to the graph(Optional operation).
addVertex(Object) - Method in class HashDirectedGraph
Adds vertex to the graph(Optional operation).
adjustBeginLineColumn(int, int) - Method in class SimpleCharStream
Method to adjust line and column numbers for the start of a token.
adopt(DecisionNode) - Method in class DecisionTreeImpl
interface Factory
adopt(DecisionNode) - Method in interface Factory
 
adoptChange() - Method in interface SensitivitySuggestion
 
adoptChange() - Method in class SingleCPTSuggestion
 
adoptChange() - Method in class SingleParamSuggestion
 
adoptChange(CPTParameter, double, ProbabilityInterval) - Method in class SingleParamSuggestion
 
adoptChange(double) - Method in class SingleParamSuggestion
 
agrees - Variable in class CPTInfo.Parameter
 
ALGO_HMETIS_STANDARD - Static variable in class MethodHmetis
 
ALGO_HMETIS_WEIGHTED - Static variable in class MethodHmetis
 
algorithm() - Method in enum CrouchingTiger.DynamatorImpl
 
Algorithm - Enum in il2.inf
Semantically, each "Algorithm" constant represents a distinctive implementation of an inference algorithm.
Algorithm.EliminationOrderHeuristic - Enum in il2.inf
elimination order heuristic
Algorithm.Key - Enum in il2.inf
keys to identify properties of Settings
Algorithm.Order2JoinTree - Enum in il2.inf
induce a join tree from an elimination order
Algorithm.Query - Enum in il2.inf
kind of query that an inference engine might support
Algorithm.Result - Enum in il2.inf
the inference engine itself and other intermediate side-effects
Algorithm.Setting - Enum in il2.inf
control inference engine compilation
ALGORITHM_DEFAULT - Static variable in class EDAlgorithm
2008-10-30 4:33 PM PDT -- first time successfully running EDBP with RC sub-algorithm
ALGORITHM_DEFAULT - Static variable in class EDMPAlgorithm
 
ALL - Static variable in class Classifier
 
ALL - Static variable in class Pedigree
 
ALL - Variable in class ProbabilityQueryCoder.MarginalScopeOption
 
allContexts() - Method in class RC
 
allContextsMinusLeafs() - Method in class RC
 
allNegative() - Method in class Interval
 
allocateCaches(Set) - Method in class RC
 
allocateCaches(Set) - Method in class RCEngine
 
allocatedCacheEntries() - Method in class RCInfo
 
allocatedCacheEntries() - Method in class CachingScheme
 
allocateGreedily(long) - Method in class RCInfo
 
allocateGreedily(long) - Method in class CachingScheme
 
allocateMemory(RCDtree, CachingScheme.RCCreateListener) - Method in class CachingDFBnB
 
allocateMemory(RCDtree, CachingScheme.RCCreateListener, double, Map) - Method in class CachingDFBnB
 
allocateMemory(RCDgraph, CachingScheme.RCCreateListener) - Method in class CachingDFBnB
 
allocateMemory(RCDgraph, CachingScheme.RCCreateListener, double, Map) - Method in class CachingDFBnB
 
allocateMemory(RC, CachingScheme.RCCreateListener) - Method in class CachingDFBnB
 
allocateMemory(RC, CachingScheme.RCCreateListener, double, Map) - Method in class CachingDFBnB
 
allocateMemory(RC, CachingScheme.RCCreateListener) - Method in class CachingGreedy
 
allocateMemory(RC, long) - Method in class CachingGreedy
This function ignores the cache factor, and uses the integer cachesRequested as the maximum Acceptable number of caches.
allocateMemory(RC, CachingScheme.RCCreateListener) - Method in class CachingNone
 
allocateMemory(RC, CachingScheme.RCCreateListener) - Method in class CachingNonOptimalSize
 
allocateMemory(RCDtree, CachingScheme.RCCreateListener) - Method in class CachingScheme
Have this CachingScheme allocate the memory for the RC object.
allocateMemory(RCDgraph, CachingScheme.RCCreateListener) - Method in class CachingScheme
Have this CachingScheme allocate the memory for the RC object.
allocateMemory(RC, CachingScheme.RCCreateListener) - Method in class CachingScheme
Have this CachingScheme allocate the memory for the RC object.
allocateMemory(RC, CachingScheme.RCCreateListener) - Method in class CachingUniform
 
allocateRCDgraphInThread(RCDgraph, CachingScheme, CachingScheme.RCCreateListener, double, Map) - Static method in class RCDgraph
 
allocateRCDtreeInThread(RCDtree, CachingScheme, CachingScheme.RCCreateListener, double, Map) - Static method in class RCDtree
 
allocRCCaches() - Method in class RC
 
allocRCCaches() - Method in class RCNode
 
allocRCCaches() - Method in class RCNodeInternalBinaryCache
 
allocRCDgraphInThread(BeliefNetwork) - Method in class Settings
 
allocRCDtreeInThread(BeliefNetwork) - Method in class Settings
 
allocRCMPE3Caches() - Method in class RC
 
allocRCMPE3Caches() - Method in class RCNode
 
allocRCMPE3Caches() - Method in class RCNodeInternalBinaryCache
 
allocRCMPE4Caches() - Method in class RC
 
allocRCMPE4Caches() - Method in class RCNode
 
allocRCMPE4Caches() - Method in class RCNodeInternalBinaryCache
 
allocRCMPECaches() - Method in class RC
 
allocRCMPECaches() - Method in class RCNode
 
allocRCMPECaches() - Method in class RCNodeInternalBinaryCache
 
allowKB - Variable in class RC
 
allowKB - Variable in class RC.RCCreationParams
 
allowKBinst - Variable in class RC2.RCCreationParams
 
allowKBsat - Variable in class RC2.RCCreationParams
 
allowPartialDerivatives - Variable in class RC2.RCCreationParams
 
allPositive() - Method in class Interval
 
analyzeAncestors(DecisionNode) - Method in class Stats
 
analyzeDescendants(DecisionNode) - Method in class Stats
 
AND - Variable in class CSITypeProperty
 
AND_LIT - Static variable in interface HuginLogReaderConstants
 
anonymousCount - Variable in class XmlbifParser.Variable
 
append(Appendable) - Method in class Macros.Recoverable
 
append(BeliefNetwork, Appendable) - Method in class Macros.Recoverable
 
append(StringBuffer, VariableStringifier) - Method in class CPTParameter
 
append(StringBuffer) - Method in class Stats.Stat
 
append(EOGenerator.EO) - Method in class EOGenerator.EO
 
append(StringBuffer, VariableStringifier, NumberFormat) - Method in class SingleParamSuggestion
 
append(StringBuffer, NumberFormat) - Method in class Interval
 
appendAdd(int) - Method in class IntSet
 
appendExtension(File) - Method in class FileType
 
appendFull(StringBuffer) - Method in class Stats.Stat
 
appendHint(SoftwareEntity) - Method in class SoftwareEntity
 
appendLog(Appendable, char) - Method in class EdgeDeletionInferenceEngine
 
apply(Object) - Method in interface Function
 
apply(int[], int[]) - Static method in class IntArrays
returns an array which is basically values[inds].
apply(int[], int[], int[]) - Static method in class IntArrays
 
applyLogOddsChange(double, double) - Static method in class Prob
 
ApproxCut - Class in edu.ucla.belief.approx
 
ApproxCut(FiniteVariable[], FiniteVariable[], double[][], CPTShell[], double, double, double) - Constructor for class ApproxCut
 
ApproxEngine - Class in edu.ucla.belief.approx
 
ApproxEngine(BeliefNetwork, InferenceEngine) - Constructor for class ApproxEngine
 
ApproxEngine(BeliefNetwork, InferenceEngine, PrintWriter) - Constructor for class ApproxEngine
 
ApproxEngineGenerator<E extends Enum<E> & Setting> - Class in edu.ucla.belief.approx
 
ApproxEngineGenerator() - Constructor for class ApproxEngineGenerator
 
ApproxEngineGenerator.Properties - Class in edu.ucla.belief.approx
 
ApproxEngineGenerator.Properties() - Constructor for class ApproxEngineGenerator.Properties
 
approximateMap(BeliefNetwork, JoinTreeInferenceEngineImpl, Set, Map, SearchMethod, InitializationMethod, int) - Method in class MapRunner
 
approximateMap(BeliefNetwork, BeliefCompilation, Set, Map, SearchMethod, InitializationMethod, int) - Method in class MapRunner
 
ApproxReport - Class in edu.ucla.belief.approx
 
ApproxReport(List, List, boolean, int, double, CPTShell[], ApproxCut, Stack, Map) - Constructor for class ApproxReport
 
approxTheta(double[], double[]) - Static method in class ApproxEngine
 
args - Variable in class HuginFunction
 
arguments - Variable in class Test
 
ARITHMETIC_OPERATORS - Static variable in class SensitivityConstraint
 
ARITHMETIC_OPERATORS - Static variable in class SensitivityEngine
 
ArithmeticExpression - Interface in edu.ucla.belief.inference
 
ARRAY - Static variable in class MessagePassingScheduler
 
ARRAY - Static variable in class EliminationHeuristic
 
ARRAY - Static variable in class InitializationMethod
 
ARRAY - Static variable in class SearchMethod
 
ARRAY - Static variable in class RCComparator
 
ARRAY - Static variable in class SetOperation
 
array2array(Object) - Static method in class Macros
 
ARRAY_BALANCE_FACTOR_ITEMS - Static variable in class MethodHmetis
 
ARRAY_BALANCE_FACTORS - Static variable in class MethodHmetis
 
ARRAY_CACHE_SCHEMES - Static variable in class Settings
 
ARRAY_DTREE_STYLES - Static variable in class MethodHuginLog
 
ARRAY_DYNAMATOR_CLASSNAMES - Static variable in class Test
 
ARRAY_FLAGS - Static variable in class Test
 
ARRAY_HMETIS_ALGOS - Static variable in class MethodHmetis
 
ARRAY_ID_ALPHABET - Static variable in class ParameterImpl
 
ARRAY_POLS - Variable in class Optimizer
 
ARRAY_SAX_AVOIDABLE_PROPERTIES - Static variable in class XmlbifParser
 
ARRAY_SOFTEVIDENCE_MARGINAL - Static variable in class Macros.Bridge
 
ARRAY_TAGS_POTENTIAL - Static variable in class XmlbifParser
 
ARRAY_VALID_ROOT_ELEMENT - Static variable in class XmlbifParser
 
ARRAY_VALUES - Variable in class ModelCoder.LibraryVersionOption
 
ARRAY_VALUES - Variable in class ProbabilityQueryCoder.MarginalScopeOption
 
ARRAY_VALUES_OPTION_AMOUNT - Variable in class OptionBreadth
 
ARRAY_VERSIONS_SUPPORTED - Static variable in class XmlbifParser
 
arrayToCode(Object[], PrintStream) - Static method in class MAPCoder
 
arrayToCodePlusString(Object[], PrintStream) - Static method in class MAPCoder
 
ArrayUtils - Class in il2.util
Static utility methods acting on arrays of primitive types.
ArrayUtils() - Constructor for class ArrayUtils
 
asArray(BeliefNetwork) - Method in class Macros.Recoverable
 
asArray() - Method in class Macros.RecoveryInfo
 
asIL2Algorithm() - Method in class Dynamator
 
asJavaCode(MessagePassingScheduler) - Static method in class MessagePassingScheduler
 
asJComponent() - Method in interface Dynamator.Commitable
 
asJoinTreeIL1() - Method in class JoinTree
 
asJoinTreeIL1() - Method in class EliminationOrders.JT
 
asJoinTreeIL1() - Method in interface JTUnifier
 
asJTIL2() - Method in class JoinTree
 
asJTIL2() - Method in class EliminationOrders.JT
 
asJTIL2() - Method in interface JTUnifier
 
Assert - Class in edu.ucla.util
 
Assert() - Constructor for class Assert
 
assertLearnedPositive(int, int) - Method in interface KnowledgeBase.KnowledgeBaseListener
This is called if the KB learns about a variable from unit propagation, and was not told about this from the user.
assertLearnedPositive(int, int) - Method in interface KnowledgeBase.KnowledgeBaseListener
This is called if the KB learns about a variable from unit propagation, and was not told about this from the user.
assertLearnedPositive(int, int) - Method in class RC
 
assertNegative(int, int) - Method in class KnowledgeBase
Asserts var!=state as true.
assertNegative(int, int) - Method in class KnowledgeBaseImpl
Asserts var!=state as true.
assertPathExists(String) - Static method in class ProbabilityQueryCoder
 
assertPositive(int, int) - Method in class KnowledgeBase
Asserts var=state as true.
assertPositive(int, int) - Method in interface KnowledgeBase
Asserts var=state as true.
assertPositive(int, int) - Method in class KnowledgeBaseImpl
Asserts var=state as true.
assertUnLearnedPositive(int) - Method in interface KnowledgeBase.KnowledgeBaseListener
Called when transitioning from 1 possible state to two possibe states (for any variable, whether the KB learned it or was told it).
assertUnLearnedPositive(int) - Method in interface KnowledgeBase.KnowledgeBaseListener
Called when transitioning from 1 possible state to two possibe states (for any variable, whether the KB learned it or was told it).
assertUnLearnedPositive(int) - Method in class RC
 
assign(String, FiniteVariable) - Method in class CPTImport
 
ASSIGNMENT_CHANGE - Static variable in class DecisionEvent
 
ASSIGNMENTS_DECL_LIT1 - Static variable in interface HuginLogReaderConstants
 
ASSIGNMENTS_DECL_LIT2 - Static variable in interface HuginLogReaderConstants
 
ASSIGNMENTS_DELETED - Static variable in class DecisionEvent
 
ASSIGNMENTS_LIT - Static variable in interface HuginLogReaderConstants
 
assignmentsBlock(int) - Method in class HuginLogReader
 
assume(UserEnumProperty) - Method in class UserEnumProperty
 
assumeOne - Static variable in class CachingDFBnB.HeurFunct
 
asynchronous - Variable in enum EdgeDeletionInferenceEngine.Command
 
audit(BeliefNetwork, Variable, Variable, Macros.RecoveryInfo, String, String) - Static method in class Macros
 
audit(BeliefNetwork, Variable, Variable, Collection, BeliefNetwork.Auditor.Deed) - Method in class Macros.Recoverables
 
audit(BeliefNetwork, Variable, Variable, Collection, BeliefNetwork.Auditor.Deed) - Method in interface BeliefNetwork.Auditor
 
augmentedForCompilation() - Method in class MultiValuedCNF
 
AugmentForCompilation(MultiValuedCNF, BeliefNetwork, boolean) - Static method in class MultiValuedCNF
WARNING: This will add variables and adjust sizes, so it will no longer be "valid" with the BeliefNetwork passed in.
AUXILIARY - Static variable in class DiagnosisType
 
AUXILIARY - Static variable in class SMILEReader
 

B

backstroke - Variable in enum Macros.Category
 
backup(int) - Method in class SimpleCharStream
 
BALANCED - Static variable in class MethodHuginLog
 
banIncomingEdges(List, List) - Static method in class UaiEdgeCutter
 
baseline() - Method in class InstanceIterator.IterationRec
 
baselineIndex(Index) - Method in class Index
 
baselineOffsetIndex(Index) - Method in class Index
 
BasicInference - Class in il2.inf
 
BasicInference() - Constructor for class BasicInference
 
BASICOBJECT - Static variable in class AbstractStringifier
 
BatchScriptGenius - Class in edu.ucla.util.code
 
BatchScriptGenius() - Constructor for class BatchScriptGenius
 
BayesianNetwork - Class in il2.model
 
BayesianNetwork(Table[]) - Constructor for class BayesianNetwork
 
beget - Static variable in class BeliefNetwork.Auditor.Intention
 
begin(int[], int[][], int[], boolean[]) - Method in class MinfillEoe
 
beginColumn - Variable in class Token
beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.
beginLine - Variable in class Token
beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.
BeginToken() - Method in class SimpleCharStream
 
belief - Static variable in class BeliefNetwork.Auditor.Unit
 
BeliefCompilation - Class in edu.ucla.belief.inference
 
BeliefCompilation(BeliefNetwork, ArithmeticExpression, TableIndex[], Map, Map) - Constructor for class BeliefCompilation
Creates a new BeliefCompilation.
BeliefCompilation(BeliefNetwork, ArithmeticExpression, TableIndex[], Map, Map, JoinTree, Table[]) - Constructor for class BeliefCompilation
 
BeliefNetwork - Interface in edu.ucla.belief
Encapsulates information necessary to specify a belief network.
beliefNetwork() - Method in class RunReadSMILE
 
beliefNetwork() - Method in class HuginReader
 
beliefNetwork() - Method in class RunReadHugin
 
beliefNetwork() - Method in class RunReadNetwork
 
beliefNetwork() - Method in class RunReadBIF
 
beliefNetwork(File, NodeLinearTask) - Method in interface RunReadBIF.MonitorableReusableParser
 
beliefNetwork(InputStream, NodeLinearTask) - Method in interface RunReadBIF.MonitorableReusableParser
 
beliefNetwork(File, NodeLinearTask) - Method in class XmlbifParser
 
beliefNetwork(InputStream, NodeLinearTask) - Method in class XmlbifParser
 
BeliefNetwork.Auditor - Interface in edu.ucla.belief
 
BeliefNetwork.Auditor.Deed - Class in edu.ucla.belief
 
BeliefNetwork.Auditor.Intention - Class in edu.ucla.belief
 
BeliefNetwork.Auditor.Unit - Class in edu.ucla.belief
 
BeliefNetworkImpl - Class in edu.ucla.belief
Encapsulates information necessary to specify a belief network.
BeliefNetworkImpl(boolean) - Constructor for class BeliefNetworkImpl
Creates an empty network.
BeliefNetworkImpl(BeliefNetworkImpl) - Constructor for class BeliefNetworkImpl
 
BeliefNetworkImpl() - Constructor for class BeliefNetworkImpl
 
BeliefNetworkImpl(Map) - Constructor for class BeliefNetworkImpl
Creates a BeliefNetwork by inducing the graph structure from a mapping from the Variable to its CPT.
BeliefNetworkImpl(DirectedGraph, Map) - Constructor for class BeliefNetworkImpl
Creates a belief network.
BeliefNetworkImpl(DirectedGraph) - Constructor for class BeliefNetworkImpl
 
BeliefNetworks - Class in edu.ucla.belief
Contains a collection of static methods relating to belief networks that are sometimes useful.
BeliefPropagation - Class in il2.inf.bp
some implementation notes: = we perform message-passing on the factor graph representation of a given Table[] array.
BeliefPropagation(Table[], MessagePassingScheduler, int, long, double) - Constructor for class BeliefPropagation
 
BeliefPropagation(Table[], int, long, double) - Constructor for class BeliefPropagation
 
BeliefPropagationSettings - Class in edu.ucla.belief.approx
 
BeliefPropagationSettings() - Constructor for class BeliefPropagationSettings
default IBP settings: timeout = 10 sec max iterations = 100 convergence threshold = 10e-8 use max iterations as stopping condition
BeliefPropagationSettings(long, int, double) - Constructor for class BeliefPropagationSettings
IBP settings to use max iterations as stopping condition.
BeliefPropagationSettings(long, int, double, MessagePassingScheduler) - Constructor for class BeliefPropagationSettings
 
bestCFSetting() - Method in class CachingDFBnB.CacheFactorInstance
 
bestCost() - Method in class CachingDFBnB.CacheFactorInstance
 
betheFreeEnergy() - Method in class PropagationInferenceEngineImpl
This method computes the Bethe free energy approximation to the probability of evidence.
biased(String, String, Object, Object) - Static method in class VariableComparator
 
bigDecimalLog(BigDecimal) - Static method in class UaiMain
 
BIGGEST_POSSIBLE_CLUSTER - Static variable in class Util
A constant for the largest cluster possible.
BIGINTEGER_DOUBLE_MAX_VALUE - Static variable in class Index
 
BIGINTEGER_INT_MAX_VALUE - Static variable in class Index
 
BIGINTEGER_LONG_MAX_VALUE - Static variable in class Index
 
BIGINTEGER_TWO - Static variable in class JoinTreeStats
 
bijectiveInverse(Map, Map) - Static method in class Maps
 
bijectiveInverse(Map) - Static method in class Maps
 
bijectiveInverse(List) - Static method in class Maps
 
binaryNode_MinContext - Static variable in class DecompositionStructureUtils.CreateNodeMethod
 
binaryNode_MinRCCalls - Static variable in class DecompositionStructureUtils.CreateNodeMethod
 
binaryNode_Random - Static variable in class DecompositionStructureUtils.CreateNodeMethod
 
binarySearch(int, int[], int, int) - Static method in class IntArrays
searches for value in a sorted array between minloc and maxloc inclusive.
Binner - Class in il2.inf.structure
 
Binner(Domain) - Constructor for class Binner
 
blankOutComments(StringBuilder) - Static method in class XmlbifParser
 
blockSize(int) - Method in class TableIndex
Returns the change in index of incrementing the value of the ith dimension by 1 while holding all others constant.
blockSize(FiniteVariable) - Method in class TableIndex
Returns the change in index of incrementing the value of the dimension corresponding to var by 1 while holding all others constant.
blockSizeOfVar(int) - Method in class RC2Index
 
blockSizes - Variable in class InstanceIterator.IterationRec
 
bn - Variable in class Macros.RankingArgs
 
bn - Variable in class Pedigree.GeneticNetwork
 
bn - Variable in class RC2.RCCreationParams
 
bn - Variable in class RC.RCCreationParams
 
bn - Variable in class UaiMain
 
bn - Variable in class Test
 
bnbMode - Static variable in class UaiMain
 
bogusMinFill(BeliefNetwork) - Static method in class EliminationOrders
 
BooleanArrays - Class in edu.ucla.util
 
BooleanArrays() - Constructor for class BooleanArrays
 
booleanValue(CodeOptionValue) - Method in class OptionBreadth
 
BOTH - Variable in class ModelCoder.LibraryVersionOption
 
boundedConstrainedMinFill(Collection, IntSet, double) - Static method in class EliminationOrders
 
BoundedConstrainedOrderGenerator - Class in il2.inf.structure
 
BoundedConstrainedOrderGenerator(Graph, Domain, IntSet, double) - Constructor for class BoundedConstrainedOrderGenerator
 
BourneScriptGenius - Class in edu.ucla.util.code
 
BourneScriptGenius() - Constructor for class BourneScriptGenius
 
breadth() - Method in class AbstractCodeGenius
 
breadth() - Method in interface CodeGenius
 
bridge() - Method in class EdgeDeletionInferenceEngine
 
bridge - Variable in class Macros.RankingArgs
 
bridge() - Method in class RecoveryInferenceEngine
 
broadens(FileType) - Method in class FileType
a.k.a.: generalizes()
BucketEliminator - Class in edu.ucla.util
 
BucketEliminator() - Constructor for class BucketEliminator
Creates new BucketEliminator
BucketEliminator(List, Collection, boolean) - Constructor for class BucketEliminator
 
Bucketer - Class in il2.inf.structure
 
Bucketer(IntList) - Constructor for class Bucketer
 
bucketerJoinTree(Collection, IntList) - Static method in class EliminationOrders
This method is an alternative to traditionalJoinTree.
bucketIndex(int) - Method in class Bucketer
 
bucketLabel(int) - Method in class Bucketer
 
buckets - Variable in class UaiEdgeCutter.MyRecord
 
BUFFER - Static variable in class NetworkIO
 
bufpos - Variable in class SimpleCharStream
 
Builder - Class in edu.ucla.belief.decision
 
Builder(BeliefNetwork, Attributes) - Constructor for class Builder
 
Bundle - Class in edu.ucla.belief.recursiveconditioning
 
Bundle() - Constructor for class Bundle
 
BY_PARAMETER - Static variable in class ExcludePolicy
 
BY_VARIABLE - Static variable in class ExcludePolicy
 

C

c01 - Static variable in class CachingDFBnB.ChildExpansion
 
c10 - Static variable in class CachingDFBnB.ChildExpansion
 
cache() - Method in class RCNode
 
CACHE_SCHEME_DFBnB - Static variable in class Settings
 
CACHE_SCHEME_UNIFORM - Static variable in class Settings
 
cachedNodes() - Method in class RCInfo
 
cachedNodes() - Method in class CachingScheme
 
cacheEntriesFullCaching() - Method in class RCInfo
 
cacheEntriesFullCaching() - Method in class CachingScheme
 
CachingDFBnB - Class in edu.ucla.belief.recursiveconditioning
 
CachingDFBnB() - Constructor for class CachingDFBnB
 
CachingDFBnB(double) - Constructor for class CachingDFBnB
 
CachingDFBnB.CacheFactorInstance - Class in edu.ucla.belief.recursiveconditioning
 
CachingDFBnB.CacheFactorInstance(double, BigInteger) - Constructor for class CachingDFBnB.CacheFactorInstance
 
CachingDFBnB.CacheFactorInstance() - Constructor for class CachingDFBnB.CacheFactorInstance
 
CachingDFBnB.ChildExpansion - Class in edu.ucla.belief.recursiveconditioning
 
CachingDFBnB.DFBnB_TmpVars - Class in edu.ucla.belief.recursiveconditioning
 
CachingDFBnB.DFBnB_TmpVars(RC, CachingDFBnB.OrderingAlgo) - Constructor for class CachingDFBnB.DFBnB_TmpVars
 
CachingDFBnB.HeurFunct - Class in edu.ucla.belief.recursiveconditioning
 
CachingDFBnB.HeurResult - Class in edu.ucla.belief.recursiveconditioning
 
CachingDFBnB.HeurResult() - Constructor for class CachingDFBnB.HeurResult
 
CachingDFBnB.OrderingAlgo - Class in edu.ucla.belief.recursiveconditioning
 
CachingDFBnB.RCNodeComparator_Size - Class in edu.ucla.belief.recursiveconditioning
Not consistent with equals!
CachingDFBnB.RCNodeComparator_Size() - Constructor for class CachingDFBnB.RCNodeComparator_Size
 
CachingDFBnB.SearchGraph - Class in edu.ucla.belief.recursiveconditioning
 
CachingDFBnB.SearchGraph(RC, CachingDFBnB.OrderingAlgo) - Constructor for class CachingDFBnB.SearchGraph
 
CachingFull - Class in edu.ucla.belief.recursiveconditioning
 
CachingFull() - Constructor for class CachingFull
 
CachingGreedy - Class in edu.ucla.belief.recursiveconditioning
 
CachingGreedy() - Constructor for class CachingGreedy
 
CachingGreedy(double) - Constructor for class CachingGreedy
 
CachingNone - Class in edu.ucla.belief.recursiveconditioning
 
CachingNone() - Constructor for class CachingNone
 
CachingNonOptimalSize - Class in edu.ucla.belief.recursiveconditioning
 
CachingNonOptimalSize(boolean) - Constructor for class CachingNonOptimalSize
 
CachingNonOptimalSize() - Constructor for class CachingNonOptimalSize
 
CachingNonOptimalSize(double) - Constructor for class CachingNonOptimalSize
 
CachingNonOptimalSize.RCNodeComparator_Size - Class in edu.ucla.belief.recursiveconditioning
Not consistent with equals!
CachingNonOptimalSize.RCNodeComparator_Size() - Constructor for class CachingNonOptimalSize.RCNodeComparator_Size
 
CachingScheme - Class in edu.ucla.belief.recursiveconditioning
This abstract class creates RC objects (RCDtrees and RCDgraphs) by giving assigning the caching to the nodes.
CachingScheme(double) - Constructor for class CachingScheme
 
CachingScheme - Class in il2.inf.rc
 
CachingScheme(DGraph, boolean) - Constructor for class CachingScheme
 
CachingScheme.RCCreateListener - Interface in edu.ucla.belief.recursiveconditioning
 
CachingUniform - Class in edu.ucla.belief.recursiveconditioning
 
CachingUniform() - Constructor for class CachingUniform
 
CachingUniform(double) - Constructor for class CachingUniform
 
calcExpectedNumberOfRCCalls(RC) - Method in class Computation.All
 
calcExpectedNumberOfRCCalls(RC) - Method in class Computation
 
calcExpectedNumberOfRCCalls(RC) - Method in class Computation.Pe
 
calcFraction(int, int) - Static method in class Stats
 
calcFraction() - Method in class Stats.Stat
 
calcProductBig(Set) - Static method in class JoinTree
 
calcProductDouble(Set) - Static method in class JoinTree
 
calculateCutsetFromChildren(RC2NodeInternal, Collection) - Static method in class RC2Utils
Calculates the cutset of a variable based only on its children.
calculateCutsetFromChildren(RCNodeInternalBinaryCache, Collection) - Static method in class RCUtilities
Calculates the cutset of a variable based only on its children.
calculateStats() - Method in class RC.RCStats
 
calculateStats() - Method in class IntList
 
callsToLookAhd - Variable in class RC.RCCounters
 
callsToRCInternalCacheHit - Variable in class RC.RCCounters
 
callsToRCInternalCompute - Variable in class RC.RCCounters
 
callsToRCInternalComputeAndSave - Variable in class RC.RCCounters
 
callsToRCLeaf - Variable in class RC.RCCounters
 
cancel() - Method in class Interruptable
 
canComputeFamilyMarginals() - Method in class RC
 
canComputeFamilyMarginals() - Method in class RCDgraph
 
canonical() - Method in class AbstractInferenceEngine
 
canonical() - Method in class SynchronizedInferenceEngine
 
canonical() - Method in interface InferenceEngine
 
canonical(Object) - Static method in class LearningDataOld
 
caption - Variable in class Stats.Stat
 
CAPTION_COMPARE2EXACT() - Static method in enum EdgeDeletionBeliefPropagationSetting
 
cardinality(int) - Method in class TableIndex
 
CF_LOW_TO_HIGH - Variable in class CachingNonOptimalSize
From brief experimentation, Low_To_High=true tends to do better than false, however, sometimes false can do better.
cfi() - Method in class CachingDFBnB.DFBnB_TmpVars
 
ChangeBroadcaster - Interface in edu.ucla.util
 
changeCacheFactor(double) - Method in class RCNode
 
changeCacheFactor(double) - Method in class RCNodeInternalBinaryCache
 
changeRecomS1(double, double) - Method in class Pedigree.GeneticNetwork
Returns the set of variables which had their cpts updated.
changeRecomS2(double, double) - Method in class Pedigree.GeneticNetwork
Returns the set of variables which had their cpts updated.
CHAR_MAP_PREPOSITION - Static variable in class AbstractStringifier
 
CHAR_SEPARATOR - Static variable in class AbstractStringifier
 
CHAR_SPACE - Static variable in class AbstractStringifier
 
CHAR_TAB - Static variable in class XmlWriter
 
characters(char[], int, int) - Method in class AbstractSaxHandler
 
characters(char[], int, int) - Method in interface CharactersHandler
 
CharactersHandler - Interface in edu.ucla.belief.io
Moved from SamIam package edu.ucla.belief.ui.util since 020105
checkValidProbabilities() - Method in interface BeliefNetwork
 
checkValidProbabilities() - Method in class BeliefNetworkImpl
 
child() - Method in class DtreeNodeLeaf
 
childExpansion - Variable in class CachingDFBnB
 
childIterator() - Method in class RCNodeInternalBinaryCache
 
children() - Method in class RCNodeInternalBinaryCache
 
children(int) - Method in class EliminationTree
 
children(int) - Method in class JoinTree
 
children(Pair) - Method in class JoinTree
 
childrenArr() - Method in class RCNodeInternalBinaryCache
 
chooseBestExecutable(List) - Method in class ParanoidFileFinder
 
chooseBestJavaExecutable(String) - Method in class ParanoidFileFinder
 
chooseBestJavaExecutable(String, File) - Method in class ParanoidFileFinder
 
choosePropertySuperintendent(PropertySuperintendent) - Method in class Dynamator
 
chromoOrd(int) - Method in class Pedigree.PseudoLoci
 
chromosomeOrder - Variable in class Loci.Header
 
CLASS - Static variable in interface HuginReaderConstants
 
classBlock(Map, Collection) - Method in class HuginReader
 
classfile - Variable in class JDKRun.CompiledClassInfo
 
Classifier - Class in edu.ucla.belief.decision
 
ClassModule - Class in edu.ucla.util.code
 
ClassModule(String, String, String, String) - Constructor for class ClassModule
 
classname - Variable in class JDKRun.CompiledClassInfo
 
clausesIndex - Variable in class MultiValuedCNF
 
clazz() - Method in class ApproxEngineGenerator
 
clazz() - Method in class EdgeDeletionEngineGenerator
 
clazz - Variable in enum EdgeDeletionInferenceEngine.Attribute
 
clazz - Variable in enum Macros.Doubler
A particular Doubler is designed to convert arrays with component type assignable from this type.
clazz() - Method in class RecoveryEngineGenerator
 
clazz - Variable in enum CrouchingTiger.DynamatorImpl
 
clazz - Variable in enum PropertyKey
 
clazz() - Method in interface Setting.Settings
 
clazz() - Method in class SettingsImpl
 
clazz - Variable in enum Algorithm
engine class
clazz - Variable in enum Algorithm.Key
 
clazz - Variable in enum Flavor
the implementation class
cleanClearedReferences() - Method in class WeakLinkedList
 
cleanup() - Method in interface RunReadBIF.MonitorableReusableParser
 
cleanup() - Method in class XmlbifParser
interface RunReadBIF.MonitorableReusableParser
cleanupAbstractSaxHandler() - Method in class AbstractSaxHandler
 
clear() - Method in class BeliefNetworkImpl
 
clear() - Method in class DecisionTreeImpl
interface Collection
clear() - Method in class Stats
 
clear() - Method in class GenieNetImpl
 
clear() - Method in class XmlbifParser
 
clear() - Method in class LearningData
 
clear() - Method in class HashDirectedGraph
 
clear() - Method in class HashGraph
 
clear() - Method in class IdentityArrayMap
 
clear() - Method in class MappedList
Removes all of the elements from this list.
clear(int) - Method in class MappedList
sets the value at location i to null
clear() - Method in class CPTShells
 
clear() - Method in class DataSetStatistic
 
clear() - Method in class WeakLinkedList
Removes all of the elements from this list.
clear() - Method in class IntPriorityQueue
 
clear(int[], double[]) - Method in class IntPriorityQueue
Clears the priority queue and then adds the given elements.
clear() - Method in class PriorityQueue
Resets the priority queue.
clear() - Method in class DoubleList
 
clear() - Method in class IntList
 
clear() - Method in class IntMap
 
clear() - Method in class IntSet
 
clearEvidence(int) - Method in class JoinTreeInference
 
clearKB() - Method in class RC
 
CLIQUE_DECL_LIT1 - Static variable in interface HuginLogReaderConstants
 
CLIQUE_DECL_LIT2 - Static variable in interface HuginLogReaderConstants
 
CLIQUE_DECL_LIT3 - Static variable in interface HuginLogReaderConstants
 
CLIQUES_LIT1 - Static variable in interface HuginLogReaderConstants
 
CLIQUES_LIT2 - Static variable in interface HuginLogReaderConstants
 
cliquesBlock() - Method in class HuginLogReader
 
clone() - Method in class Macros.Recoverable
 
clone(BeliefNetwork) - Method in class Macros.Recoverable
 
clone() - Method in class Macros.Recoverables
 
clone() - Method in class Macros.RecoveryInfo
 
clone() - Method in interface BeliefNetwork
 
clone() - Method in class BeliefNetworkImpl
As of 061002, this method simply calls deepClone().
clone() - Method in class DecisionInternal
 
clone() - Method in class DecisionLeaf
 
clone(int) - Method in class DecisionLeaf
 
clone() - Method in interface DecisionNode
 
clone() - Method in class DecisionNodeAbstract
 
clone() - Method in class DecisionTreeImpl
interface DirectedGraph
clone(Parameter) - Method in class DecisionTreeImpl
interface Factory
clone(DecisionNode) - Method in class DecisionTreeImpl
interface Factory
clone(DecisionNode) - Method in interface Factory
 
clone(Parameter) - Method in interface Factory
 
clone() - Method in class DecisionShell
 
clone() - Method in class EOGenerator.EO
 
clone() - Method in class EvidenceController
 
clone() - Method in class FiniteVariableImpl
 
clone() - Method in class DSLNodeImpl
 
clone() - Method in class HuginNodeImpl
 
clone() - Method in class NoisyOrShellHenrion
 
clone() - Method in class NoisyOrShellPearl
 
clone() - Method in interface Potential
 
clone() - Method in class RCGenerator.EO
 
clone() - Method in class RCGenerator.RC
 
clone() - Method in class Table
 
clone() - Method in class TableIndex
 
clone() - Method in class TableScaled
 
clone() - Method in class TableShell
 
clone() - Method in interface Variable
 
clone() - Method in class VariableImpl
 
clone() - Method in class VariableInstance
 
clone() - Method in class AbstractDirectedGraph
interface DirectedGraph
clone() - Method in interface DirectedGraph
 
clone() - Method in class HashDirectedGraph
 
clone() - Method in class HashGraph
 
clone() - Method in class MappedList
 
clone() - Method in class WeakLinkedList
Returns a shallow copy of this WeakLinkedList.
clone(Converter, BayesianNetwork) - Method in class EliminationOrders.JT
 
cloneAdjacencyMap(Map) - Method in class HashDirectedGraph
 
cloneAllCPTShells() - Method in interface BeliefNetwork
 
cloneAllCPTShells() - Method in class BeliefNetworkImpl
 
cloneConditional(int) - Method in class EDAlgorithm
 
clones2edgeindices - Variable in class Macros.Bridge
 
cloneVarOfEdge(int) - Method in class EDNetwork
 
close(PrintStream) - Method in enum XmlbifWriter.Element
 
close(PrintStream, boolean) - Method in enum XmlbifWriter.Element
 
close() - Method in class RC2
This will clean up all resources used by RC (currently the SAT engine).
closestToZero() - Method in class Interval
 
cluster(int) - Method in class JoinTree
 
cluster(int) - Method in class JoinTree
 
cluster(Object) - Method in class JoinTree
 
cluster(int) - Method in class JoinTree
 
clusterCount() - Method in class JoinTree
 
clusters - Variable in class UaiEdgeCutter.MyRecord
 
clusters - Variable in class EliminationOrders.JT
 
clusters - Variable in class EliminationOrders.Record
 
clusters() - Method in class JoinTree
 
clusterSize(RCNode) - Static method in class RCUtilities
 
clusterStats - Variable in class EliminationOrders.JT
 
CodeGenius - Interface in edu.ucla.util.code
 
CodeOption - Interface in edu.ucla.util.code
 
CodeOptionValue - Class in edu.ucla.util.code
 
CodeOptionValue(String) - Constructor for class CodeOptionValue
 
collapse(Graph, Object, Object) - Static method in class Graphs
 
collect(int) - Method in class Messenger
Performs a collect evidence on the specified vertex.
collectionToString(Collection) - Method in class AbstractStringifier
 
collectionToString(Collection) - Method in interface Stringifier
 
collectOptimizedStats(BeliefNetwork) - Method in class Optimizer
 
collOfFinVarsToStateSpace(Collection) - Static method in class RC2Utils
Will return the state space of all the variables in the collection, and if the collection is empty it will return 1.
collOfFinVarsToStateSpace(Collection) - Static method in class RC
Will return the state space of all the variables in the collection, and if the collection is empty it will return 1.
colOfColOfFVarsToColDtreeNodes(Map, Collection) - Static method in class Dtree
Convert a Collection of Collections of FiniteVariables (Collection of Families or UndirectedEdges) to a Collection of DtreeNodes.
combine(Object[], double[][]) - Method in class LinearFunction
Old number of arguments = combinators[i].length
combine(JoinTreeStats.Stat) - Method in class JoinTreeStats.StatImpl
 
combineWith(Index) - Method in class Index
 
command(EdgeDeletionInferenceEngine.Command) - Method in class EdgeDeletionInferenceEngine
 
command(EdgeDeletionInferenceEngine.Command, boolean) - Method in class EdgeDeletionInferenceEngine
 
COMMENT - Static variable in interface HuginLogReaderConstants
 
COMMENT - Static variable in interface HuginReaderConstants
 
COMMENT - Static variable in interface NeticaReaderConstants
 
commit(boolean, boolean) - Method in class CPTInfo
 
commitChanges() - Method in interface Dynamator.Commitable
 
commitEditComponent() - Method in class ApproxEngineGenerator
 
commitEditComponent() - Method in class PropagationEngineGenerator
 
commitEditComponent() - Method in class Dynamator
 
ComparatorHeap - Class in il2.util
 
ComparatorHeap(Comparator) - Constructor for class ComparatorHeap
 
compare(Object, Object) - Method in class Dtree.DtreeComparatorHeightLowToHigh
 
compare(Object, Object) - Method in class IDComparator
 
compare(Object, Object) - Method in class LabelComparator
 
compare(Object, Object) - Method in class CachingDFBnB.RCNodeComparator_Size
 
compare(Object, Object) - Method in class CachingNonOptimalSize.RCNodeComparator_Size
 
compare(Object, Object) - Method in class SensitivitySuggestionComparator
 
compare(Object, Object) - Method in class UaiEdgeCutter.BpInstanceComparator
 
compare(Object, Object) - Method in class UaiEdgeCutter.BpVarComparator
 
compare(Object, Object) - Method in class VariableComparator
 
compare(int[], int[]) - Method in class EdgeComparator
 
compareLowerBound(Object) - Method in class Interval
 
compareTo(Object) - Method in class CPTParameter
 
compareTo(Object) - Method in class Optimizer.Unsortable
 
compareTo(Object) - Method in class LearningData.Struct
 
compareTo(Object) - Method in class RC2Node
 
compareTo(Object) - Method in class VariableImpl
 
compareTo(Object) - Method in class VariableInstance
 
compareTo(Object) - Method in class SoftwareEntity
interface Comparable
compareUpperBound(Object) - Method in class Interval
 
COMPARISON_OPERATORS - Static variable in class SensitivityConstraint
 
COMPARISON_OPERATORS - Static variable in class SensitivityEngine
 
compatibilityGraph(Collection) - Static method in class EliminationOrders
 
compilationStatus(PropertySuperintendent) - Method in class AbstractInferenceEngine
 
compilationStatus(PropertySuperintendent) - Method in class PropagationInferenceEngineImpl
 
compilationStatus(PropertySuperintendent) - Method in class RecoveryInferenceEngine
 
compilationStatus(PropertySuperintendent) - Method in class RCEngine
 
compilationStatus(PropertySuperintendent) - Method in class SynchronizedInferenceEngine
 
compilationStatus(PropertySuperintendent) - Method in interface InferenceEngine
 
compilationStatus(PropertySuperintendent) - Method in class RCInferenceEngine
 
compile(BeliefNetwork, DynaListener) - Method in class Dynamator
 
compile(BeliefNetwork, int, Random) - Static method in class JEngineGenerator
 
compile(BeliefNetwork, List) - Static method in class JEngineGenerator
 
compile(BeliefNetwork, List, QuantitativeDependencyHandler) - Static method in class JEngineGenerator
 
compile(BeliefNetwork, JoinTree, QuantitativeDependencyHandler) - Static method in class JEngineGenerator
 
compile(BeliefNetwork, List) - Static method in class S4Compiler
 
compile(BeliefNetwork, List, QuantitativeDependencyHandler) - Static method in class S4Compiler
 
compile(BeliefNetwork, JoinTree) - Static method in class S4Compiler
 
compile(BeliefNetwork, JoinTree, QuantitativeDependencyHandler) - Static method in class S4Compiler
 
compile(BayesianNetwork, Map<Algorithm.Setting, ?>) - Method in enum Algorithm
create (i.e.
compile(BayesianNetwork, EliminationOrders.JT) - Method in enum Flavor
compile a JoinTreeAlgorithm JointEngine
Compiled_MLink - Class in edu.ucla.belief.rc2.tools
 
Compiled_MLink(Compiled_MLink.CmdLn) - Constructor for class Compiled_MLink
 
compileIL1(BeliefNetwork, Map<CrouchingTiger.DynamatorImpl, Dynamator>) - Method in enum CrouchingTiger.DynamatorImpl
 
compileIL2(BeliefNetwork, Converter, Map<CrouchingTiger.DynamatorImpl, Dynamator>) - Method in enum CrouchingTiger.DynamatorImpl
 
complement(Macros.Bridge, Collection<FiniteVariable>) - Method in enum Macros.Category
 
complement(Collection, boolean) - Method in class DecisionLeaf
 
complement(SensitivityEquation, SensitivityEquation[], int) - Static method in class SensitivityEquation
 
COMPLEMENT - Static variable in class SetOperation
 
complementaryIndex(Index) - Method in class Index
 
complementaryIndex(IntSet) - Method in class Index
 
complementEdgeList(BayesianNetwork, int[][]) - Static method in class EDEdgeDeleter
Returns all BN edges not given in inputEdges
complementEdgeList(Table[], int[][]) - Static method in class EDEdgeDeleter
Returns all factor graph edges not given in inputEdges
compose(Map, Map, Map) - Static method in class Maps
 
compose(Map, Map) - Static method in class Maps
 
compose(Function, Map, Map) - Static method in class Maps
 
compose(Function, Map) - Static method in class Maps
 
CompoundTask - Class in edu.ucla.util
A task that is the serial combination of two or more subtasks.
CompoundTask(String, ProgressMonitorable[], float[]) - Constructor for class CompoundTask
 
compress() - Method in class Graph
 
compStats() - Method in class RC2
 
Computation - Class in edu.ucla.belief.recursiveconditioning
 
Computation(RC, String) - Constructor for class Computation
 
Computation.All - Class in edu.ucla.belief.recursiveconditioning
 
Computation.All(RC) - Constructor for class Computation.All
 
Computation.Pe - Class in edu.ucla.belief.recursiveconditioning
 
Computation.Pe(RC) - Constructor for class Computation.Pe
 
compute_CutMarginal(int) - Method in class RC2
If the root rt is a leaf node, it will return null.
compute_MPEValue() - Method in class RC2
Does not run with scaling enabled.
compute_ParDer(int) - Method in class RC2
 
compute_Pe() - Method in class RC2
This will return the scaled version if scaling is enabled, the caller is responsible for converting it, as that conversion could cause an underflow to occur.
compute_Pe_sat() - Method in class RC2
 
computeAlphas(PartialDerivativeEngine, FiniteVariable) - Static method in class SensitivityEquation
 
computeDownMessage(int) - Method in class ShenoyShaferAlgorithm
 
computeHashCode() - Method in class Optimizer.EquivalenceKey
 
computeLeafs(RC2Node, Collection) - Static method in class RC2Utils
Compute leaf nodes in the subtree rooted at rt (will include rt if it is a leaf node).
computeLeafs(RCNode, Collection) - Static method in class RCUtilities
Compute leaf nodes in the subtree rooted at rt (will include rt if it is a leaf node).
computeMap(BeliefNetwork, Set, Map, double) - Static method in class ExactMap
 
computeMap(BeliefNetwork, Set, Map, double, int) - Static method in class ExactMap
 
computeMap(BeliefNetwork, Set, Map, double, int, List) - Static method in class ExactMap
 
computeMap(Random, BeliefNetwork, Map<FiniteVariable, Object>, Set<FiniteVariable>) - Method in interface UaiMapEngine
Computes MAP for the given network, evidence, and map variables.
computeMAP(Collection, IntSet, IntList, double, double, double) - Static method in class MapSearch
Runs the map search algorithm and returns a list of MapResults, each describing an instantiation of the map variables, sorted from max probability to min probability.
computeMAP(Collection, IntSet, IntList, double, double) - Static method in class MapSearch
 
computeMapSloppy(BeliefNetwork, Set, Map, double, int, double) - Static method in class ExactMap
 
computeMapSloppy(BeliefNetwork, Set, Map, double, int, double, List) - Static method in class ExactMap
 
computeMessageSpecial(Table[]) - Method in class MaxProductLinearSmoothness
 
computeMpe(Random, BeliefNetwork, Map<FiniteVariable, Object>, UaiPreprocessResult) - Method in class TestMpeEngine
Computes MAP for the given network, evidence, and map variables.
computeMpe(Random, BeliefNetwork, Map<FiniteVariable, Object>, UaiPreprocessResult) - Method in interface UaiMpeEngine
Computes MPE for the given network and evidence.
computeNoisyOr(double[], int) - Method in class NoisyOrShellHenrion
 
computeNoisyOr(int, int, int, int[], int[][]) - Method in class NoisyOrShellPearl
 
computeParentsInTree(RC2Node, Map) - Static method in class RC2Utils
When finished, ret will include a mapping from all nodes to their parents in the subtree rooted at rt.
computeParentsInTree(RCNode, Map) - Static method in class RCUtilities
When finished, ret will include a mapping from all nodes to their parents in the subtree rooted at rt.
computePe(Random, BeliefNetwork, Map<FiniteVariable, Object>, UaiPreprocessResult) - Method in class RC_Link_UAI2006
 
computePe(Random, BeliefNetwork, Map<FiniteVariable, Object>, UaiPreprocessResult) - Method in class RC_Link2PeEngine
Computes MAP for the given network, evidence, and map variables.
computePe(Random, BeliefNetwork, Map<FiniteVariable, Object>, UaiPreprocessResult) - Method in class TestPeEngine
Computes MAP for the given network, evidence, and map variables.
computePe(Random, BeliefNetwork, Map<FiniteVariable, Object>, UaiPreprocessResult) - Method in interface UaiPeEngine
Computes P(e) for the given network and evidence.
computePeKB(BeliefNetwork, Map<FiniteVariable, Object>) - Method in class RC_Link_UAI2006
 
computePeNonGenetic(BeliefNetwork, Map<FiniteVariable, Object>, int) - Method in class RC_Link_UAI2006
 
computeQuery() - Method in class UaiMain
 
computeQuery() - Method in class UaiMpeMain
 
computeQuery() - Method in class UaiPeMain
 
computeResult() - Method in class RunReadNetwork
 
computeSize(Collection, IntList) - Static method in class EliminationOrders
 
computeStatsDtree(RC2) - Static method in class RC2Utils
 
computeSuggestedValues(double) - Method in class SingleParamSuggestion
 
computeUpMessage(int) - Method in class ShenoyShaferAlgorithm
 
condition(boolean) - Static method in class Assert
 
condition(boolean, String) - Static method in class Assert
 
conditional(FiniteVariable) - Method in class EdgeDeletionInferenceEngine
 
conditional(FiniteVariable) - Method in class PropagationInferenceEngineImpl
 
conditional(FiniteVariable) - Method in class RecoveryInferenceEngine
 
conditional(FiniteVariable) - Method in class JoinTreeInferenceEngineImpl
Returns P(var | observations).
conditional(FiniteVariable) - Method in class RandomInferenceEngine
 
conditional(FiniteVariable) - Method in class SynchronizedInferenceEngine
 
conditional(FiniteVariable) - Method in class WrapperInferenceEngine
Returns P(var | observations).
conditional(FiniteVariable) - Method in interface InferenceEngine
Returns P(var | observations).
conditional(FiniteVariable) - Method in class RCInferenceEngine
Returns P(var | observations).
conditionalize(Index) - Method in class Table
 
conditionals(FiniteVariable, Table[]) - Method in class AbstractInferenceEngine
In case this InferenceEngine wants to report two sets of answers, for example, approximate and exact.
conditionals(FiniteVariable, Table[]) - Method in class EdgeDeletionInferenceEngine
In case this InferenceEngine wants to report two sets of answers, for example, approximate and exact.
conditionals(FiniteVariable, Table[]) - Method in class RecoveryInferenceEngine
 
conditionals(FiniteVariable, Table[]) - Method in class SynchronizedInferenceEngine
 
conditionals(FiniteVariable, Table[]) - Method in interface InferenceEngine
In case this InferenceEngine wants to report two sets of answers, for example, approximate and exact.
conditioned - Variable in class HuginPotential
 
condVar(FiniteVariable, int, double, int) - Method in class RCGenerator.EO
 
configureFactory(SAXParserFactory) - Method in class AbstractSaxHandler
override this method if, e.g., you need to install an xml validation schema
configureFactory(SAXParserFactory) - Method in class UAI06Parser
 
configureFactory(SAXParserFactory) - Method in class XmlbifParser
 
confirmUnitResolutionKB(RC2, BeliefNetwork) - Static method in class RC2Utils
If there is anything that is wrong, this will throw an IllegalStateException.
confirmUnitResolutionRSAT(RC2, BeliefNetwork) - Static method in class RC2Utils
If there is anything that is wrong, this will throw an IllegalStateException.
conflicts - Variable in class CPTInfo.Parameter
 
ConnectivityOrderer - Class in il2.inf.structure
 
ConnectivityOrderer(int) - Constructor for class ConnectivityOrderer
 
consistent(Instantiation) - Method in class Instantiation
 
constantMPETable(Domain, double) - Static method in class MPETable
 
constantScaled() - Method in class Pedigree.GeneticNetwork
 
constantTable(Domain, double) - Static method in class Table
 
constrainedMinFill(Collection, IntSet) - Static method in class EliminationOrders
 
ConstrainedMinFillOrderGenerator - Class in il2.inf.structure
 
ConstrainedMinFillOrderGenerator(Graph, Domain, IntSet) - Constructor for class ConstrainedMinFillOrderGenerator
 
constrainedMinSize(Collection, IntSet) - Static method in class EliminationOrders
 
ConstrainedMinSizeOrderGenerator - Class in il2.inf.structure
 
ConstrainedMinSizeOrderGenerator(Graph, Domain, IntSet) - Constructor for class ConstrainedMinSizeOrderGenerator
 
constructOrder(int) - Method in class TreeSchedule
 
contains(Object) - Method in class BeliefNetworkImpl
 
contains(Object) - Method in class DecisionTreeImpl
interface DirectedGraph
contains(Object) - Method in interface FiniteVariable
 
contains(Object) - Method in class FiniteVariableImpl
 
contains(Object) - Method in class MultiValuedCNF
 
contains(Object) - Method in interface DirectedGraph
Returns whether or not a particular Object is a vertex in the graph.
contains(Object) - Method in interface Graph
Returns whether or not a particular Object is a vertex in the graph.
contains(Object) - Method in class HashDirectedGraph
Returns whether or not a particular Object is a vertex in the graph.
contains(Object) - Method in class HashGraph
Returns whether or not a particular Object is a vertex in the graph.
contains(Object) - Method in class MappedList
Returns true if this list contains the specified element.
contains(EnumValue) - Method in class CSITypeProperty
 
contains(EnumValue) - Method in interface EnumProperty
 
contains(EnumValue) - Method in class FlagProperty
 
contains(EnumValue) - Method in class InOutDegreeProperty
 
contains(double) - Method in class Interval
 
contains(EnumValue) - Method in class UserEnumProperty
 
contains(Object) - Method in class WeakLinkedList
Returns true if this list contains the specified element.
contains(int) - Method in class IntPriorityQueue
Returns whether the queue contains the given element.
contains(int) - Method in class Graph
 
contains(int) - Method in class IntSet
 
contains(IntSet, int[]) - Method in class MPE
 
containsAll(Collection) - Method in class BeliefNetworkImpl
 
containsAll(Collection) - Method in class AbstractDirectedGraph
 
containsAll(Collection) - Method in class HashGraph
 
containsAll(Collection) - Method in class MappedList
Returns true if this list contains all of the elements of the specified collection.
containsAll(IntSet) - Method in class IntSet
 
containsBannedEdges(List, List, List) - Static method in class UaiEdgeCutter
 
containsEdge(Object, Object) - Method in class BeliefNetworkImpl
 
containsEdge(Object, Object) - Method in class AbstractDirectedGraph
 
containsEdge(Object, Object) - Method in interface DirectedGraph
Returns whether or not a particular edge is in the graph.
containsEdge(Object, Object) - Method in interface Graph
Returns whether or not a particular edge is in the graph.
containsEdge(Edge) - Method in interface Graph
 
containsEdge(Object, Object) - Method in class HashDirectedGraph
Returns whether or not a particular edge is in the graph.
containsEdge(Object, Object) - Method in class HashGraph
Returns whether or not a particular edge is in the graph.
containsEdge(Edge) - Method in class HashGraph
 
containsEdge(int, int) - Method in class Graph
 
containsKey(Object) - Method in class LearningData
 
containsKey(Object) - Method in class IdentityArrayMap
 
containsSameVars(Collection) - Method in class RC2Index
 
containsValue(Object) - Method in class LearningData
 
containsValue(Object) - Method in class IdentityArrayMap
 
containsVar(Object) - Method in class DtreeNode
 
containsVarAsChild(Index, int, List) - Static method in class UaiEdgeCutter
 
containsVarAsChild(List, int, List) - Static method in class UaiEdgeCutter
 
containsVarAsChild(int, List) - Method in class UaiEdgeCutter.MyIndex
 
context() - Method in class RC2Node
 
context(Pair) - Method in class DGraph
 
contextInstantiations() - Method in class RCNode
 
CONTINUOUS - Static variable in interface HuginReaderConstants
 
converged() - Method in class PropagationInferenceEngineImpl
 
converged() - Method in class BeliefPropagation
 
converged() - Method in class EDAlgorithm
 
convergenceSummary(boolean) - Method in interface PropagationInferenceEngine
 
convergenceSummary(boolean) - Method in class PropagationInferenceEngineImpl
Returns summary of convergence and statistics.
convergenceSummary(boolean) - Method in class RecoveryInferenceEngine
interface PropagationInferenceEngine
convergenceSummary() - Method in class EDAlgorithm
Returns summary of convergence and statistics.
converges() - Method in class ApproxReport
 
ConversionException - Exception in il2.bridge
 
ConversionException(Converter, Object) - Constructor for exception ConversionException
 
convert(BeliefNetwork) - Static method in class Macros
 
convert(BeliefNetwork, Setting.Settings<EdgeDeletionBeliefPropagationSetting>, Map<CrouchingTiger.DynamatorImpl, Dynamator>) - Static method in class Macros
 
convert(BeliefNetwork) - Method in class Converter
 
convert(int) - Method in class Converter
 
convert(FiniteVariable) - Method in class Converter
 
convert(IntSet) - Method in class Converter
 
convert(IntList) - Method in class Converter
 
convert(Set) - Method in class Converter
 
convert(List) - Method in class Converter
 
convert(Map) - Method in class Converter
 
convert(IntMap) - Method in class Converter
 
convert(Table, List) - Method in class Converter
 
convert(Table) - Method in class Converter
 
convert(Table[]) - Method in class Converter
 
convert(Table) - Method in class Converter
 
convert(Table) - Method in class Factorizer
 
convert(IntMap) - Method in class Factorizer
 
convert(IntSet) - Method in class Factorizer
 
convert(IntList) - Method in class Factorizer
 
convert(Table[]) - Method in class Factorizer
 
convertDAGtoMap(DirectedGraph, Map) - Static method in class Dtree
Convert a DirectedGraph to a Map from a FiniteVariable to a collection of FiniteVariables (its family, & itself).
convertDirected(int[][]) - Method in class Converter
 
converter() - Method in class RCInfo
 
Converter - Class in il2.bridge
 
Converter() - Constructor for class Converter
012904
converter - Variable in class EliminationOrders.JT
 
convertRCtoCnfDtree(RCGenerator.RC, PrintStream, HashMap) - Static method in class RCGenerator.Util
 
convertTables(BeliefNetwork, QuantitativeDependencyHandler) - Method in class Converter
 
convertToIL1(Converter) - Method in class Instantiation
 
convertToIL1(Converter) - Method in class MPE
 
convertToList(IntSet) - Method in class Converter
 
convertToString(boolean[]) - Static method in class BooleanArrays
 
convertToString(double[]) - Static method in class DblArrays
 
convertToString(int[]) - Static method in class IntArrays
 
convertToString(Object[]) - Static method in class ObjArrays
 
convertUndirected(int[][]) - Method in class Converter
 
Copier - Interface in edu.ucla.belief
At inception, this interface abstracts the process of copying (cloning) variable objects, which is likely to be a BeliefNetwork-subclass-specific process.
copy(BeliefPropagationSettings) - Method in class BeliefPropagationSettings
 
copy(Stats) - Method in class Stats
 
copy(JoinTreeSettings) - Method in class JoinTreeSettings
 
copy(RCSettings) - Method in class RCSettings
 
copy(Bundle) - Method in class Bundle
 
copy(Computation) - Method in class Computation
 
copy(Settings) - Method in class Settings
 
copy(Setting.Settings<E>) - Method in interface Setting.Settings
 
copy(Setting.Settings<E>) - Method in class SettingsImpl
 
copy() - Method in class Table
 
copyFiniteVariable(FiniteVariable) - Method in interface Copier
 
copyFiniteVariable(FiniteVariable, BeliefNetwork, BeliefNetwork) - Method in interface Copier
 
copyFiniteVariable(FiniteVariable, BeliefNetwork, BeliefNetwork) - Method in class AbstractCopier
 
copyFiniteVariable(FiniteVariable) - Method in class AbstractCopier
 
copyFiniteVariable(FiniteVariable) - Method in class HuginCopier
 
copyFiniteVariable(FiniteVariable, BeliefNetwork, BeliefNetwork) - Method in class HuginCopier
could invert y coordinate
copyParametersInto(double[], int) - Method in class DecisionLeaf
 
copyToSystemClipboard() - Method in interface Dynamator.Commitable
 
copyVariable(Variable) - Method in interface Copier
 
copyVariable(Variable) - Method in class AbstractCopier
 
copyVarValuesToInst(int[]) - Method in class RCInstanceIterator
 
correspondingChanges(int) - Method in class SensitivityTable
 
cost(Set, Set) - Method in interface CostFunction
A non-negative function representing the cost of the edge connecting the two clusters.
CostFunction - Interface in edu.ucla.belief.tree
A cost function for the edges in a JoinTree.
count - Variable in class Macros.RankingArgs
 
count(boolean[], boolean) - Static method in class ArrayUtils
Returns the number of occurrences of the given value in the given array.
count - Variable in class IntStats
 
countDefaultEvidence(BeliefNetwork) - Static method in class StandardNodeImpl
 
countEdgesToDropTable(Index, int, List) - Static method in class UaiEdgeCutter
 
countEdgesToDropTable(List, int, List) - Static method in class UaiEdgeCutter
 
countEdgesToDropTable(int, List) - Method in class UaiEdgeCutter.MyIndex
 
counters - Variable in class RC
 
countInformationConditions() - Method in class CPTInfo
 
countInformationParameters() - Method in class CPTInfo
 
countLeafNodes(BeliefNetwork) - Static method in class UaiEdgeCutter
 
countMaxPositionCoincidence(BeliefNetwork) - Static method in class StandardNodeImpl
 
countRecoverable(BayesianNetwork) - Static method in class EDRecovery
AC: need to update, this counts the number of edges that can be recovered
countUserEnumProperties() - Method in interface BeliefNetwork
 
countUserEnumProperties() - Method in class BeliefNetworkImpl
 
covaryingFunction(LinearFunction) - Method in class CovaryingScheme
 
CovaryingScheme - Class in edu.ucla.belief.sensitivity
 
CovaryingScheme(CPTShell, Object, int[], double[]) - Constructor for class CovaryingScheme
 
CPT - Static variable in class DSLNodeType
 
CPTCoder - Class in edu.ucla.util.code
 
CPTCoder() - Constructor for class CPTCoder
 
CPTImport - Class in edu.ucla.belief.io
Import cpt data from a tab-delimited file, e.g.
CPTImport() - Constructor for class CPTImport
 
CPTImport.CompleteParameterRecorder - Class in edu.ucla.belief.io
 
CPTImport.CompleteParameterRecorder(CPTInfo) - Constructor for class CPTImport.CompleteParameterRecorder
 
CPTImport.IncompleteParameterRecorder - Class in edu.ucla.belief.io
 
CPTImport.IncompleteParameterRecorder(CPTInfo) - Constructor for class CPTImport.IncompleteParameterRecorder
 
CPTImport.ParameterRecorder - Interface in edu.ucla.belief.io
 
CPTImportColumnInfo - Class in edu.ucla.belief.io
Bundle info about a single column of a tab-delimited file containing CPT data.
CPTImportColumnInfo(String) - Constructor for class CPTImportColumnInfo
 
CPTInfo - Class in edu.ucla.belief.io
Bundle info about a CPT imported from a tab-delimited file.
CPTInfo(FiniteVariable, CPTInfo.ReadableWritableTable) - Constructor for class CPTInfo
 
CPTInfo.Parameter - Class in edu.ucla.belief.io
 
CPTInfo.Parameter() - Constructor for class CPTInfo.Parameter
 
CPTInfo.Parameter(double) - Constructor for class CPTInfo.Parameter
 
CPTInfo.ReadableWritableTable - Interface in edu.ucla.belief.io
 
CPTParameter - Class in edu.ucla.belief
Modified by Hei Chan 20030610
CPTParameter(CPTShell, int[]) - Constructor for class CPTParameter
 
CPTParameter(CPTShell, int, int, VariableInstance) - Constructor for class CPTParameter
 
CPTParameter(FiniteVariable, int) - Constructor for class CPTParameter
 
cpts() - Method in class BayesianNetwork
 
cptsChanged(Collection<FiniteVariable>, int) - Method in interface EdgeDeletionInferenceEngine.CPTPolicy.Listener
 
CPTShell - Interface in edu.ucla.belief
 
CPTShells - Class in edu.ucla.util
 
CPTShells(String) - Constructor for class CPTShells
 
create(CrouchingTiger.DynamatorImpl...) - Static method in enum CrouchingTiger.DynamatorImpl
 
create() - Method in enum CrouchingTiger.DynamatorImpl
 
create(Collection) - Method in class Dtree.Create
Create a dtree from the data.
create(Collection) - Method in class DtreeCreateEO
Create a Dtree from the data.
create(Collection) - Method in class DtreeCreateHMetis1
Create a Dtree from the data by recursively calling hMetis.
create(Collection) - Method in class DtreeCreateHMetis1wn
Create a Dtree from the data by recursively calling hMetis.
create(Collection) - Method in class DtreeCreateJT
Create a Dtree from the data.
create(Collection) - Method in class DtreeCreateString
Create a Dtree from the data.
create(Converter, BayesianNetwork, IntList) - Static method in class NormalizedMaxSSAlgorithm
 
create(BayesianNetwork, EliminationOrders.JT) - Static method in class NormalizedMaxSSAlgorithm
 
create(Table[], EliminationOrders.JT) - Static method in class NormalizedMaxSSAlgorithm
 
create(BayesianNetwork, IntSet, IntMap) - Static method in class NormalizedMaxSSAlgorithm
 
create(Converter, BayesianNetwork) - Static method in class NormalizedMaxSSAlgorithm
 
create(Table[]) - Static method in class NormalizedMaxSSAlgorithm
This method is safe to use only in the absence of a BayesianNetwork object.
create(Table[], IntList) - Static method in class NormalizedMaxSSAlgorithm
This method is safe to use only in the absence of a BayesianNetwork object.
create(Table[], EliminationOrders.JT) - Static method in class NormalizedSSAlgorithm
 
create(BayesianNetwork, EliminationOrders.JT) - Static method in class NormalizedSSAlgorithm
 
create(Table[], EliminationOrders.JT) - Static method in class NormalizedZCAlgorithm
 
create(BayesianNetwork, EliminationOrders.JT) - Static method in class NormalizedZCAlgorithm
 
create(Converter, BayesianNetwork, IntList) - Static method in class UnindexedHuginAlgorithm
 
create(BayesianNetwork, EliminationOrders.JT) - Static method in class UnindexedHuginAlgorithm
 
create(Table[], EliminationOrders.JT) - Static method in class UnindexedHuginAlgorithm
 
create(BayesianNetwork, IntSet, IntMap) - Static method in class UnindexedHuginAlgorithm
 
create(Converter, BayesianNetwork) - Static method in class UnindexedHuginAlgorithm
 
create(Converter, BayesianNetwork, IntList) - Static method in class UnindexedSSAlgorithm
 
create(BayesianNetwork, EliminationOrders.JT) - Static method in class UnindexedSSAlgorithm
 
create(Table[], EliminationOrders.JT) - Static method in class UnindexedSSAlgorithm
 
create(BayesianNetwork, IntSet, IntMap) - Static method in class UnindexedSSAlgorithm
 
create(Converter, BayesianNetwork) - Static method in class UnindexedSSAlgorithm
 
create(Table[]) - Static method in class UnindexedSSAlgorithm
This method is safe to use only in the absence of a BayesianNetwork object.
create(Table[], IntList) - Static method in class UnindexedSSAlgorithm
This method is safe to use only in the absence of a BayesianNetwork object.
create(Converter, BayesianNetwork, IntList) - Static method in class UnindexedZCAlgorithm
 
create(BayesianNetwork, EliminationOrders.JT) - Static method in class UnindexedZCAlgorithm
 
create(Table[], EliminationOrders.JT) - Static method in class UnindexedZCAlgorithm
 
create(BayesianNetwork, IntSet, IntMap) - Static method in class UnindexedZCAlgorithm
 
create(Converter, BayesianNetwork) - Static method in class UnindexedZCAlgorithm
 
create(BayesianNetwork, int, Random) - Static method in class RCEngine
 
create(Table[], IntList) - Static method in class RCEngine
 
create(Collection) - Method in class DgraphCreateHMetis
 
create(Collection) - Method in class DgraphCreateHMetis1
Create a DGraph from the data by recursively calling hMetis.
create(Collection) - Method in class DgraphCreateHMetis1wn
Create a DGraph from the data by recursively calling hMetis.
create(Index[], int, Random) - Static method in class DGraphs
 
create(Index[], IntList) - Static method in class DGraphs
 
CREATE_EDGE - Static variable in class BeliefNetwork.Auditor.Deed
 
CREATE_NODE - Static variable in class BeliefNetwork.Auditor.Deed
 
createAnonymousOutcomes(String, int) - Static method in class XmlbifParser
 
createApproxNet(BeliefNetwork, List, List, FiniteVariable[], Map<FiniteVariable, Set<FiniteVariable>>, Map<FiniteVariable, FiniteVariable>) - Static method in class UaiEdgeCutter
this method creates the structure for the network, ready for parameterization.
createBeliefNetwork(int) - Method in class Pedigree
 
createBigIndex(Collection) - Static method in class Index
 
createClassJavadocComment(CodeGenius, String) - Static method in class CPTCoder
 
createClones(List, Map<FiniteVariable, Set<FiniteVariable>>) - Static method in class UaiEdgeCutter
 
createClusters(Graph.Compressed, Integer[], Map) - Static method in class JoinTreeAlgorithm
 
createCompatible(Index) - Static method in class Table
 
createCompatibleIndex() - Method in class Table
 
createCompatibleMPE(Index) - Static method in class MPETable
 
createCompilationComment(CodeGenius) - Static method in class CPTCoder
 
createCPT(CPTInfo, String) - Method in class CPTImport
 
createDtree(BeliefNetwork, HuginLogReader) - Method in class MethodHuginLog.Style
 
createDtree(RC2.RCCreationParams, RC2CreatorEO.Params) - Static method in class RC2CreatorEO
 
createDtreeStructure(RC2, RC2CreatorEO.Params) - Static method in class RC2CreatorEO
 
createErrorMessage(BeliefNetwork) - Static method in class InferenceValidProperty
 
createFromBN(BeliefNetwork, MappedList, KnowledgeBase.KnowledgeBaseListener) - Static method in class KnowledgeBase
 
createFromBN(BeliefNetwork, MappedList) - Static method in class MultiValuedCNF
After calling this, the user should test unsatisfiable, before attempting to access the clause and literals arrays.
createFromIL2Indexes(List) - Static method in class Hypergraph
 
createIdentity(int) - Static method in class UaiEdgeCutter
 
createInferenceEngine(BeliefNetwork, List, Dynamator, QuantitativeDependencyHandler) - Static method in class JEngineGenerator
 
createInferenceEngine(BeliefNetwork, Dynamator, JoinTree, QuantitativeDependencyHandler) - Static method in class JEngineGenerator
 
createInferenceEngine(BeliefNetwork) - Static method in class RCEngineGenerator
 
createInferenceEngine(BeliefNetwork, double, boolean) - Static method in class RCEngineGenerator
 
createInferenceEngine(BeliefNetwork, Dtree, CachingScheme, double, boolean) - Static method in class RCEngineGenerator
 
createInferenceEngine(BeliefNetwork, CachingScheme, double, boolean, DecompositionStructureUtils.ParamsGraph) - Static method in class RCEngineGenerator
 
createIntDirectedGraph(DirectedGraph, Reference) - Static method in class Graphs
 
createIntGraph(Graph, Reference) - Static method in class Graphs
 
createIsomorphic(Map) - Method in interface Graph
 
createIsomorphic(Map) - Method in class HashGraph
 
createKB(MappedList, MultiValuedCNF, KnowledgeBase.KnowledgeBaseListener) - Static method in class KnowledgeBaseImpl
Will return the created KB, or null if it was unsatisfiable.
createKB(KBMap.Mapping) - Static method in class KB_SAT
 
createKB() - Method in class RC
 
createLogicEncoding(MultiValuedCNF, File, String, Map, boolean) - Static method in class KBMap
This creates a cnf file and a Mapping which allows Variables and states from a Bayesian network to be set on the cnf.
createLogicEncoding(MultiValuedCNF, File, String, Map, boolean) - Static method in class Map_EClause
This creates a cnf file and a Mapping which allows Variables and states from a Bayesian network to be set on the cnf.
createLogicEncoding(MultiValuedCNF, File, String, Map, boolean) - Static method in class Map_L
This creates a cnf file and a Mapping which allows Variables and states from a Bayesian network to be set on the cnf.
createMPEAlgorithm(BayesianNetwork, EliminationOrders.JT) - Static method in class MPEAlgorithm
 
createMyRecord(Collection, IntList) - Static method in class UaiEdgeCutter
 
createMyRecordWithinBound(Collection, IntList, double, List, List, List) - Static method in class UaiEdgeCutter
other edge deletion stuff
createMyRecordWithinBound(Collection, IntList, double, List, List, List, List) - Static method in class UaiEdgeCutter
 
createNewNetworkCpt(Table, int) - Method in class EDNetwork
this copies the CPT of the original network, translating it into the new domain
createPedigree(BeliefNetwork, HashMap) - Static method in class Pedigree
 
createPedigree(File, Loci) - Static method in class Pedigree
 
createPedigree(String, Loci) - Static method in class Pedigree
 
createRCDgraphInThread(RC.RCCreationParams, CachingScheme, CachingScheme.RCCreateListener, DecompositionStructureUtils.ParamsGraph) - Static method in class RCDgraph
This will create a thread in which an RCDgraph will be created (by using the listnr parameter, the search for CacheSchemes can be monitored and stopped which will return the best result found so far (if the cachingScheme supports it).
createRCDgraphInThread(BeliefNetwork) - Method in class Settings
 
createRCDgraphInThread(BeliefNetwork, DecompositionStructureUtils.ParamsGraph) - Method in class Settings
 
createRCDtree(BeliefNetwork, double, boolean) - Static method in class RCEngineGenerator
 
createRCDtree(Dtree, BeliefNetwork, double, boolean, CachingScheme, boolean) - Static method in class RCEngineGenerator
 
createRCDtree(RC.RCCreationParams, Dtree, CachingScheme, boolean) - Static method in class RCEngineGenerator
 
createRCDtreeInThread(RC.RCCreationParams, CachingScheme, CachingScheme.RCCreateListener, DecompositionStructureUtils.ParamsTree) - Static method in class RCDtree
This will create a thread in which an RCDtree will be created (by using the listnr parameter, the search for CacheSchemes can be monitored and stopped which will return the best result found so far (if the cachingScheme supports it).
createRCDtreeInThread(BeliefNetwork) - Method in class Settings
 
createRecord(Collection, IntList) - Static method in class EliminationOrders
 
createSeparators(IntSet[], Graph) - Static method in class JoinTreeAlgorithm
 
createStandardComments(CodeGenius) - Static method in class CPTCoder
 
createString(EnumProperty) - Static method in class UserEnumProperty
 
createStructure(DecompositionStructureUtils.ParamsTree) - Static method in class DecompositionStructureUtils
A generic function for any type of tree creation, will decide how to create it based on the class of the parameter in.
createStructure(DecompositionStructureUtils.ParamsTreeDT) - Static method in class DecompositionStructureUtils
Creates the structure of an RC object, based on the parameters.
createStructure(DecompositionStructureUtils.ParamsTreeJT) - Static method in class DecompositionStructureUtils
Creates the structure of an RC object, based on the parameters.
createStructure(DecompositionStructureUtils.ParamsTreeJT2) - Static method in class DecompositionStructureUtils
Creates the structure of an RC object, based on the parameters.
createStructure(DecompositionStructureUtils.ParamsGraph) - Static method in class DecompositionStructureUtils
A generic function for any type of graph creation, will decide how to create it based on the class of the parameter in.
createStructure(DecompositionStructureUtils.ParamsGraphDT) - Static method in class DecompositionStructureUtils
Creates the structure of an RC object, based on the parameters.
createStructure(DecompositionStructureUtils.ParamsGraphJT) - Static method in class DecompositionStructureUtils
Creates the structure of an RC object, based on the parameters.
createStructure(DecompositionStructureUtils.ParamsGraphJT2) - Static method in class DecompositionStructureUtils
Creates the structure of an RC object, based on the parameters.
createTable(TableIndex, double[], double, boolean) - Static method in class TableScaled
 
createTable(TableIndex, double) - Static method in class TableScaled
 
createTree(Graph.Compressed, Integer[]) - Static method in class JoinTreeAlgorithm
 
CreationMethod - Class in edu.ucla.belief.dtree
 
CreationMethod.Settings - Interface in edu.ucla.belief.dtree
 
CrouchingTiger - Class in edu.ucla.belief
Java 5 ("Tiger") extensions for IL1 inflib.
CrouchingTiger() - Constructor for class CrouchingTiger
 
CrouchingTiger.DynamatorImpl - Enum in edu.ucla.belief
 
CShellScriptGenius - Class in edu.ucla.util.code
 
CShellScriptGenius() - Constructor for class CShellScriptGenius
 
CSITypeProperty - Class in edu.ucla.util
Represents the category of a variable's context-specific independence.
CSITypeProperty.CSIType - Class in edu.ucla.util
 
cumProd(int[]) - Static method in class ArrayUtils
Returns the cumulative product of the given array.
cumProd(long[]) - Static method in class ArrayUtils
 
cumProdAsLong(int[]) - Static method in class ArrayUtils
 
cumProdLastBigInteger(int[]) - Static method in class ArrayUtils
 
cumProdLastLong(int[]) - Static method in class ArrayUtils
 
current() - Method in class TableIndex.Iterator
returns the current instantiation.
currentCaching() - Method in class RC2.StoredComputationStats
 
currentState() - Method in class KnowledgeBase
 
currentState() - Method in interface KnowledgeBase
Returns the current state of the KB, if retract is later called with this value, the KB will return to this state.
currentState() - Method in class KnowledgeBaseImpl
 
currentToken - Variable in exception ParseException
This is the last token that has been consumed successfully.
cutEdges(ApproxReport) - Method in class ApproxEngine
 
cutset(Pair) - Method in class DGraph
 
cutsetInstantiations() - Method in class RCNode
 
cycleToString(List, Stringifier) - Static method in class RecursiveDepthFirstIterator
 

D

dataclone() - Method in class Table
 
dataclone() - Method in class TableScaled
Will return a copy of the data array which has already been scaled to real probability values.
DataSetStatistic - Class in edu.ucla.util
Based on Chrisanna Waldrop, Copyright Officer, 805-893-7773, waldrop@research.ucsb.edu, package edu.ucsb.nmsl.tools, url http://www.nmsl.cs.ucsb.edu/autocap
DataSetStatistic(String, int) - Constructor for class DataSetStatistic
Empty data set.
DataSetStatistic(String, Collection<T>) - Constructor for class DataSetStatistic
This constructor creates a DataSetStatistic with a given name and with data from the specified collection.
dateBlock() - Method in class HuginLogReader
 
DblArrays - Class in edu.ucla.util
A class consisting of static utility functions dealing with double arrays.
DblArrays() - Constructor for class DblArrays
 
DEBUG - Static variable in class Definitions
 
debug() - Method in class Interruptable
Override this to return true to print debug messages.
DEBUG_CACHE_SIZE - Static variable in class RCNodeCache
 
DEBUG_RC_CALC - Static variable in class RC
 
DEBUG_RC_EVID - Static variable in class RC
 
debugInstance() - Static method in class FiniteVariableImpl
 
debugPrint(PrintWriter) - Method in class LearningData
 
debugPrint(Object, PrintWriter) - Method in class LearningData
 
debugStream - Variable in class HuginLogReaderTokenManager
 
debugStream - Variable in class HuginReaderTokenManager
 
debugStream - Variable in class NeticaReaderTokenManager
 
decideBest(RC, RC) - Method in class RCComparator
 
decideBest(Bundle, Bundle) - Method in class RCComparator
 
decideReflectY(BeliefNetwork, BeliefNetwork) - Static method in class HuginCopier
 
DECISION - Static variable in interface HuginReaderConstants
 
DecisionBackup - Class in edu.ucla.belief.decision
Compact representation of a DecisionNode (internal or leaf) for the purposes of cloning a fast backup.
DecisionBackup(String, FiniteVariable, boolean) - Constructor for class DecisionBackup
 
DecisionEvent - Class in edu.ucla.belief.decision
 
DecisionEvent(DecisionNode, DecisionEvent.Type) - Constructor for class DecisionEvent
 
DecisionEvent(DecisionTree, DecisionNode, DecisionEvent.Type) - Constructor for class DecisionEvent
 
DecisionEvent(DecisionNode, DecisionNode) - Constructor for class DecisionEvent
 
decisionEvent(DecisionEvent) - Method in interface DecisionListener
 
decisionEvent(DecisionEvent) - Method in class DecisionTreeImpl
interface DecisionListener
decisionEvent(DecisionEvent) - Method in class DecisionShell
interface DecisionListener
DecisionEvent.Type - Class in edu.ucla.belief.decision
 
DecisionEvent.Type(String) - Constructor for class DecisionEvent.Type
 
DecisionInternal - Class in edu.ucla.belief.decision
 
DecisionInternal(FiniteVariable, DecisionLeaf) - Constructor for class DecisionInternal
 
DecisionInternal(DecisionInternal) - Constructor for class DecisionInternal
 
DecisionLeaf - Class in edu.ucla.belief.decision
 
DecisionLeaf(FiniteVariable, Factory) - Constructor for class DecisionLeaf
 
DecisionLeaf(FiniteVariable, Parameter[], Factory) - Constructor for class DecisionLeaf
 
DecisionLeaf(DecisionLeaf) - Constructor for class DecisionLeaf
 
DecisionListener - Interface in edu.ucla.belief.decision
 
DecisionNode - Interface in edu.ucla.belief.decision
 
DecisionNodeAbstract - Class in edu.ucla.belief.decision
 
DecisionNodeAbstract() - Constructor for class DecisionNodeAbstract
 
DecisionNodeAbstract(DecisionNodeAbstract) - Constructor for class DecisionNodeAbstract
 
DecisionShell - Class in edu.ucla.belief
 
DecisionShell(DecisionTree) - Constructor for class DecisionShell
 
DecisionTree - Interface in edu.ucla.belief.decision
 
DECISIONTREE - Static variable in class DSLNodeType
 
DecisionTreeImpl - Class in edu.ucla.belief.decision
 
DecisionTreeImpl(TableIndex) - Constructor for class DecisionTreeImpl
 
DecisionTreeImpl(DecisionNode) - Constructor for class DecisionTreeImpl
 
decompose() - Method in class HuginReader
interface ProgressMonitorable
decompose() - Method in class NodeLinearTask
Simple task decomposes into only itself.
decompose() - Method in class Simulator
interface ProgressMonitorable
decompose() - Method in class CompoundTask
 
decompose() - Method in interface ProgressMonitorable
 
decompose() - Method in class WeightedTask
 
DecompositionStructureUtils - Class in edu.ucla.belief.recursiveconditioning
This is a utility class for creating RC objects (Decomposition Structures).
DecompositionStructureUtils.CreateNodeMethod - Class in edu.ucla.belief.recursiveconditioning
 
DecompositionStructureUtils.Params - Class in edu.ucla.belief.recursiveconditioning
 
DecompositionStructureUtils.ParamsGraph - Class in edu.ucla.belief.recursiveconditioning
 
DecompositionStructureUtils.ParamsGraphDT - Class in edu.ucla.belief.recursiveconditioning
Parameter to the createStructure series of functions.
DecompositionStructureUtils.ParamsGraphDT(BeliefNetwork, RCDgraph, Dtree) - Constructor for class DecompositionStructureUtils.ParamsGraphDT
 
DecompositionStructureUtils.ParamsGraphDT(BeliefNetwork, RCDgraph, Dtree, Collection) - Constructor for class DecompositionStructureUtils.ParamsGraphDT
 
DecompositionStructureUtils.ParamsGraphJT - Class in edu.ucla.belief.recursiveconditioning
Parameter to the createStructure series of functions.
DecompositionStructureUtils.ParamsGraphJT(BeliefNetwork, RCDgraph, HuginLogReader, DecompositionStructureUtils.CreateNodeMethod) - Constructor for class DecompositionStructureUtils.ParamsGraphJT
 
DecompositionStructureUtils.ParamsGraphJT2 - Class in edu.ucla.belief.recursiveconditioning
Parameter to the createStructure series of functions.
DecompositionStructureUtils.ParamsGraphJT2(BeliefNetwork, RCDgraph, BeliefCompilation, DecompositionStructureUtils.CreateNodeMethod) - Constructor for class DecompositionStructureUtils.ParamsGraphJT2
 
DecompositionStructureUtils.ParamsTree - Class in edu.ucla.belief.recursiveconditioning
 
DecompositionStructureUtils.ParamsTreeDT - Class in edu.ucla.belief.recursiveconditioning
Parameter to the createStructure series of functions.
DecompositionStructureUtils.ParamsTreeDT(BeliefNetwork, RCDtree, Dtree, boolean) - Constructor for class DecompositionStructureUtils.ParamsTreeDT
 
DecompositionStructureUtils.ParamsTreeJT - Class in edu.ucla.belief.recursiveconditioning
Parameter to the createStructure series of functions.
DecompositionStructureUtils.ParamsTreeJT(BeliefNetwork, RCDtree, HuginLogReader, boolean, DecompositionStructureUtils.CreateNodeMethod) - Constructor for class DecompositionStructureUtils.ParamsTreeJT
 
DecompositionStructureUtils.ParamsTreeJT2 - Class in edu.ucla.belief.recursiveconditioning
Parameter to the createStructure series of functions.
DecompositionStructureUtils.ParamsTreeJT2(BeliefNetwork, RCDtree, BeliefCompilation, boolean, DecompositionStructureUtils.CreateNodeMethod) - Constructor for class DecompositionStructureUtils.ParamsTreeJT2
 
decorate(InferenceEngine) - Method in interface Dynamator.Decorator
 
decorate(InferenceEngine) - Static method in class SynchronizedInferenceEngine
 
deepClone() - Method in interface BeliefNetwork
 
deepClone() - Method in class BeliefNetworkImpl
Call this method to perform a deep clone on a BeliefNetworkImpl (i.e., will clone the structure, Tables and all Variable objects.
deepClone(Factory) - Method in class DecisionInternal
 
deepClone(Factory) - Method in class DecisionLeaf
 
deepClone(Factory) - Method in interface DecisionNode
 
deepClone(Factory) - Method in class DecisionNodeAbstract
 
deepCloneMapTypesToShells(FiniteVariable) - Static method in class FiniteVariableImpl
 
deepCopyMap(Map) - Static method in class StandardNodeImpl
 
deepSize(List) - Static method in class HuginPotential
 
DEFAULT - Variable in class Optimizer
 
DEFAULT - Static variable in interface HuginLogReaderConstants
 
DEFAULT - Static variable in interface HuginReaderConstants
 
DEFAULT - Static variable in interface NeticaReaderConstants
 
DEFAULT - Static variable in class ExcludePolicy
 
DEFAULT - Static variable in enum Algorithm.EliminationOrderHeuristic
 
DEFAULT - Static variable in enum Algorithm.Order2JoinTree
 
DEFAULT - Static variable in enum Algorithm.Query
 
DEFAULT - Static variable in enum EDAlgorithm.RankingHeuristic
 
DefaultGenerator - Class in edu.ucla.belief.inference
 
DefaultGenerator() - Constructor for class DefaultGenerator
 
defaultVal() - Static method in class CachingDFBnB.ChildExpansion
 
defaultVal() - Static method in class CachingDFBnB.HeurFunct
 
defaultVal() - Static method in class CachingDFBnB.OrderingAlgo
 
DEFINE - Static variable in interface NeticaReaderConstants
 
Definitions - Class in edu.ucla.belief
Static definitions removed from BeliefNetworks in order to break circular dependencies.
deflate() - Method in class DecisionInternal
 
deflate(Map) - Method in class DecisionInternal
 
deflate() - Method in class DecisionLeaf
 
deflate(Map) - Method in class DecisionLeaf
 
deflate() - Method in class DecisionNodeAbstract
 
deflate(Map) - Method in class DecisionNodeAbstract
 
deflateOutcomes(Map, Map) - Method in class DecisionBackup
 
deflateParameters(Parameter[], Map) - Method in class DecisionBackup
 
degree(Object) - Method in class BeliefNetworkImpl
 
degree(Object) - Method in class AbstractDirectedGraph
 
degree(Object) - Method in interface DirectedGraph
Returns the degree of the vertex.
degree(Object) - Method in interface Graph
Returns the degree of vertex.
degree(Object) - Method in class HashDirectedGraph
Returns the degree of the vertex.
degree(Object) - Method in class HashGraph
Returns the degree of vertex.
degree(int) - Method in class IntGraph
 
delayedAction() - Method in class RepetitionThread
 
delete(EnumProperty) - Method in interface Variable
 
delete(EnumProperty) - Method in class VariableImpl
 
DEPENDENCIES - Static variable in class HuginEngineGenerator
 
DEPENDENCIES - Static variable in class RCEngineGenerator
 
DEPENDENCIES - Static variable in class SSEngineGenerator
 
DEPENDENCIES - Static variable in class ZCEngineGenerator
 
depth - Variable in class Person
 
depthFirstDepth(int, FiniteVariable, FiniteVariable, BeliefNetwork, Set<FiniteVariable>, int) - Static method in class Macros
 
depthFirstIterator() - Method in class AbstractDirectedGraph
 
DepthFirstIterator - Class in edu.ucla.structure
 
DepthFirstIterator(DirectedGraph) - Constructor for class DepthFirstIterator
 
deracinate() - Method in interface DecisionNode
 
deracinate() - Method in class DecisionNodeAbstract
 
DERACINATED - Static variable in class DecisionEvent
 
describe(EvidenceController) - Method in class EvidenceChangeEvent
 
describe(boolean) - Method in class AbstractCodeOption
 
describe() - Method in interface CodeGenius
 
describe() - Method in interface CodeOption
 
describe(boolean) - Method in interface CodeOption
 
describe() - Method in class CPTCoder
 
describe() - Method in class EMCoder
 
describe() - Method in class MAPCoder
 
describe() - Method in class MAPCoder.OptionPrune
 
describe(boolean) - Method in class MAPCoder.OptionPrune
 
describe() - Method in class MAPCoder.OptionTimings
 
describe(boolean) - Method in class MAPCoder.OptionTimings
 
describe() - Method in class ModelCoder
 
describe() - Method in class ModelCoder.LibraryVersionOption
 
describe() - Method in class MPECoder
 
describe() - Method in class OptionBreadth
 
describe() - Method in class OptionWithComments
 
describe(boolean) - Method in class OptionWithComments
 
describe() - Method in class ProbabilityQueryCoder
 
describe() - Method in class ProbabilityQueryCoder.MarginalScopeOption
 
describe() - Method in class SensitivityCoder
 
DESCRIBE_CONDITIONAL - Static variable in class AbstractInferenceEngine
 
DESCRIBE_CONDITIONALS - Static variable in class EdgeDeletionInferenceEngine
 
DESCRIBE_CONDITIONALS - Static variable in class RecoveryInferenceEngine
 
describeConditionals() - Method in class AbstractInferenceEngine
In case this InferenceEngine wants to report two sets of answers, for example, approximate and exact.
describeConditionals() - Method in class EdgeDeletionInferenceEngine
In case this InferenceEngine wants to report two sets of answers, for example, approximate and exact.
describeConditionals() - Method in class RecoveryInferenceEngine
 
describeConditionals() - Method in class SynchronizedInferenceEngine
 
describeConditionals() - Method in interface InferenceEngine
In case this InferenceEngine wants to report two sets of answers, for example, approximate and exact.
describeDependencies() - Method in interface CodeGenius
 
describeDependencies(Tree) - Method in interface CodeGenius
 
describeDependencies() - Method in class CPTCoder
 
describeDependencies(Tree) - Method in class CPTCoder
 
describeDependencies() - Method in class EMCoder
 
describeDependencies(Tree) - Method in class EMCoder
 
describeDependencies() - Method in class MAPCoder
 
describeDependencies(Tree) - Method in class MAPCoder
 
describeDependencies() - Method in class ModelCoder
 
describeDependencies(Tree) - Method in class ModelCoder
 
describeDependencies() - Method in class MPECoder
 
describeDependencies(Tree) - Method in class MPECoder
 
describeDependencies() - Method in class ProbabilityQueryCoder
 
describeDependencies(Tree) - Method in class ProbabilityQueryCoder
 
describeDependencies() - Method in class SensitivityCoder
 
describeDependencies(Tree) - Method in class SensitivityCoder
 
describeUserMemConcise(Computation) - Method in class Settings
 
describeUserMemoryProportion() - Method in class RCSettings
 
describeUserMemoryProportion() - Method in class Settings
 
describeUserMemoryProportion(Computation) - Method in class Settings
 
description - Variable in enum EdgeDeletionInferenceEngine.Attribute
 
description - Variable in enum EdgeDeletionInferenceEngine.Command
 
desireAbilityToComputeFamilyMarginals - Variable in class DecompositionStructureUtils.ParamsGraphDT
 
deterministicCPT(Collection, FiniteVariable) - Static method in class RandomNetworks
Returns a deterministic CPT(For each instance of the parents, one instance of the variable has value 1, the rest 0.
deterministicNetwork(DirectedGraph) - Static method in class RandomNetworks
Creates a deterministic network from the graph of variables supplied.
deterministicNetwork(int, double) - Static method in class RandomNetworks
Creates a deterministic network from the random graph generated using the supplied parameters.
deterministicNetwork(int, int) - Static method in class RandomNetworks
Generates a deterministic network from the random graph generated using the supplied parameters.
df - Static variable in class CachingDFBnB.OrderingAlgo
 
dfbnbTime_ms() - Method in class CachingDFBnB.DFBnB_TmpVars
 
dfsLeafOrder() - Method in class MiniTree
 
dgraph() - Method in class RCInfo
 
dgraph() - Method in class CachingScheme
 
dgraph() - Method in class RC
 
dgraph() - Method in class RCEngine
 
DGraph - Class in il2.inf.structure
A binary jointree basically.
DGraph(Graph, Map) - Constructor for class DGraph
Creates a DGraph from the supplied tree and cluster labels.
DgraphCreateHMetis - Class in il2.inf.structure
This abstract class can create a Dgraph, using the hMetis algorithm/library
DgraphCreateHMetis(int[], int, int, int) - Constructor for class DgraphCreateHMetis
 
DgraphCreateHMetis(int, int, int) - Constructor for class DgraphCreateHMetis
 
DgraphCreateHMetis1 - Class in il2.inf.structure
This class can create a Dtree, using the hMetis algorithm/library
DgraphCreateHMetis1(int[], int, int, int) - Constructor for class DgraphCreateHMetis1
 
DgraphCreateHMetis1(int, int, int) - Constructor for class DgraphCreateHMetis1
 
DgraphCreateHMetis1wn - Class in il2.inf.structure
This class can create a Dtree, using the hMetis algorithm/library.
DgraphCreateHMetis1wn(int[], int, int, int) - Constructor for class DgraphCreateHMetis1wn
 
DgraphCreateHMetis1wn(int, int, int) - Constructor for class DgraphCreateHMetis1wn
 
DGraphs - Class in il2.inf.structure
 
DGraphs() - Constructor for class DGraphs
 
DiagnosisType - Class in edu.ucla.belief.io.dsl
A class that represents an enumerated type over the designations of nodes in Genie Diagnosis.
diameter() - Method in class RCInfo
 
diameter() - Method in class DGraph
 
die() - Method in class AbstractInferenceEngine
 
die() - Method in class EdgeDeletionInferenceEngine
 
die() - Method in class Macros.Bridge
 
die() - Method in class PropagationInferenceEngineImpl
 
die() - Method in class RecoveryInferenceEngine
 
die() - Method in class JoinTreeInferenceEngineImpl
 
die() - Method in class RandomInferenceEngine
 
die() - Method in class SynchronizedInferenceEngine
 
die() - Method in class WrapperInferenceEngine
 
die() - Method in interface InferenceEngine
 
die() - Method in class RCInferenceEngine
 
die() - Method in class EDAlgorithm
 
die() - Method in class EDRecovery
 
diff(SensitivityEquation, SensitivityEquation) - Static method in class SensitivityEquation
 
diff(IntSet) - Method in class IntSet
 
DIFFERENCE - Static variable in class SensitivityConstraint
 
DIFFERENCE - Static variable in class SensitivityEngine
 
DIMENSION_MINIMUM - Static variable in class Macros
 
DIMENSION_SOFT_EVIDENCE - Static variable in class Macros
 
directAway(Graph, Object) - Static method in class Graphs
This method assumes the graph is connected.
DirectedEdge - Class in edu.ucla.structure
 
DirectedEdge(Object, Object) - Constructor for class DirectedEdge
 
DirectedGraph - Interface in edu.ucla.structure
The interface describing directed graphs.
directory - Variable in class JDKRun.CompiledClassInfo
 
dirty() - Method in class EdgeDeletionInferenceEngine
 
dirty() - Method in class RecoveryInferenceEngine
 
disable_tracing() - Method in class HuginLogReader
 
disable_tracing() - Method in class HuginReader
 
disable_tracing() - Method in class NeticaReader
 
discontinuityCpt(int, double, double, double) - Static method in class MaxProductLinearSmoothness
for testing purposes
DISCRETE - Static variable in interface HuginReaderConstants
 
diseaseLocusChromoOrd() - Method in class Loci
Return 0 based Chromosome Order of disease locus.
diseaseLocusInputOrd() - Method in class Loci
Return 0 based Input Order of disease locus.
display - Variable in enum EdgeDeletionInferenceEngine.Attribute
 
display - Variable in enum EdgeDeletionInferenceEngine.Command
 
display - Variable in enum EdgeDeletionInferenceEngine.CPTPolicy
 
display - Variable in enum Macros.Category
 
displayCNF(PrintStream) - Method in class MultiValuedCNF
 
displayName() - Method in enum CrouchingTiger.DynamatorImpl
 
distance(double[], double[]) - Static method in class Prob
 
distanceMeasure(CPTInfo.ReadableWritableTable, boolean) - Method in class CPTInfo
 
distanceMeasure(Table) - Method in class Table
 
distanceMeasure(double[], double[]) - Static method in class Table
 
distinct - Variable in class Stats.Stat
 
distinguishes(FileType) - Method in class FileType
alias of narrows()
distribute(int) - Method in class Messenger
Performs a distribute evidence on the specified vertex.
divide(Table) - Method in class Table
 
divideInto(Table) - Method in class Table
 
divideRelevantInto(double[]) - Method in class Table
 
doBeliefNetwork() - Method in class HuginReader
 
doConvergenceUpdates - Variable in class EDAlgorithm
 
domain() - Method in class RCInfo
 
domain() - Method in class JoinTree
 
domain() - Method in class MapJoinTree
 
domain() - Method in class MapTree
 
domain() - Method in class RC
 
domain() - Method in class RCEngine
 
domain - Variable in class EliminationOrders.JT
 
domain() - Method in class BayesianNetwork
 
Domain - Class in il2.model
 
Domain() - Constructor for class Domain
 
Domain(int) - Constructor for class Domain
 
domain() - Method in class Index
 
domain() - Method in interface SubDomain
 
Done() - Method in class SimpleCharStream
 
done(RCDgraph, BeliefNetwork, DynaListener) - Method in class RCEngineGenerator
 
DoNotCache - Static variable in class RCNodeCache
 
doOpenDtree(BeliefNetwork, File, CreationMethod.Settings) - Static method in class MethodHuginLog
 
doOpenDtree(BeliefNetwork, File) - Method in class Settings
 
doOpenRC(BeliefNetwork, File) - Method in class Settings
 
doSaveDtree(File) - Method in class Settings
 
doSaveRC(Dtree, RC, Computation, File, String) - Method in class Settings
 
doTask(FiniteVariable, DSLNodeType, CPTShell) - Method in class CPTShells
override this method
dotProduct(double[], double[]) - Static method in class DblArrays
 
dotProduct(Table) - Method in class Table
 
DOUBLE_60 - Static variable in class RCSettings
 
DOUBLE_BIAS_VALUE - Static variable in class Learning
 
DOUBLE_BYTES_PER_BYTE - Static variable in class RCSettings
 
DOUBLE_BYTES_PER_BYTE - Static variable in class Settings
 
DOUBLE_DEFAULT_FRACTION_MISSING_VALUES - Static variable in class Simulator
 
DOUBLE_DOUBLES_PER_MEGABYTE - Static variable in class RCInfo
 
DOUBLE_EPSILON - Static variable in class CPTInfo
 
DOUBLE_FILL_VALUE - Static variable in class CPTInfo
 
DOUBLE_FRACTION_MISSING_CEILING - Static variable in class Simulator
 
DOUBLE_FRACTION_MISSING_FLOOR - Static variable in class Simulator
 
DOUBLE_HOURS_PER_MILLISECOND - Static variable in class Settings
 
DOUBLE_INVALID_OPTIMAL_MEMORY - Static variable in class RCSettings
 
DOUBLE_INVALID_OPTIMAL_MEMORY - Static variable in class Settings
 
DOUBLE_INVERSE_LN_2 - Static variable in class JoinTreeStats
 
DOUBLE_KILOBYTES_PER_BYTE - Static variable in class RCSettings
 
DOUBLE_KILOBYTES_PER_BYTE - Static variable in class Settings
 
DOUBLE_MEGABYTES_PER_BYTE - Static variable in class RCSettings
 
DOUBLE_MEGABYTES_PER_BYTE - Static variable in class Settings
 
DOUBLE_MILLIS_PER_SECOND - Static variable in class JEngineGenerator
 
DOUBLE_MINUTES_PER_MILLISECOND - Static variable in class Settings
 
DOUBLE_NORMALIZE_EPSILON - Static variable in class DecisionLeaf
 
DOUBLE_ONE - Static variable in class SingleParamSuggestion
 
DOUBLE_OUTOFMEMORY - Static variable in class RC
 
DOUBLE_SECONDS_PER_MILLISECOND - Static variable in class Settings
 
DOUBLE_SUGGESTED_FLOOR - Static variable in class Optimizer
 
DOUBLE_SUGGESTED_REDUCTION_FACTOR - Static variable in class Optimizer
 
DOUBLE_THRESHOLD_DEFAULT - Static variable in class BeliefPropagationSettings
 
DOUBLE_THRESHOLD_DEFAULT - Static variable in class EDAlgorithm
 
DoubleFunction - Interface in edu.ucla.structure
 
DoubleList - Class in il2.util
 
DoubleList() - Constructor for class DoubleList
Creates a new instance of DoubleList
DoubleList(DoubleList) - Constructor for class DoubleList
 
DoubleList(double[]) - Constructor for class DoubleList
 
DoubleList(int) - Constructor for class DoubleList
 
DoubleMap - Class in il2.util
 
DoubleMap() - Constructor for class DoubleMap
 
DoubleMap(DoubleMap) - Constructor for class DoubleMap
 
DoubleMap(int) - Constructor for class DoubleMap
 
DoubleMap(IntSet, DoubleList) - Constructor for class DoubleMap
 
DoubleMap(int[], double[]) - Constructor for class DoubleMap
 
DROP_EDGE - Static variable in class BeliefNetwork.Auditor.Deed
 
DROP_NODE - Static variable in class BeliefNetwork.Auditor.Deed
 
DSL - Static variable in class FileType
 
DSL_CPT - Static variable in class SMILEReader
 
DSL_NOISY_MAX - Static variable in class SMILEReader
 
DSL_TRUTHTABLE - Static variable in class SMILEReader
 
DSLConstants - Class in edu.ucla.belief.io.dsl
 
DSLConstants() - Constructor for class DSLConstants
 
DSLNode - Interface in edu.ucla.belief.io.dsl
A class for encapsulating a hugin node description.
DSLNodeImpl - Class in edu.ucla.belief.io.dsl
Encapsulates a SMILE node description.
DSLNodeImpl(String, Map) - Constructor for class DSLNodeImpl
 
DSLNodeType - Class in edu.ucla.belief.io.dsl
A class that represents an enumerated type over the kinds of Genie nodes that inflib/samiam will currently support.
DSLSubmodel - Class in edu.ucla.belief.io.dsl
 
DSLSubmodel(int) - Constructor for class DSLSubmodel
 
DSLSubmodelFactory - Class in edu.ucla.belief.io.dsl
 
DSLSubmodelFactory() - Constructor for class DSLSubmodelFactory
 
Dtree - Class in edu.ucla.belief.dtree
This class represents dtree objects.
Dtree(DtreeNode) - Constructor for class Dtree
Create a Dtree with inRoot as the root of the tree.
Dtree(DirectedGraph, Dtree.Create) - Constructor for class Dtree
Create a Dtree using the createAlgo algorithm and the DirectedGraph dag.
Dtree(Map, Dtree.Create) - Constructor for class Dtree
Create a Dtree using the createAlgo algorithm.
dtree() - Method in class HuginLogReader
 
dtree(boolean) - Method in class HuginLogReader
 
Dtree.Create - Class in edu.ucla.belief.dtree
Each instantiation of this class represents a way of generating dtrees.
Dtree.Create() - Constructor for class Dtree.Create
 
Dtree.DtreeComparatorHeightLowToHigh - Class in edu.ucla.belief.dtree
This comparator will first sort based on height, then on hashCode, and then try a few different things before returning 0.
Dtree.DtreeComparatorHeightLowToHigh() - Constructor for class Dtree.DtreeComparatorHeightLowToHigh
 
Dtree.DtreeCreationException - Exception in edu.ucla.belief.dtree
 
Dtree.DtreeCreationException(String) - Constructor for exception Dtree.DtreeCreationException
 
DtreeCreateEO - Class in edu.ucla.belief.dtree
This class can create a Dtree, using the supplied elimination order.
DtreeCreateEO(List) - Constructor for class DtreeCreateEO
Create a DtreeCreateEO which will use the elimination order eo to generate dtrees.
DtreeCreateHMetis - Class in edu.ucla.belief.dtree
This abstract class can create a Dtree, using the hMetis algorithm/library
DtreeCreateHMetis(int[], int, int, int) - Constructor for class DtreeCreateHMetis
 
DtreeCreateHMetis(int, int, int) - Constructor for class DtreeCreateHMetis
 
DtreeCreateHMetis1 - Class in edu.ucla.belief.dtree
This class can create a Dtree, using the hMetis algorithm/library
DtreeCreateHMetis1(int[], int, int, int) - Constructor for class DtreeCreateHMetis1
 
DtreeCreateHMetis1(int, int, int) - Constructor for class DtreeCreateHMetis1
 
DtreeCreateHMetis1wn - Class in edu.ucla.belief.dtree
This class can create a Dtree, using the hMetis algorithm/library.
DtreeCreateHMetis1wn(int[], int, int, int) - Constructor for class DtreeCreateHMetis1wn
 
DtreeCreateHMetis1wn(int, int, int) - Constructor for class DtreeCreateHMetis1wn
 
DtreeCreateJT - Class in edu.ucla.belief.dtree
This class can create a Dtree, using the supplied JoinTree.
DtreeCreateJT(HuginLogReader) - Constructor for class DtreeCreateJT
Create a DtreeCreateJT which will use the HuginLogReader to generate dtrees.
DtreeCreateString - Class in edu.ucla.belief.dtree
This class can create a Dtree, using the supplied String.
DtreeCreateString(PushbackReader) - Constructor for class DtreeCreateString
Create a DtreeCreateString which will use the PushbackReader pbrFile to generate dtrees.
dtreeMethod - Variable in class FileInfo
 
DtreeNode - Class in edu.ucla.belief.dtree
 
DtreeNode(Collection) - Constructor for class DtreeNode
 
DtreeNodeInternal - Class in edu.ucla.belief.dtree
This class represents Internal DtreeNode objects.
DtreeNodeInternal(DtreeNode, DtreeNode) - Constructor for class DtreeNodeInternal
Creates a DtreeNodeInternal using the two parameters as children.
DtreeNodeLeaf - Class in edu.ucla.belief.dtree
This class represents family dtree leaf nodes.
DtreeNodeLeaf(Collection, FiniteVariable) - Constructor for class DtreeNodeLeaf
Creates a new DtreeNodeLeaf using the Collection vars.
DynaListener - Interface in edu.ucla.belief
 
Dynamator - Class in edu.ucla.belief
 
Dynamator() - Constructor for class Dynamator
 
Dynamator.Commitable - Interface in edu.ucla.belief
 
Dynamator.Decorator - Interface in edu.ucla.belief
 
Dynamator.RunCompile - Class in edu.ucla.belief
 
Dynamator.RunCompile(BeliefNetwork, DynaListener) - Constructor for class Dynamator.RunCompile
 
dynamatorForClass(String) - Static method in class Test
 
dynamicBNOrderingVEPD() - Method in class Pedigree.GeneticNetwork
 
DynamicEliminator - Class in il2.inf.structure
 
DynamicEliminator(Orderer, Domain) - Constructor for class DynamicEliminator
 
dynamicMiniSumProduct(Collection, double) - Static method in class BasicInference
 

E

eclauses() - Method in class MultiValuedCNF
 
eclausesFV() - Method in class MultiValuedCNF
 
ecTimes - Variable in class EDAlgorithm
 
edalgorithm - Variable in class Macros.Bridge
 
EDAlgorithm - Class in il2.inf.edgedeletion
 
EDAlgorithm(BayesianNetwork, int[][], int, long, double, Algorithm, Map<Algorithm.Setting, ?>) - Constructor for class EDAlgorithm
 
EDAlgorithm(BayesianNetwork) - Constructor for class EDAlgorithm
EDAlgorithm instance with all edges deleted.
EDAlgorithm(BayesianNetwork, int[][]) - Constructor for class EDAlgorithm
 
EDAlgorithm.RankingHeuristic - Enum in il2.inf.edgedeletion
 
EDEdgeDeleter - Class in il2.inf.edgedeletion
 
EDEdgeDeleter() - Constructor for class EDEdgeDeleter
 
edge - Static variable in class BeliefNetwork.Auditor.Unit
 
Edge - Class in edu.ucla.structure
 
Edge(Object, Object) - Constructor for class Edge
 
EdgeComparator - Class in il2.inf.edgedeletion
 
EdgeComparator() - Constructor for class EdgeComparator
 
EdgeComparator(int[][], double[]) - Constructor for class EdgeComparator
 
edgeConvergenceScores - Variable in class EDAlgorithm
 
edgeCorrelations() - Method in class EDAlgorithm
 
edgeCount() - Method in interface ArithmeticExpression
 
edgeCount() - Method in class BeliefCompilation
Deprecated.  
edgeCount() - Method in class S4DoubleExpression
 
edgeCount(Graph) - Static method in class Graphs
Returns the number of edges in g.
EdgeDeletionBeliefPropagationSetting - Enum in edu.ucla.belief.approx
 
EdgeDeletionEngineGenerator - Class in edu.ucla.belief.approx
 
EdgeDeletionEngineGenerator() - Constructor for class EdgeDeletionEngineGenerator
 
EdgeDeletionInferenceEngine - Class in edu.ucla.belief.approx
 
EdgeDeletionInferenceEngine(BeliefNetwork, Macros.Bridge, Setting.Settings<EdgeDeletionBeliefPropagationSetting>, Dynamator) - Constructor for class EdgeDeletionInferenceEngine
 
EdgeDeletionInferenceEngine.Attribute - Enum in edu.ucla.belief.approx
 
EdgeDeletionInferenceEngine.Command - Enum in edu.ucla.belief.approx
 
EdgeDeletionInferenceEngine.CPTPolicy - Enum in edu.ucla.belief.approx
 
EdgeDeletionInferenceEngine.CPTPolicy.Listener - Interface in edu.ucla.belief.approx
 
EdgeDeletionInferenceEngine.DateFormatFilename - Class in edu.ucla.belief.approx
 
edgeMis() - Method in class EDAlgorithm
 
edgeScore(int[]) - Method in class MaxProduct
 
edgesDeleted - Variable in class Macros.Bridge
 
edgesDeleted() - Method in class RecoveryInferenceEngine
 
edgesDeleted() - Method in class EDAlgorithm
 
edgesDeleted() - Method in class EDNetwork
statistics and settings functions
edgeSet() - Method in class Hypergraph
 
edgeTargetedMis(int) - Method in class EDAlgorithm
 
edgeToString(int[]) - Static method in class EDEdgeDeleter
 
EDMPAlgorithm - Class in il2.inf.edgedeletion
 
EDMPAlgorithm(BayesianNetwork, int[][], int, long, double, Algorithm, Map<Algorithm.Setting, ?>) - Constructor for class EDMPAlgorithm
 
edNet() - Method in class EDAlgorithm
 
EDNetwork - Class in il2.inf.edgedeletion
 
EDNetwork(BayesianNetwork, int[][]) - Constructor for class EDNetwork
 
EDNetwork(BayesianNetwork) - Constructor for class EDNetwork
 
EDRecovery - Class in il2.inf.edgedeletion
 
EDRecovery(BayesianNetwork, IntMap, EDAlgorithm.RankingHeuristic, int, int, long, double, Algorithm, Map<Algorithm.Setting, ?>, Random) - Constructor for class EDRecovery
num is the # of edges you want to _recover_
edu.ucla.belief - package edu.ucla.belief
 
edu.ucla.belief.approx - package edu.ucla.belief.approx
 
edu.ucla.belief.decision - package edu.ucla.belief.decision
 
edu.ucla.belief.dtree - package edu.ucla.belief.dtree
 
edu.ucla.belief.inference - package edu.ucla.belief.inference
 
edu.ucla.belief.inference.map - package edu.ucla.belief.inference.map
 
edu.ucla.belief.io - package edu.ucla.belief.io
 
edu.ucla.belief.io.dsl - package edu.ucla.belief.io.dsl
 
edu.ucla.belief.io.geneticlinkage - package edu.ucla.belief.io.geneticlinkage
 
edu.ucla.belief.io.hugin - package edu.ucla.belief.io.hugin
 
edu.ucla.belief.io.netica - package edu.ucla.belief.io.netica
 
edu.ucla.belief.io.xmlbif - package edu.ucla.belief.io.xmlbif
 
edu.ucla.belief.learn - package edu.ucla.belief.learn
 
edu.ucla.belief.rc2.caching - package edu.ucla.belief.rc2.caching
 
edu.ucla.belief.rc2.creation - package edu.ucla.belief.rc2.creation
 
edu.ucla.belief.rc2.io - package edu.ucla.belief.rc2.io
 
edu.ucla.belief.rc2.kb - package edu.ucla.belief.rc2.kb
 
edu.ucla.belief.rc2.kb.sat - package edu.ucla.belief.rc2.kb.sat
 
edu.ucla.belief.rc2.structure - package edu.ucla.belief.rc2.structure
 
edu.ucla.belief.rc2.tools - package edu.ucla.belief.rc2.tools
 
edu.ucla.belief.recursiveconditioning - package edu.ucla.belief.recursiveconditioning
 
edu.ucla.belief.sensitivity - package edu.ucla.belief.sensitivity
 
edu.ucla.belief.tree - package edu.ucla.belief.tree
 
edu.ucla.belief.uai2006 - package edu.ucla.belief.uai2006
 
edu.ucla.structure - package edu.ucla.structure
 
edu.ucla.util - package edu.ucla.util
 
edu.ucla.util.code - package edu.ucla.util.code
 
element() - Method in class Heap.HeapElement
returns the object the HeapElement contains.
ElementHandler - Interface in edu.ucla.belief.io
Moved from SamIam package edu.ucla.belief.ui.util since 020105
elementsContaining(Map) - Static method in class Maps
 
eliminate(BeliefNetwork, EliminationOrders.ScoreFunction) - Static method in class EliminationOrders
 
eliminate(Graph, EliminationOrders.ScoreFunction) - Static method in class EliminationOrders
 
eliminate(BeliefNetwork, Set, EliminationOrders.ScoreFunction) - Static method in class EliminationOrders
 
eliminate(Graph, Set, EliminationOrders.ScoreFunction) - Static method in class EliminationOrders
Produces an elimination order whose order is chosen by always choosing to eliminate the node with the highest score.
eliminateBruteForce(Graph, List, EliminationOrders.ScoreFunction) - Static method in class EliminationOrders
 
eliminateForMinFill(Graph, Set, int, Random) - Static method in class EliminationOrders
 
ELIMINATION_LIT - Static variable in interface HuginLogReaderConstants
 
eliminationBlock() - Method in class HuginLogReader
 
EliminationHeuristic - Class in edu.ucla.belief
Was edu.ucla.belief.dtree.MethodEliminationOrder.Algorithm
EliminationHeuristic.RandomizedBestOfNStrategy - Class in edu.ucla.belief
 
EliminationHeuristic.RandomizedBestOfNStrategy(String) - Constructor for class EliminationHeuristic.RandomizedBestOfNStrategy
 
eliminationOrder() - Method in class JoinTree
 
eliminationOrder - Variable in class UaiPreprocessResult
The elimination order.
eliminationOrder() - Method in class EliminationOrders.JT
 
eliminationOrder() - Method in interface JTUnifier
 
EliminationOrderEngine - Class in il2.inf.structure.minfill2
A base class for algorithms that produce an elimination order.
EliminationOrderEngine() - Constructor for class EliminationOrderEngine
 
EliminationOrders - Class in edu.ucla.belief
 
EliminationOrders - Class in il2.inf.structure
 
EliminationOrders() - Constructor for class EliminationOrders
 
EliminationOrders.JT - Class in il2.inf.structure
 
EliminationOrders.Record - Class in il2.inf.structure
 
EliminationOrders.Record(IntList, double, IntSet[]) - Constructor for class EliminationOrders.Record
 
EliminationOrders.ScoreFunction - Interface in edu.ucla.belief
 
EliminationTree - Class in edu.ucla.belief.tree
 
EliminationTree(DirectedGraph, TableIndex[], int[]) - Constructor for class EliminationTree
Creates an Elimination Tree.
eliminationTree(TableIndex[], List) - Static method in class Trees
Generates an elimination tree.
elimVar(FiniteVariable, int, double) - Method in class RCGenerator.EO
 
EMCoder - Class in edu.ucla.util.code
 
EMCoder() - Constructor for class EMCoder
 
EMPTY_EVENT - Static variable in class EvidenceChangeEvent
 
EMThread - Class in edu.ucla.belief.learn
Removed from Learning.java
EMThread(BeliefNetwork, LearningDataOld, Dynamator, double, int, boolean, ProgressMonitor, EMThread.LearningListener) - Constructor for class EMThread
 
EMThread(BeliefNetwork, LearningData, Dynamator, double, int, boolean, ProgressMonitor, EMThread.LearningListener) - Constructor for class EMThread
 
EMThread.LearningListener - Interface in edu.ucla.belief.learn
 
enable_tracing() - Method in class HuginLogReader
 
enable_tracing() - Method in class HuginReader
 
enable_tracing() - Method in class NeticaReader
 
enabled(EdgeDeletionInferenceEngine) - Method in enum EdgeDeletionInferenceEngine.Command
 
end() - Method in class MinfillEoe
 
endColumn - Variable in class Token
beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.
endDocument() - Method in class AbstractSaxHandler
 
endDocument() - Method in class InstantiationXmlizer
 
endElement(String, String, String) - Method in class XmlElementHandler
 
endElement(String, String, String) - Method in class AbstractSaxHandler
 
endElement(String, String, String) - Method in interface ElementHandler
 
endElement(String, String, String) - Method in class InstantiationXmlizer
 
endElement(String, String, String) - Method in class InstantiationXmlizer.RootCheckHandler
 
endElement(String, String, String) - Method in class InstantiationXmlizer.ValidRootHandler
 
endLine - Variable in class Token
beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.
engine - Variable in class Macros.RankingArgs
 
enlist(Map<CrouchingTiger.DynamatorImpl, Dynamator>) - Method in enum CrouchingTiger.DynamatorImpl
 
ensureAllocation(int) - Method in class DoubleList
 
ensureAllocation(int) - Method in class IntList
 
ensureCapacity(int) - Method in class LearningData
 
ensureCPTProperty(BeliefNetwork) - Static method in class BeliefNetworks
 
ensureCPTProperty(FiniteVariable) - Static method in class BeliefNetworks
 
ensureCPTProperty(Table, FiniteVariable) - Static method in class BeliefNetworks
 
ensureCPTProperty(FiniteVariable, double[], double[]) - Static method in class BeliefNetworks
Assumes that the CPT variable is indexed as the least significant entry.
ensureCPTProperty(FiniteVariable) - Method in class Table
 
ensureCPTProperty(BeliefNetwork) - Static method in class UaiMain
 
ensureCPTProperty(FiniteVariable) - Static method in class UaiMain
 
ensureMapSummations(MapTree.Tree, IntSet) - Method in class MapTree
 
ensureNonsingular() - Method in interface CPTShell
 
ensureNonsingular() - Method in class DecisionShell
 
ensureNonsingular() - Method in class NoisyOrShellHenrion
 
ensureNonsingular() - Method in class NoisyOrShellPearl
 
ensureNonsingular() - Method in class Table
 
ensureNonsingular() - Method in class TableShell
 
ensureNormalized() - Method in class BayesianNetwork
 
ensureRCExists(BeliefNetwork) - Method in class Settings
 
ensureSnapshot() - Method in interface DecisionTree
 
ensureSnapshot() - Method in class DecisionTreeImpl
interface DecisionTree
entriesToMB - Static variable in class RC.RCStats
 
entropy() - Method in class Table
 
entrySet() - Method in class LearningData
 
entrySet() - Method in class IdentityArrayMap
 
EnumProperty - Interface in edu.ucla.util
 
EnumValue - Interface in edu.ucla.util
 
eo() - Method in class EOGenerator.EO
 
eo() - Method in class RCGenerator.EO
 
EO_ConnectBalanced - Static variable in class RC2CreatorEO.Params
 
EO_ConnectContextMax - Static variable in class RC2CreatorEO.Params
 
EO_ConnectContextMin - Static variable in class RC2CreatorEO.Params
 
EO_ConnectRandomly - Static variable in class RC2CreatorEO.Params
 
EO_DEFAULT - Static variable in class RC2CreatorEO.Params
 
EOF - Static variable in interface HuginLogReaderConstants
 
EOF - Static variable in interface HuginReaderConstants
 
EOF - Static variable in interface NeticaReaderConstants
 
EOGenerator - Class in edu.ucla.belief
 
EOGenerator.EO - Class in edu.ucla.belief
 
EOGenerator.EO(int) - Constructor for class EOGenerator.EO
 
EOGenerator.RC - Class in edu.ucla.belief
 
EOGenerator.RC(int) - Constructor for class EOGenerator.RC
 
eoScore() - Method in class EOGenerator.EO
 
eoScore() - Method in class RCGenerator.EO
 
EPSILON - Static variable in class UaiEdgeCutter
 
epsilonContains(double, double) - Method in class Interval
 
epsilonEquals(double, double) - Method in class Optimizer
 
epsilonEquals(double, double, double) - Static method in class Optimizer
 
epsilonEquals(double, double, double) - Static method in class CPTInfo
 
epsilonEquals(Table, double) - Method in class Table
 
equals(Object) - Method in class AbstractInferenceEngine
 
equals(Object) - Method in class BeliefNetworkImpl
 
equals(Object) - Method in class CPTParameter
 
equals(Object) - Method in class Optimizer.EquivalenceKey
 
equals(Object) - Method in class SynchronizedInferenceEngine
 
equals(Object) - Method in class LearningData
 
equals(Object) - Method in class LearningData.Struct
 
equals(Object) - Method in class TableIndex
 
equals(Object) - Method in class VariableInstance
 
equals(Object) - Method in class DirectedEdge
 
equals(Object) - Method in class Edge
 
equals(Object) - Method in class HashDirectedGraph
 
equals(Object) - Method in class HashGraph
 
equals(Object) - Method in class Heap.HeapElement
 
equals(Object) - Method in class IdentityArrayMap
 
equals(Object) - Method in class MappedList
Compares the specified object with this list for equality.
equals(Object) - Method in class FlagProperty.FlagValue
 
equals(Object) - Method in class UserEnumValue
 
equals(Object) - Method in class DoubleList
 
equals(Object) - Method in class IntList
 
equals(Object) - Method in class IntMap
 
equals(Object) - Method in class IntSet
 
equals(Object) - Method in class Pair
Fulfills java.lang.Object.
equals(Object) - Method in class UPair
Fulfills java.lang.Object.
equivalenceHashCode() - Method in class DecisionBackup
 
equivalenceHashCode() - Method in class DecisionInternal
 
equivalenceHashCode() - Method in class DecisionLeaf
 
equivalenceHashCode() - Method in interface DecisionNode
 
equivalenceHashCode() - Method in class DecisionNodeAbstract
 
equivales(DecisionNode) - Method in class DecisionBackup
 
equivales(DecisionNode) - Method in class DecisionInternal
 
equivales(DecisionNode) - Method in class DecisionLeaf
 
equivales(DecisionNode) - Method in interface DecisionNode
 
equivales(DecisionNode) - Method in class DecisionNodeAbstract
 
equivPreProcessVars() - Method in class Pedigree.GeneticNetwork
 
ERGO - Static variable in class FileType
 
error(SAXParseException) - Method in class AbstractSaxHandler
 
error - Variable in class JDKRun.CompiledClassInfo
 
errorMessage(Throwable) - Method in class RunReadSMILE
 
errorMessage(Throwable) - Method in class RunReadHugin
 
errorMessage(Throwable) - Method in class RunReadNetwork
 
errorMessage(Throwable) - Method in class RunReadBIF
 
errorPrintln(String) - Static method in class UaiEdgeCutter
 
errorStream(Throwable) - Method in class RunReadNetwork
 
escape(String, PrintStream) - Method in enum XmlbifWriter.Element
see http://www.w3schools.com/xml/xml_cdata.asp see http://www.w3.org/TR/html4/types.html
escapeQuotes(String) - Method in class AbstractScriptGenius
 
escapeQuotes(String) - Method in interface ScriptGenius
 
Estimate - Interface in edu.ucla.belief.io
moved from NetworkIO 20081110
estimate() - Method in interface Estimate
 
estimate() - Method in class SkimmerEstimator
interface Estimate
estimate() - Method in class SkimmerEstimator
interface Estimate
estimatedTime - Variable in class FileInfo
 
evaluateInstantiation(BeliefNetwork, Map) - Static method in class UaiEdgeCutter
 
event - Variable in class SettingsImpl
 
EVENT_NEW_DTREE - Variable in class Settings
 
EVENT_SETTING_CHANGED - Variable in class BeliefPropagationSettings
 
EVENT_SETTING_CHANGED - Variable in class JoinTreeSettings
 
EVENT_SETTING_CHANGED - Variable in class RCSettings
 
EVENT_SETTING_CHANGED - Variable in class Settings
 
EVENT_SETTING_CHANGED - Variable in class AbstractCodeGenius
 
evidence() - Method in class EvidenceController
Returns the set of variable to value instantiations.
evidence - Variable in class UaiMain
 
evidence - Variable in class Test
 
EvidenceAssertedProperty - Class in edu.ucla.util
 
evidenceChanged(EvidenceChangeEvent) - Method in class EdgeDeletionInferenceEngine
interface EvidenceChangeListener
evidenceChanged(EvidenceChangeEvent) - Method in class Macros.Bridge
interface EvidenceChangeListener
evidenceChanged(EvidenceChangeEvent) - Method in class PropagationInferenceEngineImpl
interface EvidenceChangeListener
evidenceChanged(EvidenceChangeEvent) - Method in class RecoveryInferenceEngine
interface EvidenceChangeListener
evidenceChanged(EvidenceChangeEvent) - Method in interface EvidenceChangeListener
Invoked when there is an evidence change.
evidenceChanged(EvidenceChangeEvent) - Method in class JoinTreeInferenceEngineImpl
For interface EvidenceChangeListener
evidenceChanged(EvidenceChangeEvent) - Method in class RandomInferenceEngine
 
evidenceChanged(EvidenceChangeEvent) - Method in class SynchronizedInferenceEngine
 
evidenceChanged(EvidenceChangeEvent) - Method in class WrapperInferenceEngine
For interface EvidenceChangeListener
evidenceChanged(EvidenceChangeEvent) - Method in class RCInferenceEngine
For interface EvidenceChangeListener.
EvidenceChangeEvent - Class in edu.ucla.belief
The listener interface for evidence changes sent by EvidenceController.
EvidenceChangeEvent(Collection) - Constructor for class EvidenceChangeEvent
 
EvidenceChangeListener - Interface in edu.ucla.belief
The listener interface for evidence changes sent by EvidenceController.
evidenceComplement - Variable in class Test
 
EvidenceController - Class in edu.ucla.belief
 
EvidenceController(BeliefNetwork) - Constructor for class EvidenceController
 
evidenceMPETable(Domain, int, int) - Static method in class MPETable
 
evidenceTable(Domain, int, int) - Static method in class Table
 
evidenceVariables() - Method in class EvidenceController
 
exactConditional(FiniteVariable) - Method in class Macros.Bridge
 
exactConditional(FiniteVariable) - Method in class RecoveryInferenceEngine
 
ExactMap - Class in edu.ucla.belief.inference.map
 
ExactMap() - Constructor for class ExactMap
 
ExactMap.SizedOrder - Class in edu.ucla.belief.inference.map
 
ExactMap.SizedOrder(IntList, double) - Constructor for class ExactMap.SizedOrder
 
examineNetwork(BeliefNetwork, double) - Static method in class UaiEdgeCutter
 
exclude(FiniteVariable) - Static method in class ExcludePolicy
 
excludedIndices(IntSet) - Method in class IntSet
 
ExcludePolicy - Class in edu.ucla.belief.sensitivity
 
exec(Collection, Collection, Set) - Method in class SetOperation
 
exec(String[], File, ScriptGenius, SystemSoftwareSource) - Method in class JDKToolScript
 
exec(String[], File, ScriptGenius, SystemSoftwareSource) - Method in interface Script
 
expand(FiniteVariable) - Method in interface CPTShell
 
expand() - Method in interface DecisionTree
 
expand() - Method in class DecisionTreeImpl
interface DecisionTree
expand(FiniteVariable) - Method in class DecisionShell
 
expand(FiniteVariable) - Method in class NoisyOrShellHenrion
 
expand(FiniteVariable) - Method in class NoisyOrShellPearl
 
expand(FiniteVariable) - Method in class Table
 
expand(FiniteVariable) - Method in class TableScaled
 
expand(FiniteVariable) - Method in class TableShell
 
expand(float, int) - Static method in class CompoundTask
 
expandNoisyOr(List) - Static method in class DSLConstants
Expand noisy-Or weights into CPT.
expandNoisyOr() - Method in interface NoisyOrShell
 
expandNoisyOr() - Method in class NoisyOrShellHenrion
Expand noisy-Or weights into CPT.
expandNoisyOr() - Method in class NoisyOrShellPearl
Expand noisy-Or weights into CPT.
expectedEdges() - Method in interface Estimate
 
expectedEdges() - Method in class SkimmerEstimator
interface Estimate
expectedEdges() - Method in class SkimmerEstimator
interface Estimate
expectedMemoryUsage(Collection) - Static method in class RC2CachingSchemeUtils
Will traverse the RC2Nodes in cachedNodes and count up the size of their expected caches.
expectedNodes() - Method in interface Estimate
 
expectedNodes() - Method in class SkimmerEstimator
interface Estimate
expectedNodes() - Method in class SkimmerEstimator
interface Estimate
expectedNumberOfRCCalls() - Method in class RC.RCStats
 
expectedRCCalls_All(RC2, Collection) - Static method in class RC2Utils
If nodesCached is null, it will look to the nodes themselves to see if memory has been allocated, however if nodesCached is non-null, it will ignore the RC object and determine the number of calls based on nodesCached.
expectedRCCalls_Pe(RC2, Collection) - Static method in class RC2Utils
If nodesCached is null, it will look to the nodes themselves to see if memory has been allocated, however if nodesCached is non-null, it will ignore the RC object and determine the number of calls based on nodesCached.
expectedRCCalls_Pe_inclEvid(RC2, Collection, Collection) - Static method in class RC2Utils
 
expectedTokenSequences - Variable in exception ParseException
Each entry in this array is an array of integers.
expectedValues() - Method in interface Estimate
 
expectedValues() - Method in class SkimmerEstimator
interface Estimate
expectedValues() - Method in class SkimmerEstimator
interface Estimate
extra - Variable in enum Macros.Category
 
extractFileNameFromPath(String) - Static method in class NetworkIO
 
extractMax() - Method in class Heap
Removes the highest priority element and returns it along with its priority.
extractNetworkNameFromPath(String) - Static method in class NetworkIO
 

F

Factorizer - Class in il2.inf.map
 
Factorizer(Domain) - Constructor for class Factorizer
Creates a new instance of Binarizer
Factory - Interface in edu.ucla.belief.decision
 
FAIL - Static variable in class Macros
 
fail(String, Throwable) - Static method in class ScriptTest
 
fail(String, Throwable) - Static method in class Test
 
FALSE - Variable in class FlagProperty
 
family(DirectedGraph, Object) - Static method in class Graphs
Returns the family of vertex.
familyConditional(FiniteVariable) - Method in class EdgeDeletionInferenceEngine
 
familyConditional(FiniteVariable) - Method in class PropagationInferenceEngineImpl
This computes an approximation to familyConditional.
familyConditional(FiniteVariable) - Method in class RecoveryInferenceEngine
 
familyConditional(FiniteVariable) - Method in class JoinTreeInferenceEngineImpl
Returns P(Family(var) | evidence) where Family(var) is the set containing var and its parents.
familyConditional(FiniteVariable) - Method in class RandomInferenceEngine
 
familyConditional(FiniteVariable) - Method in class SynchronizedInferenceEngine
 
familyConditional(FiniteVariable) - Method in class WrapperInferenceEngine
Returns P(Family(var) | evidence) where Family(var) is the set containing var and its parents.
familyConditional(FiniteVariable) - Method in interface InferenceEngine
Returns P(Family(var) | evidence) where Family(var) is the set containing var and its parents.
familyConditional(FiniteVariable) - Method in class RCInferenceEngine
Returns P(Family(var) | evidence) where Family(var) is the set containing var and its parents.
familyJoint(FiniteVariable) - Method in class EdgeDeletionInferenceEngine
 
familyJoint(FiniteVariable) - Method in class PropagationInferenceEngineImpl
 
familyJoint(FiniteVariable) - Method in class RecoveryInferenceEngine
 
familyJoint(FiniteVariable) - Method in class JoinTreeInferenceEngineImpl
Returns P(Family(var),evidence) where Family(var) is the set containing var and its parents.
familyJoint(FiniteVariable) - Method in class JointWrapper
 
familyJoint(FiniteVariable) - Method in class RandomInferenceEngine
 
familyJoint(FiniteVariable) - Method in class SynchronizedInferenceEngine
 
familyJoint(FiniteVariable) - Method in class WrapperInferenceEngine
Returns P(Family(var),evidence) where Family(var) is the set containing var and its parents.
familyJoint(FiniteVariable) - Method in interface InferenceEngine
Returns P(Family(var),evidence) where Family(var) is the set containing var and its parents.
familyJoint(FiniteVariable) - Method in class RCDgraph
 
familyJoint(FiniteVariable) - Method in class RCInferenceEngine
Returns P(Family(var),evidence) where Family(var) is the set containing var and its parents.
familyOrdering() - Method in class Pedigree.GeneticNetwork
 
familyPartial(FiniteVariable) - Method in class PropagationInferenceEngineImpl
interface PartialDerivativeEngine
familyPartial(FiniteVariable) - Method in class JoinTreeInferenceEngineImpl
Returns the partial derivatives of the probability function with respect to the family table of var.
familyPartial(FiniteVariable) - Method in class PartialDerivativeWrapperEngine
 
familyPartial(FiniteVariable) - Method in class RandomInferenceEngine
 
familyPartial(FiniteVariable) - Method in class SynchronizedInferenceEngine.SynchronizedPartialDerivativeEngine
 
familyPartial(FiniteVariable) - Method in interface PartialDerivativeEngine
Returns the partial derivatives of the probability function with respect to the family table of var.
fgPairs() - Method in class MessagePassingScheduler
 
FIELDPOSITION - Static variable in class NetworkIO
 
file - Variable in class KBMap.Mapping
 
fileClassFileNames - Variable in class Test
 
FileInfo - Class in edu.ucla.belief.recursiveconditioning
 
FileInfo() - Constructor for class FileInfo
 
fileJavaFileNames - Variable in class Test
 
FileType - Class in edu.ucla.belief.io
represents a type of Bayesian network file, e.g.
fill(double) - Method in class Table
 
fill(Map, int[]) - Method in class TableIndex
 
fill(double) - Method in class TableScaled
 
fillNeighborMap(int[][], int[], int, boolean[], boolean) - Static method in class Util
Fills the given neighbor map for the given node.
fillNeighborMap(int[][], int[], int, boolean[][], boolean) - Static method in class Util
Fills the given map with the results of calling fillNeigbhorMap on each neighbor of the given node.
Filter - Interface in edu.ucla.structure
grep filter moved from FiniteVariable 20081110
find(int) - Method in class UnionFind
Returns the set that element x belongs to.
findAllNotRootedAt(DecisionNode, Set, Set) - Static method in class DecisionNodeAbstract
 
findAncestorsNotRootedAt(DecisionNode, Set, Set) - Method in class DecisionNodeAbstract
 
findBurntBridges(BeliefNetwork) - Static method in class Macros
http://en.wikipedia.org/wiki/Bridge_(graph_theory)
findCycle(Object, Object, LinkedList, Set) - Method in class RecursiveDepthFirstIterator
 
findEdgesToDropTable(Index, int, List, List, List) - Static method in class UaiEdgeCutter
 
findEdgesToDropTable(List, int, List, List, List) - Static method in class UaiEdgeCutter
 
findEdgesToDropTable(int, List, List, List) - Method in class UaiEdgeCutter.MyIndex
 
findFixedPoint(List, List, List, int) - Method in class ApproxEngine
 
findHealthVariables() - Method in class VEVariance
 
findTargetVariable() - Method in class VEVariance
 
findURL(String, String) - Static method in class NetworkIO
 
findVariables(EnumProperty, EnumValue) - Method in interface BeliefNetwork
 
findVariables(EnumProperty, EnumValue) - Method in class BeliefNetworkImpl
 
findVariablesForType(Collection, DSLNodeType, Collection) - Static method in class FiniteVariableImpl
moved from DSLNodeType 20081110
finished - Variable in class MapSearch.MapInfo
 
finishedReading() - Method in class RunReadSMILE
 
finishedReading() - Method in class RunReadHugin
 
finishedReading() - Method in class RunReadNetwork
 
finishedReading() - Method in class RunReadBIF
 
finishedValue - Variable in class Loci.Footer.Linkmap
 
finishedValue - Variable in class Loci.Footer.Mlink
 
FiniteVariable - Interface in edu.ucla.belief
A class for representing finite variables.
FiniteVariableImpl - Class in edu.ucla.belief
A class for representing finite variables.
FiniteVariableImpl(String, Object[]) - Constructor for class FiniteVariableImpl
Creates a new Finite variable.
FiniteVariableImpl(String, List) - Constructor for class FiniteVariableImpl
 
FiniteVariableImpl(FiniteVariable) - Constructor for class FiniteVariableImpl
 
FiniteVariableImpl(FiniteVariable, DSLNodeType, CPTShell) - Constructor for class FiniteVariableImpl
 
fireAudit(Variable, Variable, Collection, BeliefNetwork.Auditor.Deed) - Method in interface BeliefNetwork
 
fireAudit(Variable, Variable, Collection, BeliefNetwork.Auditor.Deed) - Method in class BeliefNetworkImpl
 
fireNewDtree() - Method in class Settings
interface ChangeBroadcaster
fireSettingChanged() - Method in class BeliefPropagationSettings
interface ChangeBroadcaster
fireSettingChanged() - Method in class JoinTreeSettings
interface ChangeBroadcaster
fireSettingChanged() - Method in class RCSettings
interface ChangeBroadcaster
fireSettingChanged() - Method in class Settings
interface ChangeBroadcaster
fireSettingChanged() - Method in interface ChangeBroadcaster
 
fireSettingChanged() - Method in class AbstractCodeGenius
interface ChangeBroadcaster
fireSettingChanged() - Method in class SettingsImpl
interface ChangeBroadcaster
firstK(Macros.RankingArgs) - Static method in class Macros
 
fixed - Variable in class InstanceIterator.IterationRec
 
fixPoint(Map) - Static method in class Maps
 
fixPropertySuperintendent(PropertySuperintendent) - Method in class Dynamator
 
FLAG_DEBUG - Static variable in class BeliefNetworkImpl
 
FLAG_DEBUG - Static variable in class EvidenceController
 
FLAG_DEBUG - Static variable in class JTtoET
 
FLAG_DEBUG - Static variable in class GenieNetImpl
 
FLAG_DEBUG - Static variable in class HuginLogReader
 
FLAG_DEBUG - Static variable in class HuginNetImpl
 
FLAG_DEBUG - Static variable in class Computation
 
FLAG_DEBUG - Static variable in class Table
 
FLAG_DEBUG - Static variable in class Trees
 
FLAG_DEBUG_DISPLAY_NAMES - Static variable in class Dynamator
 
FLAG_DEBUG_INSERT_STATE - Static variable in class TableShell
 
FLAG_DEBUG_OVERRIDE - Static variable in class Interruptable
 
FLAG_DEBUG_STATE_MODIFICATION - Static variable in class Table
 
FLAG_DEBUG_VERBOSE - Static variable in class JoinTreeSettings
 
FLAG_DEBUG_VERBOSE - Static variable in class RCSettings
 
FLAG_DEBUG_VERBOSE - Static variable in class Settings
 
FLAG_DEBUG_VERBOSE_CLONE - Static variable in class RCSettings
 
FLAG_DEBUG_VERBOSE_II - Static variable in class RCSettings
 
FLAG_DEBUG_VERBOSE_III - Static variable in class RCSettings
 
FLAG_DEBUG_VERBOSE_INFO - Static variable in class RCSettings
 
FLAG_ENABLE_DECISIONTREE - Static variable in class DSLNodeType
 
FLAG_ENABLE_LOCK_BY_PARAMETER - Static variable in class ExcludePolicy
 
FLAG_HMETIS_LOADED - Static variable in class Settings
 
FLAG_MASSAGE_SUGGESTED - Static variable in class Optimizer
 
FLAG_REDUCE_CASES - Static variable in class LearningData
 
FLAG_VALIDATE - Static variable in class Xmlizer
 
FLAG_VERBOSE - Static variable in class HuginCopier
 
FLAG_VERBOSE - Static variable in class Simulator
 
FLAG_VERBOSE_OVERRIDE - Static variable in class Interruptable
 
flagIsBoundary - Variable in class Optimizer.Unsortable
 
FlagProperty - Class in edu.ucla.util
 
FlagProperty() - Constructor for class FlagProperty
 
FlagProperty.FlagValue - Class in edu.ucla.util
 
FlagProperty.FlagValue(boolean) - Constructor for class FlagProperty.FlagValue
 
flatten(List) - Static method in class ListConverter
 
flatten(String[]) - Static method in class JDKToolScript
 
flavor - Variable in enum Algorithm
join tree flavor
Flavor - Enum in il2.inf.jointree
Join tree algorithm "flavor", ie distinctive implementation.
flipChange(IntSet) - Method in class InstanceIterator
 
flipChange(IntList) - Method in class InstanceIterator
 
flipChange - Variable in class InstanceIterator.IterationRec
 
flipChange(Index) - Method in class Index
 
flipPoints() - Method in class MPEAlgorithm
 
flipsOutput(double[], double[]) - Static method in class ApproxEngine
 
FLOAT_PIXELS_PER_INCH - Static variable in class GraphvizIO
 
flushCaches() - Method in class RC2
 
FMT - Static variable in class Macros
 
FMT1 - Static variable in class Macros
 
footer() - Method in class Loci
 
forAll(EnumProperty, EnumValue) - Method in interface BeliefNetwork
 
forAll(EnumProperty, EnumValue) - Method in class BeliefNetworkImpl
 
forAllDSLNodeTypes(FiniteVariable) - Method in class CPTShells
 
forAllFiniteVariables(Iterator) - Method in class CPTShells
 
forAllFiniteVariables(Collection) - Method in class CPTShells
 
forArray(Object) - Static method in enum Macros.Doubler
Choose the appropriate Doubler for the specified array.
forClass(Class<? extends JointEngine>) - Static method in enum Algorithm
if you've got a JointEngine Class but you need an Algorithm
forClass(Class<? extends JoinTreeAlgorithm>, BayesianNetwork, EliminationOrders.JT) - Static method in enum Flavor
convenience factory method
forestBlock(int) - Method in class HuginLogReader
 
forget(Variable) - Method in interface CPTShell
 
forget(Variable) - Method in class DecisionShell
 
forget(Variable) - Method in class NoisyOrShellHenrion
 
forget(Variable) - Method in class NoisyOrShellPearl
 
forget(Variable) - Method in class Table
 
forget(Set) - Method in class Table
 
forget(Set) - Method in class TableIndex
Returns a new index formed by removing any dimensions whose associated with the variables contained in variables.
forget(Set) - Method in class TableScaled
 
forget(Variable) - Method in class TableShell
 
forget(IntSet) - Method in class Table
 
forget(int) - Method in class Table
 
forgetIndex(int) - Method in class UaiEdgeCutter.MyIndex
 
forgetIndex(int) - Method in class Index
 
forgetIndex(IntSet) - Method in class Index
 
forgetIndex(Index) - Method in class Index
 
forHandle(int) - Method in class DSLSubmodelFactory
 
forID(String) - Method in interface BeliefNetwork
Returns the variable with the name supplied.
forID(String) - Method in class BeliefNetworkImpl
Returns the variable with the id supplied
forID(String) - Static method in class CreationMethod
 
forID(String) - Static method in class RCComparator
 
forID(String) - Static method in class VariableImpl
 
forIndex(int) - Static method in class DiagnosisType
 
forIndex(int) - Static method in class DSLNodeType
 
forIndex(int) - Method in class CSITypeProperty
 
forIndex(int) - Method in interface EnumProperty
 
forIndex(int) - Method in class FlagProperty
 
forIndex(int) - Method in class InOutDegreeProperty
 
forIndex(int) - Method in class UserEnumProperty
 
format(Date) - Method in class EdgeDeletionInferenceEngine.DateFormatFilename
 
format(Date, Appendable) - Method in class EdgeDeletionInferenceEngine.DateFormatFilename
 
format(Date) - Method in class AbstractStringifier.DateFormatFilename
 
format(Date, StringBuffer) - Method in class AbstractStringifier.DateFormatFilename
 
format(double, NumberFormat) - Static method in class DataSetStatistic
 
FORMAT_PERCENT - Static variable in class Stats
 
FORMAT_PROFILE_PERCENT - Static variable in class NetworkIO
 
FORMAT_PROFILE_TIME - Static variable in class NetworkIO
 
formatMemoryNumbers(Computation, RC) - Static method in class Settings
 
formatMemoryNumbersConcise(Computation, RC) - Static method in class Settings
 
formatPercent(float, DecimalFormat) - Static method in class NetworkIO
 
formatTime(long) - Static method in class NetworkIO
 
formSystemCall(String[]) - Method in class AbstractScriptGenius
 
formSystemCall(String[]) - Method in class PerlScriptGenius
 
formSystemCall(String[]) - Method in interface ScriptGenius
 
forName(String) - Static method in class CreationMethod
 
forSerial(Attributes) - Method in class Builder
 
forSink(FiniteVariable, BeliefNetwork) - Method in class Macros.RecoveryInfo
 
forSmileID(int) - Static method in class DiagnosisType
 
forSource(FiniteVariable, BeliefNetwork) - Method in class Macros.RecoveryInfo
 
forString(String) - Static method in class DiagnosisType
 
forString(String) - Static method in class DSLNodeType
 
forString(String) - Static method in class HuginFileVersion
 
forString(String) - Static method in class ExcludePolicy
 
forString(String) - Method in class CSITypeProperty
 
forString(String) - Method in interface EnumProperty
 
forString(String) - Method in class FlagProperty
 
forString(String) - Method in class InOutDegreeProperty
 
forString(String) - Method in class UserEnumProperty
 
forToken(String) - Method in class CPTImport
 
forVariable(int) - Method in class BayesianNetwork
 
foundTime - Variable in class MapSearch.MapResult
 
fraction - Variable in class Stats.Stat
 
FULL_CLASS - Variable in class OptionBreadth
 
fullCaching() - Method in class RCInfo
 
fullCaching() - Method in class RC2.StoredComputationStats
 
fullCaching() - Method in class CachingScheme
 
fullCaching() - Method in class RC
 
fullCaching() - Method in class RCEngine
 
function() - Method in class HuginReader
 
Function - Interface in edu.ucla.util
 
fvToColOfClauses() - Method in class MultiValuedCNF
 

G

geneFreq(int, int) - Method in class Pedigree.PseudoLoci
 
generalizes(FileType) - Method in class FileType
alias of broadens()
generate(int, int) - Static method in class RandomNetworks
 
generateConsistentAssignment() - Method in class BayesianNetwork
 
generateDtree(BeliefNetwork) - Method in class Settings
 
generateEO(BeliefNetwork, String, String, boolean, int) - Static method in class EOGenerator
 
generateEO(BeliefNetwork, String, String, boolean, Set) - Static method in class RCGenerator
 
generateGraph() - Method in class BayesianNetwork
 
generateInfo(BeliefNetwork) - Method in class RCSettings
 
generateInfoOrDie(BeliefNetwork) - Method in class RCSettings
 
generateNoisyOrSuggestions(NoisyOrShell, SensitivityTable) - Static method in class SingleParamSuggestion
 
generateNumParents(MappedList) - Method in class RC
Will not change nds if it is non-null & non-empty
generateParseException() - Method in class HuginLogReader
 
generateParseException() - Method in class HuginReader
 
generateParseException() - Method in class NeticaReader
 
generateRC(BeliefNetwork, String, String, boolean, int) - Static method in class EOGenerator
 
generateRC(BeliefNetwork, String, String, boolean, Set) - Static method in class RCGenerator
 
generateRC(BeliefNetwork, String, String, boolean, Set, Set[][]) - Static method in class RCGenerator
 
generateSchedule(DirectedGraph) - Method in class MessagePassingScheduler
 
generateSingleParamSuggestions() - Method in class SensitivityReport
 
generateSingleParamSuggestions() - Method in class SensMPEReport
 
generateTableSuggestions(TableShell, SensitivityTable) - Static method in class SingleParamSuggestion
 
generic(Attributes) - Method in class Builder
 
GenieNet - Interface in edu.ucla.belief.io.dsl
 
GenieNetImpl - Class in edu.ucla.belief.io.dsl
 
GenieNetImpl() - Constructor for class GenieNetImpl
 
GenieNetImpl(Map) - Constructor for class GenieNetImpl
 
get(PropertyKey) - Method in enum EdgeDeletionBeliefPropagationSetting
 
get(EdgeDeletionInferenceEngine) - Method in enum EdgeDeletionInferenceEngine.Attribute
 
get(Object, int) - Method in enum Macros.Doubler
Convert the element of the specified array at the specified index to a primitive double value.
get(PropertyKey) - Method in enum RecoverySetting
 
get(int) - Method in class Optimizer.EquivalenceKey
 
get(Object) - Method in class LearningData
 
get(Object) - Method in class IdentityArrayMap
 
get(int) - Method in class MappedList
Returns the element at the specified position in this list.
get(PropertyKey) - Method in interface Setting
 
get(E) - Method in interface Setting.Settings
 
get(E, PropertyKey) - Method in interface Setting.Settings
 
get(E) - Method in class SettingsImpl
 
get(E, PropertyKey) - Method in class SettingsImpl
 
get(int) - Method in class WeakLinkedList
Returns the element at the specified position in this list.
get(Algorithm.Key) - Method in enum Algorithm.Setting
 
get(int) - Method in class DoubleList
 
get(int) - Method in class DoubleMap
 
get(int, double) - Method in class DoubleMap
 
get(int) - Method in class IntList
 
get(int) - Method in class IntMap
 
get(int, int) - Method in class IntMap
 
get(int) - Method in class IntSet
 
getAbsoluteChange() - Method in interface SensitivitySuggestion
 
getAbsoluteChange() - Method in class SingleCPTSuggestion
 
getAbsoluteChange() - Method in class SingleParamSuggestion
 
getAbsoluteLowerBound() - Method in class Interval
 
getAbsoluteLowerBound() - Method in class ProbabilityInterval
 
getAbsoluteUpperBound() - Method in class Interval
 
getAbsoluteUpperBound() - Method in class ProbabilityInterval
 
getActualMemoryProportion() - Method in class RCSettings
 
getAll() - Method in class Bundle
 
getAllEdges(BayesianNetwork) - Static method in class EDEdgeDeleter
returns an int[numEdges][2] of all edges.
getAllEdges(Table[]) - Static method in class EDEdgeDeleter
returns an int[numEdges][2] of all edges.
getAllSubmodels() - Method in class DSLSubmodelFactory
 
getAlphas(FiniteVariable) - Method in class SensitivityEquation
 
getAncestors(Set, Classifier) - Method in interface DecisionNode
 
getAncestors(Set, Classifier) - Method in class DecisionNodeAbstract
 
getAnyRoot() - Method in class RC
 
getAnyRoot() - Method in class RCDgraph
 
getAnyRoot() - Method in class RCDtree
 
getApproximator() - Method in class SearchMethod
 
getArguments() - Method in class LinearFunction
 
getArray() - Static method in class CreationMethod
 
getArrayCanonical() - Static method in class FileType
 
getArrayInterconvertibleTypes(DSLNodeType) - Static method in class DSLNodeType
 
getArraySMILE() - Static method in class FileType
 
getAssignments() - Method in class HuginLogReader
 
getAutoCPTInvalidation() - Method in interface BeliefNetwork
 
getAutoCPTInvalidation() - Method in class BeliefNetworkImpl
 
getBalanceFactor() - Method in interface CreationMethod.Settings
 
getBalanceFactor() - Method in class Settings
 
getBayesianNetwork() - Method in class ModelCoder
 
getBayesianNetwork() - Method in class Converter
 
getBeginColumn() - Method in class SimpleCharStream
 
getBeginLine() - Method in class SimpleCharStream
 
getBeliefNetwork() - Method in class EdgeDeletionInferenceEngine
 
getBeliefNetwork() - Method in class RecoveryInferenceEngine
 
getBeliefNetwork() - Method in class XmlDocumentHandler
 
getBeliefNetwork() - Method in class EvidenceController
 
getBeliefNetwork() - Method in class BeliefCompilation
 
getBeliefNetwork() - Method in class WrapperInferenceEngine
 
getBeliefNetwork() - Method in class SMILEReader
 
getBeliefNetwork() - Method in class JoinTree
 
getBeliefNetwork() - Method in class ModelCoder
 
getBeliefNetwork() - Method in class Converter
 
getBestMatch(Collection, Pattern) - Static method in class ParanoidFileFinder
 
getBucket(int) - Method in class Bucketer
 
getBucketSize(Collection, Domain) - Static method in class UaiEdgeCutter
 
getBundle() - Method in class Settings
 
getCacheFactor() - Method in class CachingScheme
 
getCacheFactor() - Method in class RCNode
 
getCacheFactor() - Method in class RCNodeInternalBinaryCache
 
getCacheHits() - Method in class PropagationInferenceEngineImpl
 
getCacheHits() - Method in class JoinTreeInferenceEngineImpl
 
getCachingScheme(RC2) - Method in class RC2CachingScheme_Collection
 
getCachingScheme(RC2) - Method in class RC2CachingScheme_DFBnB
 
getCachingScheme(RC2) - Method in class RC2CachingScheme_Full
 
getCachingScheme(RC2) - Method in class RC2CachingScheme_Greedy
 
getCachingScheme(RC2) - Method in class RC2CachingScheme_None
 
getCachingScheme(RC2) - Method in interface RC2.CachingScheme
 
getCachingScheme() - Method in class Bundle
 
getCachingScheme() - Method in class Settings
 
getCanonicalDynamator() - Method in class ApproxEngineGenerator
 
getCanonicalDynamator() - Method in class PropagationEngineGenerator
 
getCanonicalDynamator() - Method in class Dynamator
 
getCanonicalDynamator() - Method in class DefaultGenerator
 
getCanonicalDynamator() - Method in class RandomEngineGenerator
 
getCanonicalDynamator() - Method in class RCEngineGenerator
 
getCanonicalDynamator() - Method in class RCEngineGenerator
 
getCaseSensitive() - Method in class InflibFileFilter
 
getCFMap() - Method in class RC
 
getChangingS1() - Method in class Pedigree.PseudoLoci
 
getChangingS2() - Method in class Pedigree.PseudoLoci
 
getChangingVarAL(FiniteVariable) - Method in class Pedigree.GeneticNetwork
 
getCharactersHandler() - Method in class AbstractSaxHandler
 
getChildCounts() - Method in class HuginLogReader
 
getChildDecisionNodes() - Method in class DecisionInternal
 
getChildDecisionNodes() - Method in interface DecisionNode
 
getChildDecisionNodes() - Method in class DecisionNodeAbstract
 
getChildList() - Method in class ApproxReport
 
getChildSubmodels() - Method in class DSLSubmodel
 
getChromoOrd_ChangingS1() - Method in class Loci
Returns the 0 based Chromosome Order of the recom locus where the cpt of s will change (e.g.
getChromoOrd_ChangingS2() - Method in class Loci
Returns the 0 based Chromosome Order of the recom locus where the cpt of s will change (e.g.
getClassDependencies() - Method in class ApproxEngineGenerator
 
getClassDependencies() - Method in class EdgeDeletionEngineGenerator
 
getClassDependencies() - Method in class PropagationEngineGenerator
 
getClassDependencies() - Method in class RecoveryEngineGenerator
 
getClassDependencies() - Method in class Dynamator
 
getClassDependencies() - Method in class HuginEngineGenerator
 
getClassDependencies() - Method in class JEngineGenerator
 
getClassDependencies() - Method in class RandomEngineGenerator
 
getClassDependencies() - Method in class RCEngineGenerator
 
getClassDependencies() - Method in class SSEngineGenerator
 
getClassDependencies() - Method in class ZCEngineGenerator
 
getClassDependencies() - Method in class RCEngineGenerator
 
getClassName() - Method in class ClassModule
 
getClasspath(ClassModule) - Method in class GuessingSource
 
getClasspath(ClassModule) - Method in interface SystemSoftwareSource
 
getCliques() - Method in class HuginLogReader
 
getCloneCPT(int) - Method in class EDAlgorithm
Given edge index i, returns CPT of clone variable.
getCloneEdgeTable(int) - Method in class EDNetwork
functions for parametrizing the edges of a network
getCloneTable(FiniteVariable) - Method in class Macros.Bridge
 
getCluster() - Method in class DtreeNode
The Cluster is defined as: (1) vars(t) if it is a leaf node, or (2) cutset (union) context otherwise.
getClusterSize() - Method in class Dtree
 
getClusterStats() - Method in class JointWrapper
 
getClusterStats() - Method in class WrapperInferenceEngine
 
getClusterStats() - Method in class JoinTree
 
getClusterStats() - Method in class EDAlgorithm
 
getClusterStats() - Method in interface JointEngine
 
getClusterStats() - Method in class JoinTreeAlgorithm
 
getClusterStats() - Method in class RCEngine
 
getClusterStats() - Method in class EliminationOrders.JT
 
getClusterStats() - Method in interface JoinTreeStats.StatsSource
 
getCoefficients() - Method in class LinearFunction
 
getColor() - Method in class CPTInfo.Parameter
 
getColumn() - Method in class SimpleCharStream
Deprecated.  
getColumns() - Method in class CPTImport
 
getCommand(ScriptGenius, SystemSoftwareSource) - Method in class JDKToolScript
 
getCommand() - Method in class ScriptExecution
 
getCommandArray(ScriptGenius, SystemSoftwareSource) - Method in class JDKCompile
 
getCommandArray(ScriptGenius, SystemSoftwareSource) - Method in class JDKRun
 
getCommandArray(ScriptGenius, SystemSoftwareSource) - Method in class JDKToolScript
 
getCommandArray() - Method in class ScriptExecution
 
getCommentToken() - Method in class BatchScriptGenius
 
getCommentToken() - Method in class BourneScriptGenius
 
getCommentToken() - Method in class CShellScriptGenius
 
getCommentToken() - Method in class PerlScriptGenius
 
getCommentToken() - Method in interface ScriptGenius
 
getCompatibleEntry(int[]) - Method in class Table
 
getCompilationpriority() - Static method in class Dynamator
 
getCompilationTime() - Method in class JointWrapper
 
getCompilationTime() - Method in class RCInfo
 
getCompilationTime() - Method in class RCWrapper
 
getCompilationTime() - Method in class WrapperInferenceEngine
 
getCompilationTime() - Method in class BeliefPropagation
 
getCompilationTime() - Method in class EDAlgorithm
 
getCompilationTime() - Method in interface JointEngine
 
getCompilationTime() - Method in class JoinTreeAlgorithm
 
getCompilationTime() - Method in class RCEngine
 
getComplex1InputOrd(int) - Method in class Pedigree.PseudoLoci
 
getComplexPenetrance(int, String, int, int, int) - Method in class Pedigree.PseudoLoci
 
getComputationTotalTime_ms() - Method in class RC2
 
getConditional(FiniteVariable) - Method in class ApproxReport
 
getConditionalMap() - Method in class Snapshot
 
getCondKLBound() - Method in class ApproxReport
 
getCondKLTotal() - Method in class ApproxReport
 
getCondProbE() - Method in class ApproxReport
 
getConstant() - Method in class LinearFunction
 
getConstrainedOrder(IntSet, int) - Method in class VEVariance
 
getConstructionTime() - Method in class EDNetwork
 
getContext() - Method in class DtreeNode
The context is defined as vars (intersect) acutset.
getContextSize() - Method in class Dtree
 
getControlInferenceEngine() - Method in class ApproxEngine
 
getControlPanel() - Method in class AbstractInferenceEngine
 
getControlPanel() - Method in class SynchronizedInferenceEngine
 
getControlPanel() - Method in interface InferenceEngine
 
getConvergenceThreshold() - Method in class BeliefPropagationSettings
 
getConvertedInstatiation(Factorizer, Converter) - Method in class MapSearch.MapResult
 
getConvertedInstatiation() - Method in class MapSearch.MapResult
 
getConverter() - Method in class JointWrapper
 
getConverter() - Method in class ModelCoder
 
getConverter() - Method in exception ConversionException
 
getConvThreshold() - Method in class EDAlgorithm
 
getCopier() - Method in interface BeliefNetwork
 
getCopier() - Method in class BeliefNetworkImpl
 
getCopier() - Method in class HuginNetImpl
 
getCorrelationTime() - Method in class EDAlgorithm
 
getCorrespondingChanges() - Method in class SingleParamSuggestion
 
getCost() - Method in class SkimmerEstimator
 
getCost() - Method in class SkimmerEstimator
 
getCountNodeBlocks() - Method in class SkimmerEstimator
 
getCountPotentialBlocks() - Method in class SkimmerEstimator
 
getCountPotentials() - Method in class SkimmerEstimator
 
getCountProbabilityValues() - Method in class SkimmerEstimator
 
getCountProbabilityValues() - Method in class SkimmerEstimator
 
getCountVariables() - Method in class SkimmerEstimator
 
getCP(int) - Method in interface CPTShell
 
getCP(int[]) - Method in interface CPTShell
 
getCP(Object[]) - Method in interface CPTShell
 
getCP(Map) - Method in interface CPTShell
 
getCP(Object[], Object) - Method in interface CPTShell
 
getCP(int) - Method in class DecisionShell
 
getCP(int[]) - Method in class DecisionShell
 
getCP(Object[]) - Method in class DecisionShell
 
getCP(Map) - Method in class DecisionShell
 
getCP(Object[], Object) - Method in class DecisionShell
 
getCP(int) - Method in interface CPTInfo.ReadableWritableTable
 
getCP(int) - Method in class NoisyOrShellHenrion
 
getCP(int[]) - Method in class NoisyOrShellHenrion
 
getCP(Object[]) - Method in class NoisyOrShellHenrion
 
getCP(Map) - Method in class NoisyOrShellHenrion
 
getCP(Object[], Object) - Method in class NoisyOrShellHenrion
 
getCP(int) - Method in class NoisyOrShellPearl
 
getCP(int[]) - Method in class NoisyOrShellPearl
 
getCP(Object[]) - Method in class NoisyOrShellPearl
 
getCP(Map) - Method in class NoisyOrShellPearl
 
getCP(Object[], Object) - Method in class NoisyOrShellPearl
 
getCP(int) - Method in class Table
 
getCP(int) - Method in class TableScaled
 
getCP(int) - Method in class TableShell
 
getCP(int[]) - Method in class TableShell
 
getCP(Object[]) - Method in class TableShell
 
getCP(Map) - Method in class TableShell
 
getCP(Object[], Object) - Method in class TableShell
 
getCPD(int, int[]) - Method in class NoisyOrShellHenrion
 
getCPD(int, int[]) - Method in class NoisyOrShellPearl
 
getCPLength() - Method in interface CPTInfo.ReadableWritableTable
 
getCPLength() - Method in class Table
 
getCPScaled(int) - Method in interface CPTShell
 
getCPScaled(int[]) - Method in interface CPTShell
 
getCPScaled(int) - Method in class DecisionShell
 
getCPScaled(int[]) - Method in class DecisionShell
 
getCPScaled(int) - Method in class NoisyOrShellHenrion
 
getCPScaled(int[]) - Method in class NoisyOrShellHenrion
 
getCPScaled(int) - Method in class NoisyOrShellPearl
 
getCPScaled(int[]) - Method in class NoisyOrShellPearl
 
getCPScaled(int) - Method in class Table
 
getCPScaled(int[]) - Method in class Table
 
getCPScaled(int) - Method in class TableScaled
 
getCPScaled(int[]) - Method in class TableScaled
 
getCPScaled(int) - Method in class TableShell
 
getCPScaled(int[]) - Method in class TableShell
 
getCPT() - Method in interface CPTShell
 
getCPT() - Method in class DecisionShell
 
getCPT() - Method in class NoisyOrShellHenrion
 
getCPT() - Method in class NoisyOrShellPearl
 
getCPT() - Method in class TableShell
 
getCPTMap() - Method in class Snapshot
 
getCPTParameter(int) - Method in interface CPTShell
 
getCPTParameter(int[]) - Method in interface CPTShell
 
getCPTParameter(int) - Method in class DecisionShell
 
getCPTParameter(int[]) - Method in class DecisionShell
 
getCPTParameter(int) - Method in class NoisyOrShellHenrion
 
getCPTParameter(int[]) - Method in class NoisyOrShellHenrion
 
getCPTParameter(int) - Method in class NoisyOrShellPearl
 
getCPTParameter(int[]) - Method in class NoisyOrShellPearl
 
getCPTParameter() - Method in class SingleParamSuggestion
 
getCPTParameter(int) - Method in class TableShell
 
getCPTParameter(int[]) - Method in class TableShell
 
getCPTParameters() - Method in interface CPTShell
 
getCPTParameters() - Method in class DecisionShell
 
getCPTParameters() - Method in class NoisyOrShellHenrion
 
getCPTParameters() - Method in class NoisyOrShellPearl
 
getCPTParameters() - Method in class TableShell
 
getCPTPartialMap() - Method in class Snapshot
 
getCPTShell(FiniteVariable) - Method in class ApproxEngine
interface QuantitativeDependencyHandler
getCPTShell(FiniteVariable) - Method in class ApproxReport
 
getCPTShell() - Method in class CPTParameter
 
getCPTShell() - Method in interface FiniteVariable
 
getCPTShell(DSLNodeType) - Method in interface FiniteVariable
 
getCPTShell() - Method in class FiniteVariableImpl
 
getCPTShell(DSLNodeType) - Method in class FiniteVariableImpl
 
getCPTShell(FiniteVariable) - Method in interface QuantitativeDependencyHandler
 
getCPTShell() - Method in class SensitivityTable
 
getCurrentParent() - Method in class Interruptable
 
getCurrentRecord() - Method in class LearningData
 
getCurrentThreadCpuTime() - Static method in class JVMProfiler
Will return the CPU Time of the thread or else will return 0 if the profiler cannot be interfaced with.
getCurrentThreadCpuTime() - Static method in class JVMTI
Call this method from a user application to report running times to a user.
getCurrentThreadCpuTime_native() - Static method in class JVMProfiler
This will throw an unsatisfied link exception if loaded is not true.
getCurrentThreadCpuTimeMS() - Static method in class JVMProfiler
Will return the CPU Time of the thread or else will return 0 if the profiler cannot be interfaced with.
getCurrentThreadCpuTimeUnsafe() - Static method in class JVMTI
WARNING: Call this method from test code only.
getCurrentValue() - Method in interface SensitivitySuggestion
 
getCurrentValue() - Method in class SingleCPTSuggestion
 
getCurrentValue() - Method in class SingleParamSuggestion
 
getCurrentWeight() - Method in class LearningData
 
getCutset() - Method in class DtreeNode
The cutset is defined as: (1) varsL (intersect) varsR - acutset if it is a leaf node, or (2) empty Collection otherwise.
getCutset(HashSet) - Method in class RCNodeInternalBinaryCache
 
getCutsetSize() - Method in class Dtree
 
getCutsetVars(Collection) - Method in class RC2NodeInternal
 
getCycle() - Method in class RecursiveDepthFirstIterator
 
getCycle(Object) - Method in class RecursiveDepthFirstIterator
 
getCycleMembers() - Method in class RecursiveDepthFirstIterator
 
getDebugLabel() - Method in class UserEnumProperty
 
getDebugLabel(UserEnumProperty) - Static method in class UserEnumProperty
 
getDebugVariable() - Method in class LearningData
 
getDebugVariable() - Method in class LearningDataOld
 
getDecisionTree() - Method in class DecisionShell
 
getDeepVariables(DSLSubmodel) - Method in interface GenieNet
 
getDeepVariables(DSLSubmodel) - Method in class GenieNetImpl
The first call is expensive.
getDefault() - Static method in class MessagePassingScheduler
 
getDefault() - Method in class DecisionTreeImpl
interface Factory
getDefault() - Method in interface Factory
 
getDefault() - Static method in class EliminationHeuristic
 
getDefault() - Static method in class InitializationMethod
 
getDefault() - Method in class MapProperty
 
getDefault() - Static method in class SearchMethod
 
getDefault() - Static method in class RCComparator
 
getDefault() - Method in class AbstractCodeOption
 
getDefault() - Method in interface CodeOption
 
getDefault() - Method in class ModelCoder.LibraryVersionOption
 
getDefault() - Method in class OptionBreadth
 
getDefault() - Method in class ProbabilityQueryCoder.MarginalScopeOption
 
getDefault() - Method in class CSITypeProperty
 
getDefault() - Method in interface EnumProperty
 
getDefault() - Method in class EvidenceAssertedProperty
 
getDefault() - Method in class HiddenProperty
 
getDefault() - Method in class ImpactProperty
 
getDefault() - Method in class InferenceValidProperty
 
getDefault() - Method in class InOutDegreeProperty
 
getDefault() - Method in class QueryParticipantProperty
 
getDefault() - Method in class UserEnumProperty
 
getDefaultFileName() - Method in class JDKCompile
 
getDefaultFileName() - Method in class JDKRun
 
getDefaultFileName() - Method in interface Script
 
getDefaultFlag() - Method in class AbstractCodeOption
 
getDefaultFlag() - Method in interface CodeOption
 
getDefaultFlag() - Method in class MAPCoder.OptionPrune
 
getDefaultFlag() - Method in class MAPCoder.OptionTimings
 
getDefaultFlag() - Method in class OptionWithComments
 
getDefaultStateIndex() - Method in interface StandardNode
originally in DSLNode
getDefaultStateIndex() - Method in class StandardNodeImpl
 
getDependencies() - Method in class JDKToolScript
 
getDependencies() - Method in interface Script
 
getDescendants(Set, Classifier) - Method in interface DecisionNode
 
getDescendants(Set, Classifier) - Method in class DecisionNodeAbstract
 
getDescription() - Method in class HuginReader
interface ProgressMonitorable
getDescription() - Method in class InflibFileFilter
 
getDescription() - Method in class NodeLinearTask
 
getDescription() - Method in class RunReadNetwork
 
getDescription() - Method in class Simulator
interface ProgressMonitorable
getDescription() - Method in class ScriptExecution
 
getDescription() - Method in class CompoundTask
 
getDescription() - Method in interface ProgressMonitorable
 
getDescription() - Method in class WeightedTask
 
getDescriptionComment() - Method in class JDKCompile
 
getDescriptionComment() - Method in class JDKRun
 
getDescriptionComment() - Method in interface Script
 
getDescriptionShort() - Method in class SoftwareEntity
 
getDescriptionVerbose() - Method in class SoftwareEntity
 
getDescriptor() - Method in class Computation
 
getDiagnosisType() - Method in interface StandardNode
originally in DSLNode
getDiagnosisType() - Method in class StandardNodeImpl
 
getDimension(Dimension) - Method in interface StandardNode
Will return the node size listed in the HuginNet file.
getDimension(Dimension) - Method in class StandardNodeImpl
 
getDimensionIndices(Object[]) - Method in class TableIndex
Returns the dimensions that correspond to the given variables.
getDimensionIndices(TableIndex) - Method in class TableIndex
returns the dimensions that correspond to the variables in ind.
getDisplayName() - Method in class EdgeDeletionEngineGenerator
 
getDisplayName() - Method in class PropagationEngineGenerator
 
getDisplayName() - Method in class RecoveryEngineGenerator
 
getDisplayName() - Method in class Dynamator
 
getDisplayName() - Method in class HuginEngineGenerator
 
getDisplayName() - Method in class JEngineGenerator
 
getDisplayName() - Method in class RandomEngineGenerator
 
getDisplayName() - Method in class RCEngineGenerator
 
getDisplayName() - Method in class SSEngineGenerator
 
getDisplayName() - Method in class ZCEngineGenerator
 
getDisplayName() - Method in class RCEngineGenerator
 
getDistanceMeasure(boolean) - Method in class CPTInfo
 
getDomain() - Method in class Converter
 
getDouble(Object) - Method in interface DoubleFunction
 
getDSLNodeType() - Method in interface FiniteVariable
moved from DSLNode 010905
getDSLNodeType() - Method in class FiniteVariableImpl
 
getDSLNodeType() - Method in class DSLNodeImpl
Convenience method.
getDSLSubmodel() - Method in interface DSLNode
 
getDSLSubmodel() - Method in class DSLNodeImpl
 
getDSLSubmodelFactory() - Method in interface GenieNet
 
getDSLSubmodelFactory() - Method in class GenieNetImpl
 
getDtree() - Method in class Bundle
 
getDtree() - Method in class Settings
 
getDtreeCreateHMetis(int, int, int) - Method in class MethodHmetis.Algorithm
 
getDtreeHeight() - Method in class Bundle
 
getDtreeHeight() - Method in class Settings
 
getDtreeMaxCluster() - Method in class Bundle
 
getDtreeMaxCluster() - Method in class Settings
 
getDtreeMaxContext() - Method in class Bundle
 
getDtreeMaxContext() - Method in class Settings
 
getDtreeMaxCutset() - Method in class Bundle
 
getDtreeMaxCutset() - Method in class Settings
 
getDtreeMethod() - Method in class Settings
 
getDtreeStyle() - Method in interface CreationMethod.Settings
 
getDtreeStyle() - Method in class Settings
 
getDynamator() - Method in class AbstractInferenceEngine
 
getDynamator() - Method in class SynchronizedInferenceEngine
 
getDynamator() - Method in interface InferenceEngine
 
getEdgeIndex(List, List, FiniteVariable, FiniteVariable) - Static method in class UaiEdgeCutter
 
getEdgeRankingTime() - Method in class EDAlgorithm
 
getEdgesToCut(BeliefNetwork, double, List, List) - Static method in class UaiEdgeCutter
 
getEdgesToDeleteForRandomSpanningTree(Table[], Random) - Static method in class EDEdgeDeleter
 
getEdgesToDeleteForRandomSpanningTree(BayesianNetwork, Random) - Static method in class EDEdgeDeleter
 
getEditComponent(Container) - Method in class ApproxEngineGenerator
 
getEditComponent(Container) - Method in class PropagationEngineGenerator
 
getEditComponent(Container) - Method in class Dynamator
 
getEffectiveCPTData(FiniteVariable) - Method in class AbstractInferenceEngine
 
getElementHandler() - Method in class AbstractSaxHandler
 
getElimAlgo() - Method in interface CreationMethod.Settings
 
getElimAlgo() - Method in class Settings
 
getEliminationHeuristic() - Method in class JoinTreeSettings
 
getEliminationHeuristic() - Method in class RCSettings
 
getEliminationOrder(BeliefNetwork) - Method in class EliminationHeuristic
 
getEliminationOrder(Index[]) - Method in class EliminationHeuristic
 
getEliminationOrder(BeliefNetwork) - Method in class EliminationHeuristic.RandomizedBestOfNStrategy
 
getEliminationOrder(Index[]) - Method in class EliminationHeuristic.RandomizedBestOfNStrategy
 
getEliminationOrder(BeliefNetwork, int, Random) - Method in class EliminationHeuristic.RandomizedBestOfNStrategy
 
getEliminationOrder(Index[], int, Random) - Method in class EliminationHeuristic.RandomizedBestOfNStrategy
 
getEliminationOrder() - Method in class HuginLogReader
 
getEliminationTree() - Method in class JTtoET
 
getElimOrder(ArrayList) - Method in class Dtree
 
getElimOrder() - Method in class RC2
 
getElimOrder(RCNode, ArrayList) - Static method in class RCUtilities
The ArrayList ord will contain the vars in an elimination order determined by the subtree rooted at rt (it is not unique).
getElimOrderUnInitialized(RCNode, Collection, ArrayList) - Static method in class RCUtilities
The ArrayList ord will contain the vars in an elimination order determined by the subtree rooted at rt (it is not unique).
getEndColumn() - Method in class SimpleCharStream
 
getEndLine() - Method in class SimpleCharStream
 
getEngine() - Method in class JoinTreeSettings
 
getEnumProperties() - Method in interface Variable
 
getEnumProperties() - Method in class VariableImpl
 
getEpsilon() - Method in class Optimizer
 
getEstimatedHours() - Method in class Computation
 
getEstimatedMinutes() - Method in class Computation
 
getEstimatedSeconds() - Method in class Computation
 
getEstimator() - Method in class RunReadSMILE
 
getEstimator() - Method in class RunReadHugin
 
getEstimator() - Method in class RunReadNetwork
 
getEstimator() - Method in class RunReadBIF
 
getEvidence() - Method in class XmlbifParser.Variable
 
getEvidenceController() - Method in interface BeliefNetwork
 
getEvidenceController() - Method in class BeliefNetworkImpl
 
getEvidenceEq(List) - Method in class SensitivityEngine
 
getEvidenceMap() - Method in class Snapshot
 
getExactEngineGenerator() - Method in class ApproxEngineGenerator
 
getExcludeArray() - Method in interface StandardNode
 
getExcludeArray() - Method in class StandardNodeImpl
 
getExcludeArray(FiniteVariable) - Static method in class ExcludePolicy
 
getExcludePolicy() - Method in interface StandardNode
 
getExcludePolicy() - Method in class StandardNodeImpl
 
getExcludePolicy(Object) - Static method in class ExcludePolicy
 
getExecutablePath(JDKTool) - Method in class GuessingSource
 
getExecutablePath(JDKTool) - Method in interface SystemSoftwareSource
 
getExitValue() - Method in class ScriptExecution
 
getExpectedNumberOfRCCalls() - Method in class Computation
 
getExpression() - Method in class BeliefCompilation
 
getExtensions() - Method in class InflibFileFilter
 
getFactory() - Method in class AbstractSaxHandler
 
getFactory() - Static method in class SkimmerEstimator
 
getFamilyPartial(FiniteVariable) - Method in class BeliefCompilation
Returns the partial derivative of the CPT for the current values of the parameters.
getFamilyTable(FiniteVariable) - Method in class BeliefCompilation
Returns the value of the CPT for the variable.
getFile() - Method in class RunReadSMILE
 
getFile() - Method in class RunReadHugin
 
getFile() - Method in class RunReadNetwork
 
getFile() - Method in class RunReadBIF
 
getFile() - Method in class RunWriteBIF
 
getFileFilter() - Method in class FileType
 
getFileName() - Method in class ParanoidFileFinder
 
getFileSeparatorUnicode() - Static method in class ParanoidFileFinder
 
getFileType() - Method in class RunReadSMILE
 
getFileType() - Method in class RunReadHugin
 
getFileType() - Method in class RunReadNetwork
 
getFileType() - Method in class RunReadBIF
 
getFileType() - Method in class RunWriteBIF
 
getFirst() - Method in class WeakLinkedList
Returns the first element in this list.
getFixedKLBound() - Method in class ApproxReport
 
getFixedKLTotal() - Method in class ApproxReport
 
getFixedPoint(FiniteVariable) - Method in class ApproxReport
 
getFixedProbE() - Method in class ApproxReport
 
getFlag(CodeOption) - Method in class AbstractCodeGenius
 
getFlag(CodeOption) - Method in interface CodeGenius
 
getFlagControl() - Method in class EdgeDeletionInferenceEngine
 
getFormatDescription() - Method in class RunReadNetwork
 
getFVIndx() - Method in class RC2NodeLeaf
 
getFVIndx() - Method in class RC2NodeLeafEvidInd
 
getGeneralEdgeCorrection() - Method in class EDAlgorithm
 
getGeneralEdgeCorrections() - Method in class EDAlgorithm
 
getGenieConstant() - Method in class FileType
 
getGlobalGraphInfo() - Method in interface GraphvizIO.ExtraDotInfoSupplier
 
getGlobalGraphInfo() - Method in class GraphvizIO.StandardNodeDimensionSupplier
 
getGlobalNodeSize(Dimension) - Method in interface HuginNet
Will return the node size listed in the HuginNet file.
getGlobalNodeSize(Dimension) - Method in class HuginNetImpl
Will return the node size listed in the HuginNetImpl file.
getHandle() - Method in class DSLSubmodel
 
getHeight() - Method in class Dtree
 
getHeight() - Method in class DtreeNode
This height is calculated by how many levels of nodes there are, not by how many edges there are between them.
getHeight() - Method in class DtreeNodeInternal
 
getHeight() - Method in class DtreeNodeLeaf
 
getHeight() - Method in class RCNode
This height is calculated by how many levels of nodes there are, not by how many edges there are between them.
getHeight() - Method in class RCNodeInternalBinaryCache
 
getHeight() - Method in class RCNodeLeaf
 
getHelpText() - Method in interface CodeOption
 
getHelpText() - Method in class MAPCoder.OptionPrune
 
getHelpText() - Method in class MAPCoder.OptionTimings
 
getHelpText() - Method in class ModelCoder.LibraryVersionOption
 
getHelpText() - Method in class OptionBreadth
 
getHelpText() - Method in class OptionWithComments
 
getHelpText() - Method in class ProbabilityQueryCoder.MarginalScopeOption
 
getHints() - Method in class SoftwareEntity
 
getHMeTiSAlgo() - Method in interface CreationMethod.Settings
 
getHMeTiSAlgo() - Method in class Settings
 
getHmetisTime() - Method in class DtreeCreateHMetis
Returns the amount of time (in seconds) spent in the hMetis library (just the c++ calls to the library) since the last call to resetTiming or construction.
getHmetisTime() - Method in class DgraphCreateHMetis
Returns the amount of time (in seconds) spent in the hMetis library (just the c++ calls to the library) since the last call to resetTiming or construction.
getHoursPerRCCall() - Static method in class Settings
 
getHuginLogFile() - Method in interface CreationMethod.Settings
 
getHuginLogFile() - Method in class Settings
 
getIconFileName() - Method in interface CodeGenius
 
getIconFileName() - Method in class CPTCoder
 
getIconFileName() - Method in class EMCoder
 
getIconFileName() - Method in class MAPCoder
 
getIconFileName() - Method in class ModelCoder
 
getIconFileName() - Method in class MPECoder
 
getIconFileName() - Method in class ProbabilityQueryCoder
 
getIconFileName() - Method in class SensitivityCoder
 
getID() - Method in interface Parameter
 
getID() - Method in class ParameterImpl
 
getID() - Method in class CreationMethod
 
getID() - Method in class MapProperty
 
getID() - Method in class DSLNodeImpl
Convenience method.
getID(Object) - Static method in class InstantiationXmlizer
 
getID() - Method in class XmlbifParser.Variable
 
getID() - Method in interface Variable
 
getID() - Method in class VariableImpl
 
getID() - Method in class CSITypeProperty
 
getID() - Method in interface EnumProperty
 
getID() - Method in class EvidenceAssertedProperty
 
getID() - Method in class HiddenProperty
 
getID() - Method in class ImpactProperty
 
getID() - Method in class InferenceValidProperty
 
getID() - Method in class InOutDegreeProperty
 
getID() - Method in class QueryParticipantProperty
 
getID() - Method in class UserEnumProperty
 
GetImage() - Method in class SimpleCharStream
 
getIncoming(int) - Method in class RC
 
getIndex() - Method in interface DecisionTree
 
getIndex() - Method in class DecisionTreeImpl
interface DecisionTree
getIndex() - Method in class VariableInstance
 
getIndex() - Method in class Converter
 
getIndexes() - Method in class NoisyOrShellPearl
 
getIndexFromFullInstance(int[]) - Method in class Index
 
getIndexOfCondition() - Method in class CPTParameter
 
getIndexWithinCondition() - Method in class CPTParameter
 
getIndices() - Method in class CPTParameter
 
getInflibModule() - Static method in class ClassModule
 
getInfo() - Method in class RCSettings
 
getInitial(BeliefNetwork, Map, Set, BeliefCompilation) - Method in class InitializationMethod
 
getInputFile() - Method in class CPTImport
 
getInputOrd_ChangingS1() - Method in class Loci.Footer.BinaryILink
 
getInputOrd_ChangingS1() - Method in class Loci.Footer.GH
 
getInputOrd_ChangingS1() - Method in class Loci.Footer.Linkmap
 
getInputOrd_ChangingS1() - Method in class Loci.Footer.Mlink
 
getInputOrd_ChangingS1() - Method in class Loci.Footer.ProgData
Input order of the 1st locus containing a changing recombination value (1 based).
getInputOrd_ChangingS2() - Method in class Loci.Footer.BinaryILink
 
getInputOrd_ChangingS2() - Method in class Loci.Footer.GH
 
getInputOrd_ChangingS2() - Method in class Loci.Footer.Linkmap
 
getInputOrd_ChangingS2() - Method in class Loci.Footer.Mlink
 
getInputOrd_ChangingS2() - Method in class Loci.Footer.ProgData
Input order of the 2nd locus containing a changing recombination value (1 based).
getInstance() - Static method in class EdgeDeletionInferenceEngine.DateFormatFilename
 
getInstance(BeliefNetwork, CreationMethod.Settings) - Method in class CreationMethod
 
getInstance(BeliefNetwork, CreationMethod.Settings) - Method in class MethodEliminationOrder
 
getInstance(BeliefNetwork, CreationMethod.Settings) - Method in class MethodHmetis
 
getInstance(BeliefNetwork, CreationMethod.Settings) - Method in class MethodHuginLog
 
getInstance() - Method in class MapEngine
 
getInstance() - Static method in class HuginCopier
 
getInstance() - Static method in class VariableComparator
 
getInstance() - Method in class VariableInstance
 
getInstance() - Static method in class AbstractStringifier.DateFormatFilename
 
getInstance() - Static method in class OptionWithComments
 
getInstanceID() - Static method in class IDComparator
 
getInstanceLabel() - Static method in class LabelComparator
 
getInternalHistory() - Method in class DecisionTreeImpl
interface Factory
getInternalHistory() - Method in interface Factory
 
getInterval() - Method in class SingleParamSuggestion
 
getIntoMessage(int) - Method in class MapJoinTree
 
getIterator() - Method in class RC
 
getIteratorParentChild() - Method in class RC
 
getIteratorRoots() - Method in class RC
 
getIteratorRoots() - Method in class RCDgraph
 
getIteratorRoots() - Method in class RCDtree
 
getIteratorTraversal() - Method in class RC
 
getIteratorTraversal() - Method in class RCDgraph
 
getIteratorTraversal() - Method in class RCDtree
 
getIteratorTree() - Method in class RC
 
getIteratorTree() - Method in class RCDgraph
Iterator only over the first root
getIteratorTree() - Method in class RCDtree
 
getJarName() - Method in class ClassModule
 
getJavaCodeName() - Method in class EliminationHeuristic
 
getJavaCodeName() - Method in class InitializationMethod
 
getJavaCodeName() - Method in class SearchMethod
 
getJavacTool() - Static method in class JDKTool
 
getJavaTool() - Static method in class JDKTool
 
getJMenu() - Method in class ApproxEngineGenerator
 
getJMenu() - Method in class PropagationEngineGenerator
 
getJMenu() - Method in class Dynamator
 
getJoinForest() - Method in class HuginLogReader
 
getJoint() - Method in class CPTInfo
 
getJoint() - Method in class TableIndex
Returns the child variable.
getJointEngine() - Method in class JointWrapper
 
getJointInstance() - Method in class CPTParameter
 
getJoinTree() - Method in class BeliefCompilation
 
getJoinTree() - Method in class JoinTreeSettings
 
getJoinTree() - Method in class JoinTreeAlgorithm
 
getJoinTreeStats() - Method in interface JoinTreeInferenceEngine
 
getJoinTreeStats() - Method in class JoinTreeInferenceEngineImpl
 
getJoinTreeStats() - Method in class WrapperInferenceEngine
 
getJointWrapper() - Method in class WrapperInferenceEngine
 
getJointYEq(List, FiniteVariable, Object) - Method in class SensitivityEngine
 
getKeepBest() - Method in class Settings
 
getKey() - Method in class EdgeDeletionEngineGenerator
 
getKey() - Method in class PropagationEngineGenerator
 
getKey() - Method in class RecoveryEngineGenerator
 
getKey() - Method in class Dynamator
 
getKey() - Method in class HuginEngineGenerator
 
getKey() - Method in class JEngineGenerator
 
getKey() - Method in class RandomEngineGenerator
 
getKey() - Method in class RCEngineGenerator
 
getKey() - Method in class SSEngineGenerator
 
getKey() - Method in class ZCEngineGenerator
 
getKey() - Method in class RCEngineGenerator
 
getKeyStatic() - Static method in class EdgeDeletionEngineGenerator
 
getKeyStatic() - Static method in class PropagationEngineGenerator
 
getKeyStatic() - Static method in class RecoveryEngineGenerator
 
getKeyStatic() - Static method in class RandomEngineGenerator
 
getKeyStatic() - Static method in class RCEngineGenerator
 
getKeyStatic() - Static method in class RCEngineGenerator
 
getLabel() - Method in class DSLNodeImpl
Convenience method.
getLabel() - Method in class HuginNodeImpl
Will get the label from a HuginNodeImpl.
getLabel() - Method in interface StandardNode
Will get the label from a HuginNode.
getLabel() - Method in class XmlbifParser.BifNode
 
getLanguage() - Method in class ScriptExecution
 
getLargestCluster(int) - Method in class DtreeNode
Returns the largest cluster (actually the first it finds which is at least as big as the parameter largest).
getLargestCluster(int) - Method in class DtreeNodeInternal
 
getLargestCluster(int) - Method in class DtreeNodeLeaf
 
getLast() - Method in class WeakLinkedList
Returns the last element in this list.
getLastLikelihood() - Static method in class Learning
Returns the -log(Likelihood) for the last call to learnParamsEM().
getLastScore() - Method in class MapRunner
 
getLatestReport() - Method in class ApproxEngine
 
getLeaf(int[]) - Method in interface DecisionTree
 
getLeaf(int[]) - Method in class DecisionTreeImpl
interface DecisionTree
getLeaf(DecisionNode, int[]) - Method in class DecisionTreeImpl
 
getLeafDerivative(int) - Method in class MiniTree
 
getLeafHistory() - Method in class DecisionTreeImpl
interface Factory
getLeafHistory() - Method in interface Factory
 
getLeafValue(int) - Method in class MiniTree
 
getLeafVar() - Method in class RC2NodeLeaf
 
getLeafVar() - Method in class RC2NodeLeafEvidInd
 
getLeafVar() - Method in class RCNodeLeaf
Get the "child" variable of this leaf (family).
getLeaks() - Method in class NoisyOrShellHenrion
 
getLeaks() - Method in class NoisyOrShellPearl
 
getLeaves(Set) - Method in interface DecisionNode
 
getLeaves(Set) - Method in class DecisionNodeAbstract
 
getLikelihood(FiniteVariable) - Method in class BeliefCompilation
Returns the likelihoods(Evidence indicators) for the given variable.
getLikelihood(int) - Method in class MapJoinTree
 
getLine() - Method in class SimpleCharStream
Deprecated.  
getLinearIndex() - Method in class CPTParameter
 
getLocation(Point) - Method in class DSLSubmodel
 
getLocation(Point) - Method in interface StandardNode
Will get the location from a HuginNode.
getLocation(Point) - Method in class StandardNodeImpl
 
getLociType(int) - Method in class Pedigree.PseudoLoci
 
getLogOddsChange() - Method in interface SensitivitySuggestion
 
getLogOddsChange() - Method in class SingleCPTSuggestion
 
getLogOddsChange() - Method in class SingleParamSuggestion
 
getLogSizes(IntSet) - Method in class Domain
 
getLogZeroMiCorrection() - Method in class EDAlgorithm
 
getLogZeroMiCorrection() - Method in class EDMPAlgorithm
 
getLoops() - Method in class ApproxReport
 
getLowerBound() - Method in class Interval
 
getMandatory() - Method in interface DSLNode
 
getMandatory() - Method in class DSLNodeImpl
Convenience method.
getMap(File) - Method in class InstantiationXmlizer
 
getMax() - Method in class DataSetStatistic
 
getMax() - Method in interface JoinTreeStats.Stat
 
getMax() - Method in class JoinTreeStats.StatImpl
 
getMaxDegree() - Method in class IntGraph
 
getMaxDomainCardinality() - Method in interface BeliefNetwork
 
getMaxDomainCardinality() - Method in class BeliefNetworkImpl
 
getMaxIterations() - Method in class BeliefPropagationSettings
 
getMaxIterations() - Method in class EDAlgorithm
 
getMaxTheoreticalCPTSize() - Method in interface BeliefNetwork
 
getMaxTheoreticalCPTSize() - Method in class BeliefNetworkImpl
 
getMean() - Method in class DataSetStatistic
This method returns the mean of all data points in the set.
getMedian() - Method in class DataSetStatistic
This method calculates and returns the median value of the data points in the set.
getMemoryRequirements() - Method in interface ArithmeticExpression
 
getMemoryRequirements() - Method in class BeliefCompilation
 
getMemoryRequirements() - Method in class JointWrapper
 
getMemoryRequirements() - Method in class RCInfo
 
getMemoryRequirements() - Method in class RCWrapper
 
getMemoryRequirements() - Method in class S4DoubleExpression
 
getMemoryRequirements() - Method in class WrapperInferenceEngine
 
getMemoryRequirements() - Method in interface JointEngine
 
getMemoryRequirements() - Method in class JoinTreeAlgorithm
 
getMemoryRequirements() - Method in class UnindexedHuginAlgorithm
 
getMemoryRequirements() - Method in class UnindexedSSAlgorithm
 
getMemoryRequirements() - Method in class UnindexedZCAlgorithm
 
getMemoryRequirements() - Method in class RCEngine
 
getMessage() - Method in exception ParseException
This method has the standard behavior when this object has been created using the standard constructors.
getMessage() - Method in error TokenMgrError
You can also modify the body of this method to customize your error messages.
getMessage() - Method in class ScriptExecution
 
getMessage() - Method in exception ConversionException
 
getMethod() - Method in class EDRecovery
 
getMin() - Method in class DataSetStatistic
 
getMinDomainCardinality() - Method in interface BeliefNetwork
 
getMinDomainCardinality() - Method in class BeliefNetworkImpl
 
getMinTheoreticalCPTSize() - Method in interface BeliefNetwork
 
getMinTheoreticalCPTSize() - Method in class BeliefNetworkImpl
 
getMinutesPerRCCall() - Static method in class Settings
 
getMissing() - Method in exception ConversionException
 
getMode() - Method in class DataSetStatistic
 
getModeFrequency() - Method in class DataSetStatistic
 
getMPE() - Method in class SensMPEReport
 
getMPE() - Method in class MPEAlgorithm
 
getName() - Method in class DecisionEvent.Type
 
getName() - Method in class MapProperty
 
getName() - Method in class DSLSubmodel
 
getName() - Method in class FileType
 
getName() - Method in class JDKCompile
 
getName() - Method in class JDKRun
 
getName() - Method in class JDKTool
 
getName() - Method in interface Script
 
getName() - Method in class CSITypeProperty
 
getName() - Method in interface EnumProperty
 
getName() - Method in class EvidenceAssertedProperty
 
getName() - Method in class HiddenProperty
 
getName() - Method in class ImpactProperty
 
getName() - Method in class InferenceValidProperty
 
getName() - Method in class InOutDegreeProperty
 
getName() - Method in class Interruptable
For identification purposes
getName() - Method in class LinearFunction
 
getName() - Method in class QueryParticipantProperty
 
getName() - Method in class UserEnumProperty
 
getNameMethodOfInterest() - Method in class Interruptable
Override this to help print meaningful verbose messages.
getNewestFirstComparator() - Static method in class ParanoidFileFinder
 
getNewOrder(Collection) - Static method in class UaiEdgeCutter
 
getNext(int) - Method in class DecisionInternal
 
getNext(Object) - Method in class DecisionInternal
 
getNext(int) - Method in interface DecisionNode
 
getNext(Object) - Method in interface DecisionNode
 
getNext(int) - Method in class DecisionNodeAbstract
 
getNext(Object) - Method in class DecisionNodeAbstract
 
getNextToken() - Method in class HuginLogReader
 
getNextToken() - Method in class HuginLogReaderTokenManager
 
getNextToken() - Method in class HuginReader
 
getNextToken() - Method in class HuginReaderTokenManager
 
getNextToken() - Method in class NeticaReader
 
getNextToken() - Method in class NeticaReaderTokenManager
 
getNodeType() - Method in interface HuginNode
 
getNodeType() - Method in class HuginNodeImpl
 
getNormalizedMax() - Method in interface JoinTreeStats.Stat
 
getNormalizedMax() - Method in class JoinTreeStats.StatImpl
 
getNote() - Method in class HuginReader
interface ProgressMonitorable
getNote() - Method in class NodeLinearTask
 
getNote() - Method in class Simulator
interface ProgressMonitorable
getNote() - Method in class CompoundTask
 
getNote() - Method in interface ProgressMonitorable
 
getNote() - Method in class WeightedTask
 
getNumAlgos() - Static method in class CachingDFBnB.OrderingAlgo
 
getNumAlleles(int) - Method in class Pedigree.PseudoLoci
 
getNumberInternalNodes() - Method in class DtreeNode
Returns the number of internal nodes including (possibly) this one and all below it.
getNumberInternalNodes() - Method in class DtreeNodeInternal
 
getNumberInternalNodes() - Method in class DtreeNodeLeaf
 
getNumberLeafNodes() - Method in class DtreeNode
Returns the number of leaf nodes including (possibly) this one and all below it.
getNumberLeafNodes() - Method in class DtreeNodeInternal
 
getNumberLeafNodes() - Method in class DtreeNodeLeaf
 
getNumberNodes() - Method in class DtreeNode
Returns the number of DtreeNodes including this one and all below it.
getNumberNodes() - Method in class DtreeNodeInternal
 
getNumCacheEntries(RC) - Method in class Computation.All
 
getNumCacheEntries(RC) - Method in class Computation
 
getNumCacheEntries(RC) - Method in class Computation.Pe
 
getNumChanged() - Method in class CPTInfo
 
getNumChildSubmodels() - Method in class DSLSubmodel
 
getNumConditionsInFile() - Method in class CPTImport
 
getNumConflicts() - Method in class CPTInfo
 
getNumDtrees() - Method in interface CreationMethod.Settings
 
getNumDtrees() - Method in class Settings
 
getNumExpansions() - Static method in class CachingDFBnB.ChildExpansion
 
getNumLoci() - Method in class Pedigree.PseudoLoci
 
getNumMaxCacheEntries() - Method in class Computation
 
getNumPartitions() - Method in interface CreationMethod.Settings
 
getNumPartitions() - Method in class Settings
 
getNumPheno() - Method in class Pedigree.PseudoLoci
 
getNumProperties() - Static method in class VariableImpl
 
getNumRCCallsMaxCache() - Method in class Computation
 
getNumRCNodes_All() - Method in class RC2
Can use this and getRCNode_All to iterate through nodes.
getNumRCNodes_Pe() - Method in class RC2
Can use this and getRCNode_Pe to iterate through nodes.
getNumRecovered() - Method in class EDRecovery
 
getNumRedundant() - Method in class CPTInfo
 
getNumSpared() - Method in class CPTInfo
 
getNumSubmodels() - Method in class DSLSubmodelFactory
 
getNumTypes() - Static method in class DiagnosisType
 
getNumTypes() - Static method in class CachingDFBnB.HeurFunct
 
getNumVariables() - Method in class TableIndex
 
getNumVars() - Method in class RCInstanceIterator
 
getObject() - Method in interface SensitivitySuggestion
 
getObject() - Method in class SingleCPTSuggestion
 
getObject() - Method in class SingleParamSuggestion
 
getOptimalMemoryRequirement() - Method in class Computation
 
getOption(CodeOption) - Method in class AbstractCodeGenius
 
getOption(CodeOption) - Method in interface CodeGenius
 
getOptionBreadth() - Method in interface CodeGenius
 
getOptionBreadth() - Method in class CPTCoder
 
getOptionBreadth() - Method in class EMCoder
 
getOptionBreadth() - Method in class MAPCoder
 
getOptionBreadth() - Method in class ModelCoder
 
getOptionBreadth() - Method in class MPECoder
 
getOptionBreadth() - Method in class ProbabilityQueryCoder
 
getOptionBreadth() - Method in class SensitivityCoder
 
getOptions() - Method in interface CodeGenius
 
getOptions() - Method in class CPTCoder
 
getOptions() - Method in class EMCoder
 
getOptions() - Method in class MAPCoder
 
getOptions() - Method in class ModelCoder
 
getOptions() - Method in class MPECoder
 
getOptions() - Method in class ProbabilityQueryCoder
 
getOptions() - Method in class SensitivityCoder
 
getOriginalTables() - Method in class JoinTreeAlgorithm
 
getOrigProbE() - Method in class ApproxReport
 
getOutcome(DecisionNode, int) - Method in class XmlWriter.GroupedDecisionWriter
 
getOutcome(DecisionNode, int) - Method in class XmlWriter.GroupedOutcomeWriter
 
getOutcome(DecisionNode, int) - Method in class XmlWriter.GroupedParameterWriter
 
getOutcomes(Set) - Method in class DecisionInternal
 
getOutcomes(Set) - Method in class DecisionLeaf
 
getOutcomes(Set) - Method in interface DecisionNode
 
getOutcomes(Set) - Method in class DecisionNodeAbstract
 
getOutcomes() - Method in class XmlbifParser.Variable
 
getOutputClassName() - Method in class AbstractCodeGenius
 
getOutputClassName() - Method in interface CodeGenius
 
getOutputClassNameDefault() - Method in interface CodeGenius
 
getOutputClassNameDefault() - Method in class CPTCoder
 
getOutputClassNameDefault() - Method in class EMCoder
 
getOutputClassNameDefault() - Method in class MAPCoder
 
getOutputClassNameDefault() - Method in class ModelCoder
 
getOutputClassNameDefault() - Method in class MPECoder
 
getOutputClassNameDefault() - Method in class ProbabilityQueryCoder
 
getOutputClassNameDefault() - Method in class SensitivityCoder
 
getPanFilter() - Static method in class FileType
 
getParameter(int) - Method in class DecisionLeaf
 
getParameter(Object) - Method in class DecisionLeaf
 
getParameter(int) - Method in interface DecisionNode
 
getParameter(Object) - Method in interface DecisionNode
 
getParameter(int) - Method in class DecisionNodeAbstract
 
getParameter(Object) - Method in class DecisionNodeAbstract
 
getParameter(int[]) - Method in interface DecisionTree
 
getParameter(int[]) - Method in class DecisionTreeImpl
interface DecisionTree
getParameter(int) - Method in interface ArithmeticExpression
 
getParameter(int) - Method in class S4DoubleExpression
 
getParameter(int) - Method in class CPTInfo
 
getParameterHistory() - Method in class DecisionTreeImpl
interface Factory
getParameterHistory() - Method in interface Factory
 
getParameterOptimizationLevel() - Method in class Optimizer
 
getParams() - Method in class NoisyOrShellHenrion
 
getParams() - Method in class NoisyOrShellPearl
 
getParanoidFileFinder() - Static method in class JDKTool
 
getParent() - Method in class DSLSubmodel
 
getParentInstances() - Method in class CPTParameter
 
getParentList() - Method in class ApproxReport
 
getParents() - Method in interface DecisionNode
 
getParents() - Method in class DecisionNodeAbstract
 
getParents() - Method in class TableIndex
Returns an array containing the variable associated with each dimension.
getParentsSet() - Method in class TableIndex
 
getParser() - Method in class RunReadBIF
 
getPartial(int) - Method in interface ArithmeticExpression
 
getPartial(FiniteVariable) - Method in class BeliefCompilation
Returns the partial derivative of the likelihoods for the current values of the parameters.
getPartial(int) - Method in class S4DoubleExpression
 
getPartial(int) - Method in class JoinTreeInference
 
getPartial(int) - Method in class ShenoyShaferAlgorithm
 
getPath(SoftwareEntity) - Method in class GuessingSource
 
getPath() - Method in class SoftwareEntity
 
getPath(SoftwareEntity) - Method in interface SystemSoftwareSource
 
getPathPattern() - Static method in class JDKRun
 
getPe() - Method in class Bundle
 
getPenalty() - Method in class InitializationMethod
 
getPenetrance(int, String, int, int) - Method in class Pedigree.PseudoLoci
 
getPeRootNode() - Method in class RC2
 
getPmTable(int) - Method in class EDNetwork
 
getPrEOnly() - Method in class RCSettings
 
getPriorityEvidenceChangeListeners(List) - Method in class EvidenceController
 
getProb() - Method in class SensitivityEquation
 
getProb(int) - Method in class SensitivityTable
 
getProbEvidence() - Method in class Snapshot
 
getProcess() - Method in class ScriptExecution
 
getProgress() - Method in class CPTImport
 
getProgress() - Method in class HuginReader
interface ProgressMonitorable
getProgress() - Method in class NodeLinearTask
 
getProgress() - Method in class Simulator
interface ProgressMonitorable
getProgress() - Method in class CompoundTask
 
getProgress() - Method in interface ProgressMonitorable
 
getProgress() - Method in class WeightedTask
 
getProgressIncrementNodeBlock() - Method in class SkimmerEstimator
 
getProgressIncrementNodeBlock() - Method in class SkimmerEstimator
 
getProgressIncrementPoteBlock() - Method in class SkimmerEstimator
 
getProgressIncrementPoteBlock() - Method in class SkimmerEstimator
 
getProgressMax() - Method in class HuginReader
interface ProgressMonitorable
getProgressMax() - Method in class SkimmerEstimator
 
getProgressMax() - Method in class NodeLinearTask
 
getProgressMax() - Method in class SkimmerEstimator
 
getProgressMax() - Method in class Simulator
interface ProgressMonitorable
getProgressMax() - Method in class CompoundTask
 
getProgressMax() - Method in interface ProgressMonitorable
 
getProgressMax() - Method in class WeightedTask
 
getPropagationTime() - Method in interface ArithmeticExpression
 
getPropagationTime() - Method in class BeliefCompilation
 
getPropagationTime() - Method in class JointWrapper
 
getPropagationTime() - Method in class S4DoubleExpression
 
getPropagationTime() - Method in class WrapperInferenceEngine
 
getPropagationTime() - Method in class BeliefPropagation
 
getPropagationTime() - Method in class EDAlgorithm
 
getPropagationTime() - Method in interface JointEngine
 
getPropagationTime() - Method in class JoinTreeAlgorithm
 
getPropagationTime() - Method in class RCEngine
 
getProperties() - Method in class ApproxEngineGenerator.Properties
 
getProperties() - Method in class BeliefNetworkImpl
 
getProperties() - Method in class DSLNodeImpl
 
getProperties() - Method in class HuginNodeImpl
 
getProperties() - Method in interface PropertySuperintendent
 
getProperties() - Method in class XmlbifParser.BifNode
 
getProperty(EnumProperty) - Method in interface Variable
 
getProperty(EnumProperty) - Method in class VariableImpl
 
getQuantitativeDependencyHandler() - Method in class AbstractInferenceEngine
 
getQuantitativeDependencyHandler() - Method in class SynchronizedInferenceEngine
 
getQuantitativeDependencyHandler() - Method in interface InferenceEngine
 
getRandom() - Method in class Test
 
getRandomSpanningTree(BayesianNetwork, Random) - Static method in class EDEdgeDeleter
Samples a random spanning forest uniformly from the set of all spanning forests of the undirected network.
getRandomSpanningTree(Table[], Random) - Static method in class EDEdgeDeleter
 
getRandomStatic() - Static method in class Test
 
getRanked() - Method in interface DSLNode
 
getRanked() - Method in class DSLNodeImpl
Convenience method.
getRC() - Method in class Bundle
 
getRC() - Method in class Settings
 
getRCComparator() - Method in class Settings
 
getRCCreateListener() - Method in class Settings
 
getRCFactory() - Method in class Settings
 
getRCFilePath() - Method in class Bundle
 
getRCInfo() - Method in class RCWrapper
 
getRCNode_All(int) - Method in class RC2
Can use this and getNumRCNodes_All to iterate through nodes.
getRCNode_Pe(int) - Method in class RC2
Can use this and getNumRCNodes_Pe to iterate through nodes.
getReadTask() - Method in class RunReadSMILE
 
getReadTask() - Method in class RunReadHugin
 
getReadTask() - Method in class RunReadNetwork
 
getReadTask() - Method in class RunReadBIF
 
getRecombF(String, int) - Method in class Pedigree.PseudoLoci
 
getRecombM(String, int) - Method in class Pedigree.PseudoLoci
 
getRelevant(int[]) - Method in interface CPTShell
 
getRelevant(Object[]) - Method in interface CPTShell
 
getRelevant(Map) - Method in interface CPTShell
 
getRelevant(Object[], Object) - Method in interface CPTShell
 
getRelevant(int[]) - Method in class DecisionShell
 
getRelevant(Object[]) - Method in class DecisionShell
 
getRelevant(Map) - Method in class DecisionShell
 
getRelevant(Object[], Object) - Method in class DecisionShell
 
getRelevant(int[]) - Method in class NoisyOrShellHenrion
 
getRelevant(Object[]) - Method in class NoisyOrShellHenrion
 
getRelevant(Map) - Method in class NoisyOrShellHenrion
 
getRelevant(Object[], Object) - Method in class NoisyOrShellHenrion
 
getRelevant(int[]) - Method in class NoisyOrShellPearl
 
getRelevant(Object[]) - Method in class NoisyOrShellPearl
 
getRelevant(Map) - Method in class NoisyOrShellPearl
 
getRelevant(Object[], Object) - Method in class NoisyOrShellPearl
 
getRelevant(int[]) - Method in class TableShell
 
getRelevant(Object[]) - Method in class TableShell
 
getRelevant(Map) - Method in class TableShell
 
getRelevant(Object[], Object) - Method in class TableShell
 
getRepetitions() - Method in class EliminationHeuristic.RandomizedBestOfNStrategy
 
getResult() - Method in class RunReadNetwork
 
getResult() - Method in class RunWriteBIF
 
getResults(FiniteVariable, Object, FiniteVariable, Object, Object, Object, double, boolean, boolean) - Method in class SensitivityEngine
 
getResults(SensitivityConstraint) - Method in class SensitivityEngine
 
getResults() - Method in class SensMPEEngine
 
getResultsMap() - Method in class SensMPEReport
 
getResultsOld() - Method in class SensMPEEngine
 
getRoot() - Method in class Builder
 
getRoot() - Method in class DecisionNodeAbstract
 
getRoot() - Method in interface DecisionTree
 
getRoot() - Method in class DecisionTreeImpl
interface DecisionTree
getRootNodes() - Method in class RC2
 
getRoots() - Method in class HuginLogReader
 
getRoots() - Method in class RC
 
getSAXParser() - Method in class AbstractSaxHandler
 
getSAXParser() - Static method in class SkimmerEstimator
 
getScheduler() - Method in class BeliefPropagationSettings
 
getSchema() - Static method in class XmlbifParser
 
getScript() - Method in class ScriptExecution
 
getScriptFileExtension() - Method in class BatchScriptGenius
 
getScriptFileExtension() - Method in class BourneScriptGenius
 
getScriptFileExtension() - Method in class CShellScriptGenius
 
getScriptFileExtension() - Method in class PerlScriptGenius
 
getScriptFileExtension() - Method in interface ScriptGenius
 
getScriptLanguageDescription() - Method in class BatchScriptGenius
 
getScriptLanguageDescription() - Method in class BourneScriptGenius
 
getScriptLanguageDescription() - Method in class CShellScriptGenius
 
getScriptLanguageDescription() - Method in class PerlScriptGenius
 
getScriptLanguageDescription() - Method in interface ScriptGenius
 
getSecondsPerRCCall() - Static method in class RCSettings
 
getSecondsPerRCCall() - Static method in class Settings
 
getSeparatorStats() - Method in class JointWrapper
 
getSeparatorStats() - Method in class WrapperInferenceEngine
 
getSeparatorStats() - Method in class JoinTree
 
getSeparatorStats() - Method in class EDAlgorithm
 
getSeparatorStats() - Method in interface JointEngine
 
getSeparatorStats() - Method in class JoinTreeAlgorithm
 
getSeparatorStats() - Method in class RCEngine
 
getSeparatorStats() - Method in class EliminationOrders.JT
 
getSeparatorStats() - Method in interface JoinTreeStats.StatsSource
 
getSeTable(int) - Method in class EDNetwork
 
getSetOfAllCachedNodes(RC2) - Static method in class RC2Utils
 
getSetOfAllNodes(RC2) - Static method in class RC2Utils
 
getSetOfAllNonLeafNodes(RC2) - Static method in class RC2Utils
 
getSettings(PropertySuperintendent) - Method in class ApproxEngineGenerator
 
getSettings(Object, Class<E>, PropertySuperintendent, boolean) - Static method in class ApproxEngineGenerator
 
getSettings(PropertySuperintendent, boolean) - Static method in class EdgeDeletionEngineGenerator
 
getSettings(PropertySuperintendent) - Static method in class PropagationEngineGenerator
 
getSettings(PropertySuperintendent, boolean) - Static method in class PropagationEngineGenerator
 
getSettings(PropertySuperintendent) - Method in class RecoveryEngineGenerator
 
getSettings(PropertySuperintendent, boolean) - Static method in class RecoveryEngineGenerator
 
getSettings(PropertySuperintendent) - Method in class DefaultGenerator
 
getSettings(PropertySuperintendent, boolean) - Method in class DefaultGenerator
 
getSettings(PropertySuperintendent) - Static method in class RCEngineGenerator
 
getSettings(PropertySuperintendent, boolean) - Static method in class RCEngineGenerator
 
getSettings(BeliefNetwork) - Static method in class RCEngineGenerator
 
getSettings(PropertySuperintendent) - Static method in class RCEngineGenerator
 
getSettings(PropertySuperintendent, boolean) - Static method in class RCEngineGenerator
 
getShortDescription() - Method in interface CodeGenius
 
getShortDescription() - Method in class CPTCoder
 
getShortDescription() - Method in class EMCoder
 
getShortDescription() - Method in class MAPCoder
 
getShortDescription() - Method in class ModelCoder
 
getShortDescription() - Method in class MPECoder
 
getShortDescription() - Method in class ProbabilityQueryCoder
 
getShortDescription() - Method in class SensitivityCoder
 
getShortest(List) - Static method in class ParanoidFileFinder
 
getSingleCPTMap() - Method in class SensitivityReport
 
getSingleParamMap() - Method in class SensitivityReport
 
getSizes(IntSet) - Method in class Domain
 
getSizesLong(IntSet) - Method in class Domain
 
getSmileID() - Method in class DiagnosisType
 
getSnapshot() - Method in interface DecisionTree
 
getSnapshot() - Method in class DecisionTreeImpl
interface DecisionTree
getSoftEvidenceCPT(int) - Method in class EDAlgorithm
Given edge index i, returns CPT of soft evidence variable.
getSoftEvidenceEdgeTable(int) - Method in class EDNetwork
 
getSoftEvidenceTable(FiniteVariable) - Method in class Macros.Bridge
 
getStaticTagName() - Static method in class RCDgraph
 
getStaticTagName() - Static method in class RCDtree
 
getStatistics() - Method in class RC
 
getStatistics(boolean) - Method in class RC
 
getStats(boolean) - Method in class Bundle
 
getStats(IntSet[], Domain) - Static method in class JoinTreeAlgorithm
 
getStatsBig(Set[]) - Static method in class JoinTree
 
getStatsDouble(Set[]) - Static method in class JoinTree
 
getStdDev() - Method in class DataSetStatistic
This method calculates are returns the standard deviation of all the data in the set.
getStringifier() - Static method in class VariableImpl
 
getSubalgorithmPropertySuperintendent(PropertySuperintendent) - Method in class ApproxEngineGenerator
 
getSubDomainSize(Index, Domain) - Static method in class UaiEdgeCutter
 
GetSuffix(int) - Method in class SimpleCharStream
 
getSuggestedParameterValue() - Method in class SingleParamSuggestion
 
getSuggestedValue() - Method in interface SensitivitySuggestion
 
getSuggestedValue() - Method in class SingleCPTSuggestion
 
getSuggestedValue() - Method in class SingleParamSuggestion
 
getSuggestedValue(double, ProbabilityInterval) - Static method in class SingleParamSuggestion
 
getSynch() - Method in class Interruptable
We use a single, devoted Object to synchronize calls to Interruptable.runImpl(Object).
getSyntaxErrors() - Method in class AbstractSaxHandler
 
getSyntaxErrors() - Method in class RunReadNetwork
 
getSyntaxErrors() - Method in class RunReadBIF
 
getSyntaxErrors() - Method in interface RunReadBIF.MonitorableReusableParser
 
getSystemSoftwareSource() - Method in class ScriptExecution
 
getTab(int) - Static method in class XmlWriter
 
getTable(int) - Method in class RC
 
getTable(int) - Method in class RCEngine
 
getTables() - Method in class BeliefCompilation
 
getTableSizes() - Method in class AbstractSSAlgorithm
 
getTagName() - Static method in class Dtree
 
getTagName() - Method in class RC
 
getTagName() - Method in class RCDgraph
 
getTagName() - Method in class RCDtree
 
getTargetList() - Method in interface DSLNode
 
getTargetList() - Method in class DSLNodeImpl
Convenience method.
getTentativeHuginLogFilePath() - Method in interface CreationMethod.Settings
 
getTentativeHuginLogFilePath() - Method in class Settings
 
getTheoreticalCPTSize(FiniteVariable) - Method in interface BeliefNetwork
 
getTheoreticalCPTSize(FiniteVariable) - Method in class BeliefNetworkImpl
 
getTheta() - Method in class SingleParamSuggestion
 
getThreadGroup() - Method in interface DynaListener
 
getThreadGroup() - Method in interface NetworkIO.BeliefNetworkIOListener
 
getThreadGroup() - Method in interface EMThread.LearningListener
 
getThreadGroup() - Static method in class SystemGCThread
 
getThreadRunning() - Method in class RC
 
getTimeoutMillis() - Method in class BeliefPropagationSettings
 
getTimeoutMillis() - Method in class EDAlgorithm
 
getTiming() - Method in class DtreeCreateHMetis
Currently returns an array of length one, containing the same information as getHmetisTime()
getTiming() - Method in class DgraphCreateHMetis
Currently returns an array of length one, containing the same information as getHmetisTime()
getToken() - Method in class CPTImportColumnInfo
 
getToken(int) - Method in class HuginLogReader
 
getToken(int) - Method in class HuginReader
 
getToken(int) - Method in class NeticaReader
 
getTotal() - Method in interface JoinTreeStats.Stat
 
getTotal() - Method in class JoinTreeStats.StatImpl
 
getTotalCliqueTableSize() - Method in class HuginLogReader
 
getTotalSeparatorTableSize() - Method in class HuginLogReader
 
getTree(FiniteVariable) - Method in class XmlDocumentHandler
 
getTypeForFile(File) - Static method in class FileType
 
getTypeForFilter(FileFilter) - Static method in class FileType
 
getUforS(FiniteVariable) - Method in class Macros.Bridge
 
getUpperBound() - Method in class Interval
 
getURL() - Method in class FileType
 
getUsage() - Method in class JDKCompile
 
getUsage() - Method in class JDKRun
 
getUsage() - Method in interface Script
 
getUsageExample() - Method in class JDKCompile
 
getUsageExample() - Method in class JDKRun
 
getUsageExample() - Method in interface Script
 
getUseKB() - Method in class Settings
 
getUserEnumProperties() - Method in interface BeliefNetwork
 
getUserEnumProperties() - Method in class BeliefNetworkImpl
 
getUserMemoryProportion() - Method in class RCSettings
 
getUserMemoryProportion() - Method in class Settings
 
getUserObject() - Method in class BeliefNetworkImpl
 
getUserObject() - Method in interface Variable
 
getUserObject() - Method in class VariableImpl
 
getUserObject2() - Method in class BeliefNetworkImpl
 
getUtilIndices() - Method in class CPTInfo
 
getUtilMap() - Method in class CPTInfo
 
getValid() - Method in class AbstractInferenceEngine
 
getValid() - Method in class SynchronizedInferenceEngine
 
getValid() - Method in interface InferenceEngine
 
getValidRootHandler(String, Attributes) - Method in class XmlDocumentHandler
 
getValidRootHandler(String, Attributes) - Method in class AbstractSaxHandler
 
getValidRootHandler(String, Attributes) - Method in class UAI06Parser
 
getValidRootHandler(String, Attributes) - Method in class XmlbifParser
 
getValue() - Method in class CPTParameter
 
getValue() - Method in interface Parameter
 
getValue() - Method in class ParameterImpl
 
getValue(Variable) - Method in class EvidenceController
 
getValue() - Method in interface ArithmeticExpression
 
getValue() - Method in class BeliefCompilation
 
getValue() - Method in class JoinTreeInferenceEngineImpl
 
getValue() - Method in class S4DoubleExpression
 
getValue() - Method in class WrapperInferenceEngine
 
getValue(String) - Method in class NeticaObject
 
getValue(Attributes, String[]) - Static method in class XmlbifParser
 
getValue() - Method in class RCInferenceEngine
 
getValue(boolean) - Method in class FlagProperty
 
getValue() - Method in class MapJoinTree
 
getValue() - Method in class MapTree
 
getValue() - Method in class MiniTree
 
getValueIgnoreCase(Attributes, String) - Static method in class XmlbifParser
 
getValues() - Method in class CPTImportColumnInfo
 
getValues() - Method in class AbstractCodeOption
 
getValues() - Method in interface CodeOption
 
getValues() - Method in class ModelCoder.LibraryVersionOption
 
getValues() - Method in class OptionBreadth
 
getValues() - Method in class ProbabilityQueryCoder.MarginalScopeOption
 
getValueType() - Method in interface HuginNode
 
getValueType() - Method in class HuginNodeImpl
 
getVariable() - Method in class CPTParameter
 
getVariable() - Method in interface CPTShell
 
getVariable() - Method in class DecisionBackup
 
getVariable() - Method in class DecisionInternal
 
getVariable() - Method in class DecisionLeaf
 
getVariable() - Method in interface DecisionNode
 
getVariable() - Method in class DecisionNodeAbstract
 
getVariable() - Method in class DecisionShell
 
getVariable() - Method in class CPTImportColumnInfo
 
getVariable() - Method in class NoisyOrShellHenrion
 
getVariable() - Method in class NoisyOrShellPearl
 
getVariable() - Method in interface SensitivitySuggestion
 
getVariable() - Method in class SingleCPTSuggestion
 
getVariable() - Method in class SingleParamSuggestion
 
getVariable() - Method in class TableShell
 
getVariable() - Method in class VariableInstance
 
getVariables(DSLSubmodel) - Method in interface GenieNet
 
getVariables(DSLSubmodel) - Method in class GenieNetImpl
 
getVars(Collection) - Static method in class Dtree
Get all the vars contained within a collection of DtreeNodes.
getVars(Collection, Collection) - Static method in class Dtree
Get all the vars contained within a collection of DtreeNodes.
getVars() - Method in class DtreeNode
Returns a nonModifiableCollection containing the variables below this node.
getVars(Collection) - Static method in class RC
Get all the vars contained within a collection of RCNodes.
getVars(Collection, Collection) - Static method in class RC
Get all the vars contained within a collection of RCNodes.
getVars(Collection) - Method in class RCInstanceIterator
 
getVars(Collection) - Static method in class BasicInference
 
getVersion() - Method in interface HuginNet
 
getVersion() - Method in class HuginNetImpl
 
getVertexInfo(Object) - Method in interface GraphvizIO.ExtraDotInfoSupplier
 
getVertexInfo(Object) - Method in class GraphvizIO.StandardNodeDimensionSupplier
 
getWarnings() - Method in class AbstractCodeGenius
 
getWarnings() - Method in interface CodeGenius
 
getWarnings() - Method in class ModelCoder
 
getWeight(Object) - Method in class Hypergraph
 
getWeight(int) - Method in class LearningData
 
getWeightParameter(int) - Method in interface NoisyOrShell
 
getWeightParameter(int) - Method in class NoisyOrShellHenrion
 
getWeightParameter(int) - Method in class NoisyOrShellPearl
 
getWeightParameters() - Method in interface NoisyOrShell
 
getWeightParameters() - Method in class NoisyOrShellHenrion
 
getWeightParameters() - Method in class NoisyOrShellPearl
 
getWidth() - Method in class Dtree
Same as getClusterSize - 1.
getWildArgumentToken() - Method in class BatchScriptGenius
 
getWildArgumentToken() - Method in class BourneScriptGenius
 
getWildArgumentToken() - Method in class CShellScriptGenius
 
getWildArgumentToken() - Method in class PerlScriptGenius
 
getWildArgumentToken() - Method in interface ScriptGenius
 
getWorkingDirectory() - Method in class ScriptExecution
 
getWriter() - Method in class RunWriteBIF
 
getZeroFrequency() - Method in class DataSetStatistic
 
getZeroMiCorrection() - Method in class EDAlgorithm
Edge Corrections
getZeroMiCorrections() - Method in class EDAlgorithm
 
getZeroMiCorrections() - Method in class EDMPAlgorithm
 
givens - Variable in class XmlbifParser.Definition
 
gleanLayoutFromDot(File, Map) - Method in class GraphvizIO
 
GLOBAL - Variable in class Optimizer
 
Graph - Interface in edu.ucla.structure
The interface describing undirected graphs.
Graph - Class in il2.util
 
Graph(int) - Constructor for class Graph
 
graph - Variable in class Graph.Compressed
 
Graph.Compressed - Class in il2.util
 
Graphs - Class in edu.ucla.structure
A set of static routines for Graphs and DirectedGraphs.
GraphvizIO - Class in edu.ucla.belief.io
 
GraphvizIO() - Constructor for class GraphvizIO
 
GraphvizIO.ExtraDotInfoSupplier - Interface in edu.ucla.belief.io
 
GraphvizIO.StandardNodeDimensionSupplier - Class in edu.ucla.belief.io
 
GraphvizIO.StandardNodeDimensionSupplier(Collection) - Constructor for class GraphvizIO.StandardNodeDimensionSupplier
 
grep(Filter, Collection) - Method in interface FiniteVariable
 
grep(Pattern, boolean, Collection) - Method in interface FiniteVariable
 
grep(Matcher, boolean, Collection) - Method in interface FiniteVariable
 
grep(Filter, Collection) - Method in class FiniteVariableImpl
 
grep(Pattern, boolean, Collection) - Method in class FiniteVariableImpl
 
grep(Matcher, boolean, Collection) - Method in class FiniteVariableImpl
 
grep(Filter, Collection) - Method in class MappedList
 
grep(Pattern, boolean, Collection) - Method in class MappedList
 
grep(Matcher, boolean, Collection) - Method in class MappedList
 
groupInstancesByOutcome(Map) - Method in interface DecisionNode
 
groupInstancesByOutcome(Map) - Method in class DecisionNodeAbstract
 
guaranteedOptimal() - Method in class CachingDFBnB.CacheFactorInstance
 
GuessingSource - Class in edu.ucla.util.code
 
GuessingSource() - Constructor for class GuessingSource
 
guessLocation() - Method in class ClassModule
 
guessLocation() - Method in class JDKTool
 
guessLocation() - Method in class SoftwareEntity
 
guessLocationIfNecessary() - Method in class SoftwareEntity
 

H

HANDLE_MAIN - Static variable in class DSLSubmodelFactory
 
handleBeliefNetworkIOError(String) - Method in interface NetworkIO.BeliefNetworkIOListener
 
handleCancelation() - Method in interface NetworkIO.BeliefNetworkIOListener
 
handledClone(QuantitativeDependencyHandler) - Method in class EdgeDeletionInferenceEngine
 
handledClone(QuantitativeDependencyHandler) - Method in class PropagationInferenceEngineImpl
 
handledClone(QuantitativeDependencyHandler) - Method in class RecoveryInferenceEngine
 
handledClone(QuantitativeDependencyHandler) - Method in class HuginEngine
 
handledClone(QuantitativeDependencyHandler) - Method in class HuginWrapper
 
handledClone(QuantitativeDependencyHandler) - Method in class JoinTreeInferenceEngineImpl
 
handledClone(QuantitativeDependencyHandler) - Method in class RandomInferenceEngine
 
handledClone(QuantitativeDependencyHandler) - Method in class RCEngine
 
handledClone(QuantitativeDependencyHandler) - Method in class RCWrapper
 
handledClone(QuantitativeDependencyHandler) - Method in class SSEngine
 
handledClone(QuantitativeDependencyHandler) - Method in class SSWrapper
 
handledClone(QuantitativeDependencyHandler) - Method in class SynchronizedInferenceEngine
 
handledClone(QuantitativeDependencyHandler) - Method in class ZCEngine
 
handledClone(QuantitativeDependencyHandler) - Method in class ZCWrapper
 
handledClone(QuantitativeDependencyHandler) - Method in interface InferenceEngine
 
handledClone(QuantitativeDependencyHandler) - Method in class RCInferenceEngine
 
handleError(String) - Method in interface DynaListener
 
handleInferenceEngine(InferenceEngine) - Method in interface DynaListener
 
handleLearningError(String) - Method in interface EMThread.LearningListener
 
handleNewBeliefNetwork(BeliefNetwork, File) - Method in interface NetworkIO.BeliefNetworkIOListener
 
handleProgress(ProgressMonitorable, Estimate) - Method in interface NetworkIO.BeliefNetworkIOListener
 
handleSyntaxErrors(String[], FileType) - Method in interface NetworkIO.BeliefNetworkIOListener
 
hardBoundedConstrainedFill(Collection, IntSet, double) - Static method in class EliminationOrders
 
hasActiveVars() - Method in class DynamicEliminator
 
hasBinaryParents(BeliefNetwork, FiniteVariable) - Static method in class UaiMpeMain
 
hasDeterministicCpt(FiniteVariable) - Static method in class UaiEdgeCutter
 
hashCode() - Method in class AbstractInferenceEngine
 
hashCode() - Method in class BeliefNetworkImpl
 
hashCode() - Method in class CPTParameter
 
hashCode(Object[]) - Static method in class DecisionLeaf
 
hashcode - Variable in class Optimizer.EquivalenceKey
 
hashCode() - Method in class Optimizer.EquivalenceKey
 
hashCode(Object[]) - Static method in class Optimizer
based on jdk1.5.0 Arrays.hashCode()
hashCode() - Method in class SynchronizedInferenceEngine
 
hashCode() - Method in class LearningData
 
hashCode() - Method in class LearningData.Struct
 
hashCode() - Method in class RC2Node
 
hashCode() - Method in class TableIndex
 
hashCode() - Method in class VariableInstance
 
hashCode() - Method in class DirectedEdge
Swapping the vertices must result in a distinct hash.
hashCode() - Method in class Edge
 
hashCode() - Method in class HashDirectedGraph
 
hashCode() - Method in class HashGraph
 
hashCode() - Method in class Heap.HeapElement
Returns the hashCode of the object it contains.
hashCode() - Method in class IdentityArrayMap
 
hashCode() - Method in class MappedList
Returns the hash code value for this list.
hashCode() - Method in class FlagProperty.FlagValue
 
hashCode() - Method in class UserEnumValue
 
hashCode() - Method in class DoubleList
 
hashCode() - Method in class IntList
 
hashCode() - Method in class IntSet
 
hashCode() - Method in class Pair
Fulfills java.lang.Object.
hashCode() - Method in class UPair
Fulfills java.lang.Object.
hashCodeSpecial() - Method in class DtreeNode
 
HashDirectedGraph - Class in edu.ucla.structure
An implementation of a dirrected graph which stores the nodes and edges in a hash table to allow O(1) testing for inclusion, insertion, removal etc.
HashDirectedGraph() - Constructor for class HashDirectedGraph
Creates new HashDirectedGraph
HashDirectedGraph(int) - Constructor for class HashDirectedGraph
 
HashDirectedGraph(DirectedGraph) - Constructor for class HashDirectedGraph
 
HashGraph - Class in edu.ucla.structure
An implementation of a Graph which stores the nodes and edges in a hash table to allow O(1) testing for inclusion,insertion, removal etc.
HashGraph() - Constructor for class HashGraph
Creates new HashGraph
HashGraph(Graph) - Constructor for class HashGraph
 
HashGraph(int) - Constructor for class HashGraph
 
hasNext() - Method in class RCIterator
 
hasNext() - Method in class RCIteratorArray
 
hasNext() - Method in class RCIteratorTraversal
 
hasNext() - Method in class RCNodeInternalBinaryCache.ChildIterator
 
hasNext() - Method in class TableIndex.Iterator
returns true if some index values still remain to be visited.
hasNext() - Method in class DepthFirstIterator
 
hasNext() - Method in class RecursiveDepthFirstIterator
 
hasNext() - Method in interface IntIterator
 
hasOutcome(Object) - Method in class DecisionInternal
 
hasOutcome(Object) - Method in class DecisionLeaf
 
hasOutcome(Object) - Method in interface DecisionNode
 
hasOutcome(Object) - Method in class DecisionNodeAbstract
 
hasPath(BeliefNetwork, Map<String, Set<String>>, String, Variable) - Method in class Macros.Recoverables
 
hasPath(Object, Object) - Method in class BeliefNetworkImpl
 
hasPath(Object, Object) - Method in class AbstractDirectedGraph
Determines if there is a directed path from vertex1 to vertex2.
hasPath(Object, Object) - Method in interface DirectedGraph
Determines if there is a directed path from vertex1 to vertex2.
header() - Method in class Loci
 
HEALTH_ST - Variable in class VEVariance
 
Heap - Class in edu.ucla.structure
A class implementing a binary heap.
Heap() - Constructor for class Heap
Creates an empty heap.
Heap(Object[], double[]) - Constructor for class Heap
Creates a heap consisting made up of the objects, with corresponding priorities.
Heap - Class in il2.util
A class implementing the logic for a binary heap.
Heap() - Constructor for class Heap
Creates an empty heap.
Heap.HeapElement - Class in edu.ucla.structure
Helper class for implementing an object priority pair.
height - Variable in class Stats
 
height() - Method in class RCInfo
 
height - Variable in class RC2Node
This height is calculated by how many levels of nodes there are, not by how many edges there are between them.
height() - Method in class DGraph
 
heur - Variable in class CachingDFBnB
 
heur() - Method in class CachingDFBnB.HeurFunct
 
heuristic - Variable in class Macros.RankingArgs
 
HiddenProperty - Class in edu.ucla.util
 
highest() - Method in class IntPriorityQueue
Returns the highest priority element.
highestKey() - Method in class IntPriorityQueue
Returns the highest priority key.
HILL - Static variable in class SearchMethod
 
Hmetis - Class in edu.ucla.belief.dtree
This class is an interface library to the C++ hMeTiS library.
HMETIS_PartKway(int, int, int[], int[], int[], int[], int, int, int[], int[], int[], double[]) - Static method in class Hmetis
Call the hMetis function, and return 0 if success, or nonzero if an error happened.
HMETIS_PartKway(Hypergraph, int[], int, int[], double[]) - Static method in class Hmetis
Returns an integer array where each element is 0..numPartitions-1, representing the partition that hypernode was assigned.
HMETIS_PartKway(Hypergraph, int[], int, int[], int[], double[]) - Static method in class Hmetis
Returns an integer array where each element is 0..numPartitions-1, representing the partition that hypernode was assigned.
HMETIS_PartRecursive(int, int, int[], int[], int[], int[], int, int, int[], int[], int[], double[]) - Static method in class Hmetis
Call the hMetis function, and return 0 if success, or nonzero if an error happened.
HMETIS_PartRecursive(Hypergraph, int[], int, int[], double[]) - Static method in class Hmetis
Returns an integer array where each element is 0..numPartitions-1, representing the partition that hypernode was assigned.
HMETIS_PartRecursive(Hypergraph, int[], int, int[], int[], double[]) - Static method in class Hmetis
Returns an integer array where each element is 0..numPartitions-1, representing the partition that hypernode was assigned.
hookRCNodeInternalBinary(RCNode, Element, Document, Element, Map) - Method in class Xmlizer
 
hookRCNodeLeaf(RCNode, Element, Document) - Method in class Xmlizer
 
HUGIN - Static variable in class FileType
 
HUGIN57 - Static variable in class FileType
 
HuginClique - Class in edu.ucla.belief.io.hugin
 
HuginClique(int, List, int) - Constructor for class HuginClique
 
HuginCopier - Class in edu.ucla.belief.io.hugin
Copier for HuginNets.
HuginEngine - Class in edu.ucla.belief.inference
 
HuginEngine(BeliefNetwork, Dynamator) - Constructor for class HuginEngine
 
HuginEngine(BeliefNetwork, Dynamator, List) - Constructor for class HuginEngine
 
HuginEngine(BeliefNetwork, Dynamator, EliminationOrders.JT) - Constructor for class HuginEngine
 
HuginEngine(BeliefNetwork, Collection, Map, Dynamator) - Constructor for class HuginEngine
 
HuginEngineGenerator - Class in edu.ucla.belief.inference
 
HuginEngineGenerator() - Constructor for class HuginEngineGenerator
 
HuginFileVersion - Class in edu.ucla.belief.io.hugin
A class that represents an enumerated type over Hugin file versions.
HuginFunction - Class in edu.ucla.belief.io.hugin
 
HuginFunction(String, List) - Constructor for class HuginFunction
 
HuginLogReader - Class in edu.ucla.belief.io.hugin
HuginLogReader - a class that parses Hugin ".hlg" files and returns a String representation of a dtree.
HuginLogReader(InputStream) - Constructor for class HuginLogReader
 
HuginLogReader(Reader) - Constructor for class HuginLogReader
 
HuginLogReader(HuginLogReaderTokenManager) - Constructor for class HuginLogReader
 
HuginLogReaderConstants - Interface in edu.ucla.belief.io.hugin
 
HuginLogReaderTokenManager - Class in edu.ucla.belief.io.hugin
 
HuginLogReaderTokenManager(SimpleCharStream) - Constructor for class HuginLogReaderTokenManager
 
HuginLogReaderTokenManager(SimpleCharStream, int) - Constructor for class HuginLogReaderTokenManager
 
HuginNet - Interface in edu.ucla.belief.io.hugin
 
HuginNetImpl - Class in edu.ucla.belief.io.hugin
 
HuginNetImpl() - Constructor for class HuginNetImpl
 
HuginNetImpl(boolean) - Constructor for class HuginNetImpl
 
HuginNetImpl(Map) - Constructor for class HuginNetImpl
 
HuginNetImpl(BeliefNetworkImpl) - Constructor for class HuginNetImpl
 
HuginNode - Interface in edu.ucla.belief.io.hugin
A class for encapsulating a hugin node description.
HuginNodeImpl - Class in edu.ucla.belief.io.hugin
Encapsulates a hugin node description.
HuginNodeImpl(String, List, Map, int, int) - Constructor for class HuginNodeImpl
 
HuginNodeImpl(String, Map) - Constructor for class HuginNodeImpl
Constructs with default values: type NODE and DISCRETE.
HuginNodeImpl(String, Map, int, int) - Constructor for class HuginNodeImpl
 
HuginNodeImpl(String, List, Map) - Constructor for class HuginNodeImpl
 
HuginNodeImpl(FiniteVariable) - Constructor for class HuginNodeImpl
 
HuginPotential - Class in edu.ucla.belief.io.hugin
 
HuginPotential(List, List, Map) - Constructor for class HuginPotential
 
HuginPotential(List, List, Map, boolean) - Constructor for class HuginPotential
 
HuginReader - Class in edu.ucla.belief.io.hugin
 
HuginReader(InputStream) - Constructor for class HuginReader
 
HuginReader(InputStream, String) - Constructor for class HuginReader
 
HuginReader(Reader) - Constructor for class HuginReader
 
HuginReader(HuginReaderTokenManager) - Constructor for class HuginReader
 
HuginReaderConstants - Interface in edu.ucla.belief.io.hugin
 
HuginReaderTokenManager - Class in edu.ucla.belief.io.hugin
 
HuginReaderTokenManager(SimpleCharStream) - Constructor for class HuginReaderTokenManager
 
HuginReaderTokenManager(SimpleCharStream, int) - Constructor for class HuginReaderTokenManager
 
HuginWrapper - Class in edu.ucla.belief.inference
 
HuginWrapper(BeliefNetwork) - Constructor for class HuginWrapper
 
HuginWrapper(BeliefNetwork, Collection, Map) - Constructor for class HuginWrapper
 
HuginWrapper(BeliefNetwork, List) - Constructor for class HuginWrapper
 
HuginWrapper(BeliefNetwork, EliminationOrders.JT) - Constructor for class HuginWrapper
 
HuginWrapper(BeliefNetwork, EliminationOrders.JT, QuantitativeDependencyHandler) - Constructor for class HuginWrapper
 
Hypergraph - Class in edu.ucla.belief.dtree
This class represents Hypergraph objects.
Hypergraph(List) - Constructor for class Hypergraph
Create a Hypergraph from a List of DtreeNodeLeafs.
Hypergraph(Map, int) - Constructor for class Hypergraph
Create a Hypergraph.
Hypergraph(int) - Constructor for class Hypergraph
Create a Hypergraph.
hyperNodes() - Method in class Hypergraph
 

I

id(T, Object) - Static method in class Macros
 
id - Variable in class HuginClique
 
ID - Static variable in interface HuginLogReaderConstants
 
ID - Static variable in interface HuginReaderConstants
 
ID - Static variable in interface NeticaReaderConstants
 
id - Variable in class XmlbifParser.Variable
 
id - Variable in class VariableImpl
 
IDComparator - Class in edu.ucla.belief
 
IDComparator() - Constructor for class IDComparator
 
identifierChanged(String, Variable) - Method in interface BeliefNetwork
 
identifierChanged(String, Variable) - Method in class BeliefNetworkImpl
 
IdentityArrayMap - Class in edu.ucla.structure
Cheap but slow.
IdentityArrayMap() - Constructor for class IdentityArrayMap
 
identityMap(Collection) - Static method in class Maps
 
idList() - Method in class HuginLogReader
 
idList() - Method in class HuginReader
 
idString - Variable in class XmlbifParser.Variable
 
idToVariableMap(BeliefNetwork) - Static method in class Prune
Returns a map from id to variable for the given belief network.
ignore(File) - Method in class ParanoidFileFinder
 
IL1 - Variable in class ModelCoder.LibraryVersionOption
 
IL2 - Variable in class ModelCoder.LibraryVersionOption
 
il2.bridge - package il2.bridge
 
il2.inf - package il2.inf
 
il2.inf.bp - package il2.inf.bp
 
il2.inf.bp.schedules - package il2.inf.bp.schedules
 
il2.inf.edgedeletion - package il2.inf.edgedeletion
 
il2.inf.experimental - package il2.inf.experimental
 
il2.inf.jointree - package il2.inf.jointree
 
il2.inf.map - package il2.inf.map
 
il2.inf.mini - package il2.inf.mini
 
il2.inf.rc - package il2.inf.rc
 
il2.inf.structure - package il2.inf.structure
 
il2.inf.structure.minfill2 - package il2.inf.structure.minfill2
 
il2.model - package il2.model
 
il2.util - package il2.util
 
il2Partials() - Static method in enum CrouchingTiger.DynamatorImpl
 
il2s() - Static method in enum CrouchingTiger.DynamatorImpl
 
image - Variable in class Token
The string image of the token.
image(Set, Map) - Static method in class Prune
Returns the image of the given set according to the given map.
imagefilename - Variable in enum EdgeDeletionInferenceEngine.Command
 
ImpactProperty - Class in edu.ucla.util
 
inc - Variable in class Loci.Footer.Mlink
 
INCLUDE - Static variable in class ExcludePolicy
 
inComing(Object) - Method in class BeliefNetworkImpl
 
inComing(Object) - Method in class DecisionTreeImpl
interface DirectedGraph
inComing(Object) - Method in interface DirectedGraph
Constructs an Iterator over the vertices adjacent to edges entering the specified vertex.
inComing(Object) - Method in class HashDirectedGraph
Constructs an Iterator over the vertices adjacent to edges entering the specified vertex.
inComing(int) - Method in class IntDirectedGraph
 
INCREMENTAL_STACK_GROWTH - Variable in class KnowledgeBase
Must be a positive value.
INCREMENTAL_STACK_GROWTH - Variable in class KnowledgeBaseImpl
Must be a positive value.
incrementKey(int, double) - Method in class IntPriorityQueue
Changes the key of the given element by the given value.
inDegree(Object) - Method in class BeliefNetworkImpl
 
inDegree(Object) - Method in class AbstractDirectedGraph
 
inDegree(Object) - Method in interface DirectedGraph
Returns the number of edges entering the vertex.
inDegree(Object) - Method in class HashDirectedGraph
Returns the number of edges entering the vertex.
inDegree(int) - Method in class IntDirectedGraph
 
INDENTATION - Static variable in class XmlbifWriter
 
index() - Method in interface CPTShell
 
index - Variable in class Optimizer.Unsortable
 
index() - Method in class DecisionShell
 
index(Object) - Method in interface FiniteVariable
Returns the index associated with the instance.
index(Object) - Method in class FiniteVariableImpl
Returns the index associated with the instance.
index(FiniteVariable) - Method in class CPTInfo
 
index() - Method in class NoisyOrShellHenrion
 
index() - Method in class NoisyOrShellPearl
 
index() - Method in class Table
Returns the TableIndex of this Table.
index(int[]) - Method in class TableIndex
Converts the multidimensional index to the corresponding linear index.
index(Map) - Method in class TableIndex
 
index(Object[]) - Method in class TableIndex
 
index() - Method in class TableShell
 
index(int) - Method in class EliminationTree
 
index(EnumProperty) - Static method in class VariableImpl
 
index(double[]) - Static method in class DblArrays
Sets values[i]=i for all indices.
index(int) - Static method in class DblArrays
returns an array of length size where result[i]=i.
index(int[]) - Static method in class IntArrays
Sets values[i]=i for all indices.
index(int) - Static method in class IntArrays
returns an array of length size where result[i]=i.
index(String) - Method in class Domain
 
Index - Class in il2.model
 
Index(Domain, IntSet) - Constructor for class Index
 
Index(Domain, int) - Constructor for class Index
 
Index(Index) - Constructor for class Index
 
Index.Partition - Class in il2.model
 
Index.Partition(Index[], int[]) - Constructor for class Index.Partition
 
IndexedHeap - Class in il2.util
 
IndexedHeap() - Constructor for class IndexedHeap
 
IndexedJoinTree - Class in il2.inf.map
 
IndexedJoinTree(Index[], IntList) - Constructor for class IndexedJoinTree
 
indexFirstOccurrence - Variable in class LearningData.Struct
 
indexForToken(String) - Method in class CPTImportColumnInfo
 
indexingList() - Method in class MultiValuedCNF
This returns a list of all vars in the BN, not only those in the CNF.
indexObserved - Variable in class XmlbifParser.Variable
 
indexOf(EnumValue) - Static method in class DiagnosisType
 
indexOf(EnumValue) - Static method in class DSLNodeType
 
indexOf(Object) - Method in class MappedList
Returns the index in this list of the first occurence of the specified element or -1 if this list does not contain this element.
indexOf(EnumValue) - Method in class CSITypeProperty
 
indexOf(EnumValue) - Method in interface EnumProperty
 
indexOf(EnumValue) - Method in class FlagProperty
 
indexOf(EnumValue) - Method in class InOutDegreeProperty
 
indexOf(EnumValue) - Method in class UserEnumProperty
 
indexOf(Object) - Method in class WeakLinkedList
Returns the index in this list of the first occurrence of the specified element, or -1 if the List does not contain this element.
indexOf(int) - Method in class IntSet
 
indicators() - Method in class JoinTreeInference
 
indicatorTable(Domain, int) - Static method in class Table
 
indices - Variable in class Partition
The index of each partition
indices - Variable in class Index.Partition
 
indices(IntSet) - Method in class IntSet
Returns the indices in this set of the items in the subset
indicesAsStrings(int, int, char, String) - Static method in class ModelCoder
 
induce(BayesianNetwork, IntList) - Method in enum Algorithm.Order2JoinTree
 
inducedGraph(Map) - Static method in class BeliefNetworks
Generates the graph induced by the potential map.
induceGraph(Map) - Method in interface BeliefNetwork
 
induceGraph(Map) - Method in class BeliefNetworkImpl
 
induceGraph(Map, NodeLinearTask) - Method in class BeliefNetworkImpl
 
InferenceEngine - Interface in edu.ucla.belief
 
InferenceValidProperty - Class in edu.ucla.util
 
inflate(Factory) - Method in class DecisionBackup
 
InflibFileFilter - Class in edu.ucla.belief.io
 
InflibFileFilter(String[], String) - Constructor for class InflibFileFilter
 
info - Variable in class UaiMapSolution
Additional information from the algorithm in the form of pairs.
info - Variable in class UaiPreprocessResult
Additional information returned by an algorithm in form.
init() - Method in class CPTImport.CompleteParameterRecorder
 
init() - Method in class CPTImport.IncompleteParameterRecorder
 
init() - Method in interface CPTImport.ParameterRecorder
 
init(File) - Method in interface Estimate
 
init(File) - Method in class SkimmerEstimator
interface Estimate
init(File) - Method in class SkimmerEstimator
interface Estimate
init() - Method in class CachingDFBnB.HeurResult
 
init(CachingDFBnB.OrderingAlgo) - Method in class CachingDFBnB.SearchGraph
 
init() - Method in class RC.RCCounters
 
init(Collection, Collection, boolean, ArrayList) - Method in class RCNodeLeaf
Function which should be called if using non-complete constructor.
init() - Method in class Test
 
init(Collection) - Method in class Converter
Initializes the fields without requiring a call to convert ().
initCacheOrder(ArrayList) - Method in class RCNode
 
initCacheOrder(ArrayList) - Method in class RCNodeInternalBinaryCache
 
initCacheOrder(ArrayList) - Method in class RCNodeLeaf
 
initDurationMillisElapsed - Variable in class MapRunner.MapResult
 
initDurationMillisElapsed - Variable in class MapSearch.MapInfo
 
initDurationMillisProfiled - Variable in class MapRunner.MapResult
 
initDurationMillisProfiled - Variable in class MapSearch.MapInfo
 
initGraph(int[][], int[][], int[]) - Static method in class Util
Initializes a graph in the internal representation from a graph in the external representation.
initial(Table[], IntSet, IntList) - Static method in class MapInitializer
 
INITIAL_STACK_SIZE - Variable in class KnowledgeBase
Must be a positive value.
INITIAL_STACK_SIZE - Variable in class KnowledgeBaseImpl
Must be a positive value.
InitializationMethod - Class in edu.ucla.belief.inference.map
 
InitializationMethod() - Constructor for class InitializationMethod
 
initialize(Collection) - Method in class RC2Node
Called to initialize the nodes.
initialize(Collection) - Method in class RC2NodeInternal
 
initialize(Collection) - Method in class RC2NodeLeaf
 
initialize(Collection) - Method in class RC2NodeLeafEvidInd
 
initialize(List, Collection, boolean) - Method in class BucketEliminator
 
initialize(IntSet) - Method in class IndexedHeap
 
initialize(Map) - Method in class MappedHeap
 
initializeInheritance(Map) - Method in class NeticaObject
 
initProperties() - Static method in class VariableImpl
 
initRoot(DecisionNode) - Method in class DecisionTreeImpl
 
innerProduct(Table, Table) - Static method in class Table
 
innerProduct(Table, Table) - Static method in class TableScaled
 
InOutDegreeProperty - Class in edu.ucla.util
 
InOutDegreeProperty.InOutDegree - Class in edu.ucla.util
 
inputFile - Variable in class Test
 
inputOrd(int) - Method in class Pedigree.PseudoLoci
 
inputToChromOrder - Variable in class Loci.Header
 
insert(int, Object) - Method in interface FiniteVariable
 
insert(int, Object) - Method in class FiniteVariableImpl
 
insert(Object, double) - Method in class Heap
Adds element to heap.
insert(int, double) - Method in class DoubleList
 
insert(int, int) - Method in class IntList
 
insertAt(int, int) - Method in class IntSet
 
insertParent(FiniteVariable, DecisionNode, Factory) - Method in interface DecisionNode
 
insertParent(FiniteVariable, DecisionNode, Factory) - Method in class DecisionNodeAbstract
 
insertState(FiniteVariable, int, Object) - Method in interface BeliefNetwork
 
insertState(FiniteVariable, int, Object) - Method in class BeliefNetworkImpl
 
insertState(int) - Method in interface CPTShell
 
insertState(int) - Method in class DecisionShell
 
insertState(int) - Method in class NoisyOrShellHenrion
 
insertState(int) - Method in class NoisyOrShellPearl
 
insertState(int) - Method in class Table
 
insertState(int) - Method in class TableShell
 
instance(int) - Method in interface FiniteVariable
Returns the instance associated with the index.
instance(String) - Method in interface FiniteVariable
 
instance(int) - Method in class FiniteVariableImpl
Returns the instance associated with the index.
instance(String) - Method in class FiniteVariableImpl
Returns the instance represented by the string.
instance(String) - Method in interface Variable
 
instanceIndex(int, String) - Method in class Domain
 
InstanceIterator - Class in il2.inf.structure
 
InstanceIterator(Domain, int[], IntSet) - Constructor for class InstanceIterator
 
InstanceIterator(Domain, int[], IntList) - Constructor for class InstanceIterator
 
InstanceIterator.IterationRec - Class in il2.inf.structure
 
instanceList(Attributes, List) - Method in class Builder
 
instanceName(int, int) - Method in class Domain
 
instanceNames(int) - Method in class Domain
 
instances() - Method in interface FiniteVariable
 
instances() - Method in class FiniteVariableImpl
 
instantiation - Variable in class MapRunner.MapResult
 
instantiation - Variable in class UaiMapSolution
The instantiation of MAP variables.
Instantiation - Class in il2.util
 
Instantiation() - Constructor for class Instantiation
 
Instantiation(int, int) - Constructor for class Instantiation
 
Instantiation(IntSet, int[]) - Constructor for class Instantiation
 
InstantiationXmlizer - Class in edu.ucla.belief.io
 
InstantiationXmlizer() - Constructor for class InstantiationXmlizer
 
InstantiationXmlizer.RootCheckHandler - Class in edu.ucla.belief.io
 
InstantiationXmlizer.RootCheckHandler() - Constructor for class InstantiationXmlizer.RootCheckHandler
 
InstantiationXmlizer.ValidRootHandler - Class in edu.ucla.belief.io
 
InstantiationXmlizer.ValidRootHandler() - Constructor for class InstantiationXmlizer.ValidRootHandler
 
INT_ALPHABET_LAST_INDEX - Static variable in class ParameterImpl
 
INT_ALPHABET_LENGTH - Static variable in class ParameterImpl
 
INT_ALPHABET_LENGTH_PLUS - Static variable in class ParameterImpl
 
INT_CEILING_CPT_SIZE - Static variable in class ModelCoder
 
INT_DEFAULT_NUM_CASES - Static variable in class Simulator
 
INT_DEPTH_ABANDON - Static variable in class JDKTool
 
INT_DIM_PADDING - Static variable in class GraphvizIO
 
INT_ID_COUNTER - Static variable in class Xmlizer
 
INT_INDENT_BASE - Static variable in class XmlWriter
 
INT_INDENT_DELTA - Static variable in class XmlWriter
 
INT_INVALID_DTREE_STAT - Static variable in class Stats
 
INT_MAX_ITERATIONS_DEFAULT - Static variable in class BeliefPropagationSettings
 
INT_MAX_ITERATIONS_DEFAULT - Static variable in class EDAlgorithm
 
INT_MINFILL_REPS_DEFAULT - Static variable in class EliminationHeuristic
 
INT_MINIMUM_VARIABLES - Static variable in class Dynamator
 
INT_MINUTE_HOUR_THRESHOLD - Static variable in class RCSettings
 
INT_MINUTE_HOUR_THRESHOLD - Static variable in class Computation
 
INT_MINUTE_HOUR_THRESHOLD - Static variable in class Settings
 
INT_NAME_COUNTER - Static variable in class UserEnumProperty
 
INT_NUM_CASES_CEILING - Static variable in class Simulator
 
INT_NUM_CASES_FLOOR - Static variable in class Simulator
 
INT_NUM_FILES_CEILING - Static variable in class Simulator
 
INT_NUM_FILES_DEFAULT - Static variable in class Simulator
 
INT_NUM_FILES_FLOOR - Static variable in class Simulator
 
INT_NUM_PROPERTIES - Static variable in class VariableImpl
 
INT_POSITION_PREFIX - Static variable in class XmlbifWriter
 
INT_PRIORITY_READ - Static variable in class NetworkIO
 
INT_REPETITIONS - Static variable in class SystemGCThread
 
INT_ROOT_COUNTER - Static variable in class Xmlizer
 
INT_SECOND_MINUTE_THRESHOLD - Static variable in class RCSettings
 
INT_SECOND_MINUTE_THRESHOLD - Static variable in class Computation
 
INT_SECOND_MINUTE_THRESHOLD - Static variable in class Settings
 
INT_SIZE_ACCUMULATOR_INITIAL - Static variable in class XmlbifParser
 
INT_WIDTH_DIGITS - Static variable in class Macros
 
IntArrays - Class in edu.ucla.util
A class consisting of static utility functions dealing with integer arrays.
IntArrays() - Constructor for class IntArrays
 
IntDirectedGraph - Class in edu.ucla.structure
 
IntDirectedGraph() - Constructor for class IntDirectedGraph
 
IntDirectedGraph(int[][], int[][]) - Constructor for class IntDirectedGraph
 
intDSLNodeType - Variable in class PotentialInfo
 
integerArray(int) - Static method in class IntArrays
 
integerIndex(int[]) - Static method in class IntArrays
 
intention - Variable in class BeliefNetwork.Auditor.Deed
 
INTERCHANGE - Static variable in class FileType
 
interference - Variable in class Loci.Footer
 
internal(Attributes) - Method in class Builder
 
INTERNAL - Static variable in class InOutDegreeProperty
 
internalForID(String) - Method in class DecisionTreeImpl
interface Factory
internalForID(String) - Method in interface Factory
 
INTERNALS - Static variable in class Classifier
 
internals - Variable in class Stats
 
interrupt() - Method in class Interruptable
 
Interruptable - Class in edu.ucla.util
A base class that helps you define a piece of code that might be invoked "too often", that is: a piece of code that performs an expensive task that must be restarted afresh whenever it is run at all.
Interruptable() - Constructor for class Interruptable
 
Interruptable.Veto - Interface in edu.ucla.util
Implement this interface to define a callback for deciding whether or not to go ahead with an interruption.
interruptStartGroup() - Method in class RepetitionThread
 
intersect(SensitivityTable) - Method in class SensitivityTable
 
INTERSECT - Static variable in class SetOperation
 
intersect(Interval) - Method in class Interval
 
intersection(IntSet) - Method in class IntSet
 
interval(int) - Method in class SensitivityTable
 
Interval - Class in edu.ucla.util
Class for interval.
Interval() - Constructor for class Interval
 
Interval(double) - Constructor for class Interval
 
Interval(double, double) - Constructor for class Interval
 
Interval(Interval, double) - Constructor for class Interval
 
intervalSum(double[], int, int) - Static method in class ArrayUtils
Returns the sum of the given consecutive range of values in the given array.
IntGraph - Class in edu.ucla.structure
 
IntGraph() - Constructor for class IntGraph
 
IntGraph(int[][]) - Constructor for class IntGraph
 
IntIterator - Interface in edu.ucla.util
An iterface describing an iterator over integers.
IntList - Class in il2.util
 
IntList() - Constructor for class IntList
Creates a new instance of IntList
IntList(IntList) - Constructor for class IntList
 
IntList(int[]) - Constructor for class IntList
 
IntList(int) - Constructor for class IntList
 
IntMap - Class in il2.util
 
IntMap() - Constructor for class IntMap
 
IntMap(IntMap) - Constructor for class IntMap
 
IntMap(int) - Constructor for class IntMap
 
IntMap(IntSet, IntList) - Constructor for class IntMap
 
IntMap(int[], int[]) - Constructor for class IntMap
 
intoMapping(TableIndex) - Method in class TableIndex
Returns an array where result[i] is the entry in this index that is compatible with the ith entry in ind2.
IntPriorityQueue - Class in il2.inf.structure.minfill2
A priority queue implemented with a heap where elements are ints in [0,N-1] for some N, where keys are doubles, where lower keys are higher priority, and where the queue may not contain duplicate items.
IntPriorityQueue(int, int[], double[]) - Constructor for class IntPriorityQueue
Initializes the priority queue with the given elements.
IntPriorityQueue(int) - Constructor for class IntPriorityQueue
Initializes an empty priority queue.
IntSet - Class in il2.util
 
IntSet() - Constructor for class IntSet
Creates a new instance of IntSet
IntSet(int) - Constructor for class IntSet
 
IntSet(IntSet) - Constructor for class IntSet
 
IntSet(IntList) - Constructor for class IntSet
 
IntSet(int[]) - Constructor for class IntSet
 
IntStats - Class in il2.util
 
IntStats() - Constructor for class IntStats
 
intValueOf(StringBuilder) - Static method in class XmlbifParser
 
INVALID_LEXICAL_STATE - Static variable in error TokenMgrError
Tried to change to an invalid lexical state.
invalidate(int) - Method in class Messenger
 
invalidate(int) - Method in class RC
 
invalidateAll() - Method in class Messenger
 
inverse(Map, Map) - Static method in class Maps
 
inverse(Map) - Static method in class Maps
 
inverse(IntList) - Static method in class IntMap
 
invert() - Method in class Table
 
invertInPlace() - Method in class Table
 
IO - Class in il2.bridge
 
IO() - Constructor for class IO
 
isAcyclic() - Method in class BeliefNetworkImpl
 
isAcyclic() - Method in class AbstractDirectedGraph
Determines whether or not the graph is acyclic.
isAcyclic() - Method in interface DirectedGraph
Determines whether or not the graph is acyclic.
isAcyclic() - Method in interface Graph
Determines whether or not the graph is acyclic.
isAcyclic() - Method in class HashGraph
Determines whether or not the graph is acyclic.
isAnscestor(DSLSubmodel, Variable) - Method in interface GenieNet
 
isAnscestor(DSLSubmodel, Variable) - Method in class GenieNetImpl
The first call is expensive.
isAsynchronous() - Method in class MessagePassingScheduler
 
isAsynchronous() - Method in class ParallelSchedule
 
isAsynchronous() - Method in class SequentialSchedule
 
isAsynchronous() - Method in class TreeSchedule
 
isBridge(FiniteVariable, FiniteVariable, BeliefNetwork) - Static method in class Macros
http://en.wikipedia.org/wiki/Bridge_(graph_theory)
isBridge(BeliefNetwork) - Method in class Macros.Recoverable
 
isChangingVar(FiniteVariable) - Method in class Pedigree.GeneticNetwork
 
isCoding(BeliefNetwork) - Method in class UaiMpeMain
 
isCodingCheckNode(FiniteVariable) - Static method in class UaiMpeMain
 
isCodingInfoNode(FiniteVariable) - Static method in class UaiMpeMain
 
isCodingNetwork(BeliefNetwork) - Static method in class UaiMpeMain
 
isCommitted() - Method in class CPTInfo
 
isCompilable() - Method in class AbstractCodeGenius
 
isCompilable() - Method in interface CodeGenius
 
isComplete() - Method in class LearningDataOld
Determines if every evidence map in list contains an instantiation of every variable.
isComplete(Set) - Method in class LearningDataOld
Determines if every evidence map in list contains an instantiation of every variable in subset "vars".
isComplex1(int) - Method in class Pedigree.PseudoLoci
 
isComplex2(int) - Method in class Pedigree.PseudoLoci
 
isConnected() - Method in interface Graph
Determines whether or not the graph is connected.
isConnected(Object, Object) - Method in interface Graph
Determines if there is a path from vertex1 to vertex2.
isConnected(Graph) - Static method in class Graphs
Returns true if the graph is connected.
isConnected() - Method in class HashGraph
Determines whether or not the graph is connected.
isConnected(Object, Object) - Method in class HashGraph
Determines if there is a path from vertex1 to vertex2.
isConnected(IntSet) - Method in class Graph
 
isCyclic() - Method in class RecursiveDepthFirstIterator
 
isDataCompleteFor(FiniteVariable) - Method in class CPTImport
 
isDeeplyEquivalent(DecisionNode, double, Map) - Method in interface DecisionNode
 
isDeeplyEquivalent(DecisionNode, double, Map) - Method in class DecisionNodeAbstract
 
isDescendant(DecisionNode) - Method in interface DecisionNode
 
isDescendant(DecisionNode) - Method in class DecisionNodeAbstract
 
isDeterministicCpt(double[]) - Static method in class UaiMpeMain
 
isDtreeRequired() - Method in class Settings
 
isDtreeSettingChanged() - Method in class Settings
 
isEditable() - Method in class ApproxEngineGenerator
 
isEditable() - Method in class PropagationEngineGenerator
 
isEditable() - Method in class DecisionBackup
 
isEditable() - Method in interface DecisionNode
 
isEditable() - Method in class DecisionNodeAbstract
 
isEditable() - Method in class Dynamator
 
isEmpty() - Method in class Macros.RecoveryInfo
 
isEmpty() - Method in class BeliefNetworkImpl
 
isEmpty() - Method in class EvidenceController
 
isEmpty() - Method in class LearningData
 
isEmpty() - Method in class LearningDataOld
Determines if list is empty.
isEmpty() - Method in class AbstractDirectedGraph
 
isEmpty() - Method in class HashGraph
 
isEmpty() - Method in class Heap
Returns whether or not the heap is empty.
isEmpty() - Method in class IdentityArrayMap
 
isEmpty() - Method in class MappedList
Returns true if this list contains no elements.
isEmpty() - Method in class Interval
 
isEmpty() - Method in class Heap
Returns whether or not the heap is empty.
isEmpty() - Method in class IntSet
 
isError() - Method in class ScriptExecution
 
isExact() - Method in class MiniTree
 
isExhaustive() - Method in class EdgeDeletionInferenceEngine
 
isExhaustive() - Method in class PropagationInferenceEngineImpl
 
isExhaustive() - Method in class RecoveryInferenceEngine
 
isExhaustive() - Method in class JoinTreeInferenceEngineImpl
 
isExhaustive() - Method in class RandomInferenceEngine
 
isExhaustive() - Method in class SynchronizedInferenceEngine
 
isExhaustive() - Method in class WrapperInferenceEngine
 
isExhaustive() - Method in interface InferenceEngine
 
isExhaustive() - Method in class RCInferenceEngine
 
isFinished() - Method in class HuginReader
interface ProgressMonitorable
isFinished() - Method in class NodeLinearTask
 
isFinished() - Method in class Simulator
interface ProgressMonitorable
isFinished() - Method in class CompoundTask
 
isFinished() - Method in interface ProgressMonitorable
 
isFinished() - Method in class WeightedTask
 
isFlag() - Method in class AbstractEnumProperty
 
isFlag() - Method in class AbstractCodeOption
 
isFlag() - Method in interface CodeOption
 
isFlag() - Method in class MAPCoder.OptionPrune
 
isFlag() - Method in class MAPCoder.OptionTimings
 
isFlag() - Method in class OptionWithComments
 
isFlag() - Method in interface EnumProperty
 
isFlag() - Method in class FlagProperty
 
isFlag() - Method in class UserEnumProperty
 
isFounder() - Method in class Person
 
isFrozen() - Method in class EvidenceController
 
isGenetic() - Method in class UaiPeMain
 
isGeneticNetwork(BeliefNetwork, Map<FiniteVariable, Object>) - Static method in class RC_Link_UAI2006
 
isGuess() - Method in class SoftwareEntity
 
isHidden(Variable) - Static method in class HiddenProperty
 
isHighlyDeterministic(BeliefNetwork) - Method in class UaiMpeMain
 
isHuginType() - Method in class FileType
 
isInterrupted() - Method in class ScriptExecution
 
isLeaf() - Method in class DecisionBackup
 
isLeaf() - Method in class DecisionInternal
 
isLeaf() - Method in interface DecisionNode
 
isLeaf() - Method in class DecisionNodeAbstract
 
isLeaf() - Method in class DtreeNode
 
isLeaf() - Method in class DtreeNodeInternal
 
isLeaf() - Method in class DtreeNodeLeaf
 
isLeaf() - Method in class RC2Node
 
isLeaf() - Method in class RC2NodeInternal
 
isLeaf() - Method in class RC2NodeLeaf
 
isLeaf() - Method in class RC2NodeLeafEvidInd
 
isLeaf() - Method in class RCNode
 
isLeaf() - Method in class RCNodeInternalBinaryCache
 
isLeaf() - Method in class RCNodeLeaf
 
isLeaf(int) - Method in class IntGraph
 
isLeaf(int) - Method in class JoinTree
 
isLoaded() - Static method in class JVMTI
 
isLocked() - Method in class DoubleList
 
isLocked() - Method in class IntList
 
isMAPVariable() - Method in interface StandardNode
Moved from HuginNode @since 062204
isMAPVariable() - Method in class StandardNodeImpl
Moved from HuginNodeImpl 062204 @since 071603
isMember(DecisionNode) - Method in class Classifier
 
isModified() - Method in class AbstractEnumProperty
 
isModified() - Method in interface EnumProperty
 
isModified() - Method in class UserEnumProperty
 
isMultiEvent() - Method in class SensitivityCoder
 
isNatural() - Method in enum XmlbifParser.VariableType
 
isOneOf(String, String[]) - Static method in class XmlbifParser
 
isParallel() - Method in class MessagePassingScheduler
 
isPoint() - Method in class Interval
 
isProfilerRunning() - Static method in class JVMTI
 
isQuantitativeDependencyHandled() - Method in class AbstractInferenceEngine
 
isQuantitativeDependencyHandled() - Method in class SynchronizedInferenceEngine
 
isQuantitativeDependencyHandled() - Method in interface InferenceEngine
 
isQueryParticipant(Variable) - Static method in class QueryParticipantProperty
 
isRCBetter(RC, Computation) - Method in class RCComparator
 
isReadable() - Method in class FileType
 
isRelevant(IntSet, IntMap) - Method in class BayesianNetwork
 
isRelevant(IntSet) - Method in class BayesianNetwork
 
isResolved(SystemSoftwareSource) - Method in class JDKToolScript
 
isResolved() - Method in class JDKToolScript
 
isResolved() - Method in interface Script
 
isResolved(SystemSoftwareSource) - Method in interface Script
 
isRoot() - Method in class RC2Node
 
isRoot - Variable in class RCNode
 
isRunning() - Method in class RC
 
isSinglyConnected() - Method in class BeliefNetworkImpl
 
isSinglyConnected() - Method in class AbstractDirectedGraph
Determines whether or not the graph is a singly connected.
isSinglyConnected() - Method in interface DirectedGraph
Determines whether or not the graph is a singly connected.
isSingular() - Method in class Table
 
isSMILEType() - Method in class FileType
 
isSpecifiedDimension() - Method in interface HuginNode
 
isSpecifiedDimension() - Method in class HuginNodeImpl
 
isStale() - Method in class RCSettings
 
isStale() - Method in class Bundle
 
isStringifier() - Static method in class VariableImpl
 
isSuperSetOf(RC2Index) - Method in class RC2Index
 
isTableType() - Method in class DSLNodeType
 
isTimedOut() - Method in class ScriptExecution
 
isTransient() - Method in class AbstractEnumProperty
 
isTransient() - Method in class CSITypeProperty
 
isTransient() - Method in interface EnumProperty
 
isTransient() - Method in class EvidenceAssertedProperty
 
isTransient() - Method in class InOutDegreeProperty
 
isTree() - Method in interface Graph
Determines whether or not the graph is a tree.
isTree(Graph) - Static method in class Graphs
 
isTree() - Method in class HashGraph
Determines whether or not the graph is a tree.
isTree() - Method in class Graph
 
isUniqueNodeID(String) - Method in class DecisionTreeImpl
interface Factory
isUniqueNodeID(String) - Method in interface Factory
 
isUniqueParameterID(String) - Method in class DecisionTreeImpl
interface Factory
isUniqueParameterID(String) - Method in interface Factory
 
isUserEditable() - Method in class AbstractEnumProperty
 
isUserEditable() - Method in class CSITypeProperty
 
isUserEditable() - Method in interface EnumProperty
 
isUserEditable() - Method in class EvidenceAssertedProperty
 
isUserEditable() - Method in class InOutDegreeProperty
 
isValid(int, int) - Method in class Messenger
 
isValid() - Method in class VariableInstance
 
isValidating() - Method in class XmlDocumentHandler
 
isValidating() - Method in class AbstractSaxHandler
 
isValidating() - Method in class XmlbifParser
 
isValidationErrorFatal() - Method in class AbstractSaxHandler
override this method to make syntax errors non-fatal
isValidationErrorFatal() - Method in class XmlbifParser
 
isValidID(String) - Method in class DecisionTreeImpl
interface Factory
isValidID(String) - Method in interface Factory
 
isValidProbability() - Method in class Table
 
isValidRootElementName(String) - Method in class XmlDocumentHandler
 
isValidRootElementName(String) - Method in class AbstractSaxHandler
 
isValidRootElementName(String) - Method in class UAI06Parser
 
isValidRootElementName(String) - Method in class XmlbifParser
 
isWeaklyConnected() - Method in class BeliefNetworkImpl
 
isWeaklyConnected(Object, Object) - Method in class BeliefNetworkImpl
 
isWeaklyConnected() - Method in class AbstractDirectedGraph
Determines whether or not the graph is weakly connected.
isWeaklyConnected(Object, Object) - Method in class AbstractDirectedGraph
Determines if there is an undirected path from vertex1 to vertex2.
isWeaklyConnected() - Method in interface DirectedGraph
Determines whether or not the graph is weakly connected.
isWeaklyConnected(Object, Object) - Method in interface DirectedGraph
Determines if there is an undirected path from vertex1 to vertex2.
isWeighted() - Method in class Hypergraph
 
isWritableFrom(FileType) - Method in class FileType
 
isXor(BeliefNetwork) - Method in class UaiMpeMain
 
isXorCpt(double[], int) - Static method in class UaiMpeMain
 
isXorNetwork(BeliefNetwork) - Static method in class UaiMpeMain
 
iterations() - Method in class PropagationInferenceEngineImpl
 
iterations() - Method in class BeliefPropagation
 
iterations() - Method in class EDAlgorithm
 
iterationStatusOk() - Method in class EDAlgorithm
 
iterator() - Method in class BeliefNetworkImpl
 
iterator() - Static method in class DiagnosisType
 
iterator() - Static method in class DSLNodeType
 
iterator() - Static method in class HuginFileVersion
 
iterator() - Method in class LearningDataOld
Returns an iterator over the evidence in the list.
iterator() - Method in class TableIndex
returns an iterator over the indices in the array.
iterator() - Method in class AbstractDirectedGraph
 
iterator() - Method in class HashGraph
 
iterator() - Method in class MappedList
Returns an iterator over the elements in this list in proper sequence.
iterator() - Method in class CSITypeProperty
 
iterator() - Method in interface EnumProperty
 
iterator() - Method in class FlagProperty
 
iterator() - Method in class InOutDegreeProperty
 
iterator() - Method in class UserEnumProperty
 

J

javaSpecificationVersion() - Static method in class FileType
 
JDKCompile - Class in edu.ucla.util.code
 
JDKCompile() - Constructor for class JDKCompile
 
JDKRun - Class in edu.ucla.util.code
 
JDKRun() - Constructor for class JDKRun
 
JDKRun.CompiledClassInfo - Class in edu.ucla.util.code
 
JDKRun.CompiledClassInfo(File) - Constructor for class JDKRun.CompiledClassInfo
 
JDKTool - Class in edu.ucla.util.code
 
JDKTool(String, String, String) - Constructor for class JDKTool
 
JDKToolScript - Class in edu.ucla.util.code
 
JDKToolScript() - Constructor for class JDKToolScript
 
JEngineGenerator - Class in edu.ucla.belief.inference
 
JEngineGenerator() - Constructor for class JEngineGenerator
 
jj_nt - Variable in class HuginLogReader
 
jj_nt - Variable in class HuginReader
 
jj_nt - Variable in class NeticaReader
 
jjstrLiteralImages - Static variable in class HuginLogReaderTokenManager
 
jjstrLiteralImages - Static variable in class HuginReaderTokenManager
 
jjstrLiteralImages - Static variable in class NeticaReaderTokenManager
 
join(long) - Method in class NodeLinearTask
important: relies on setFinished(true)
joint(FiniteVariable) - Method in class EdgeDeletionInferenceEngine
 
joint(FiniteVariable) - Method in class PropagationInferenceEngineImpl
 
joint(FiniteVariable) - Method in class RecoveryInferenceEngine
 
joint(FiniteVariable) - Method in class JoinTreeInferenceEngineImpl
Returns P(var,observations).
joint(FiniteVariable) - Method in class RandomInferenceEngine
 
joint(FiniteVariable) - Method in class SynchronizedInferenceEngine
 
joint(FiniteVariable) - Method in class WrapperInferenceEngine
Returns P(var,observations).
joint(FiniteVariable) - Method in interface InferenceEngine
Returns P(var,observations).
joint - Variable in class XmlbifParser.Definition
 
joint(FiniteVariable) - Method in class RCDgraph
 
joint(FiniteVariable) - Method in class RCInferenceEngine
Returns P(var,observations).
JointEngine - Interface in il2.inf
 
JoinTree - Class in edu.ucla.belief.tree
 
JoinTree(List, IntGraph, Set[], BeliefNetwork) - Constructor for class JoinTree
 
JoinTree(JoinTree) - Constructor for class JoinTree
 
JoinTree - Class in il2.inf.map
 
JoinTree(Index[], IntList) - Constructor for class JoinTree
 
JoinTree - Class in il2.inf.structure
 
JoinTree(Graph, Map) - Constructor for class JoinTree
 
JoinTreeAlgorithm - Class in il2.inf.jointree
 
JoinTreeAlgorithm(EliminationOrders.JT, Table[]) - Constructor for class JoinTreeAlgorithm
 
JoinTreeInference - Class in il2.inf.map
 
JoinTreeInference(Table[], IntList) - Constructor for class JoinTreeInference
 
JoinTreeInference(Table[], int, Random) - Constructor for class JoinTreeInference
 
JoinTreeInference(IntSet, Table[], int, Random) - Constructor for class JoinTreeInference
 
JoinTreeInference(IntSet, Table[], IntList) - Constructor for class JoinTreeInference
 
JoinTreeInferenceEngine - Interface in edu.ucla.belief.inference
 
JoinTreeInferenceEngineImpl - Class in edu.ucla.belief.inference
 
JoinTreeInferenceEngineImpl(BeliefCompilation, Dynamator) - Constructor for class JoinTreeInferenceEngineImpl
Constructs a new JoinTreeInferenceEngineImpl that wraps a BeliefCompilation.
JoinTreeSettings - Class in edu.ucla.belief.inference
 
JoinTreeSettings() - Constructor for class JoinTreeSettings
 
JoinTreeStats - Class in il2.inf.structure
il2.inf.structure.JoinTreeStats
JoinTreeStats() - Constructor for class JoinTreeStats
 
JoinTreeStats.Stat - Interface in il2.inf.structure
 
JoinTreeStats.StatImpl - Class in il2.inf.structure
 
JoinTreeStats.StatImpl(BigInteger, double, BigInteger) - Constructor for class JoinTreeStats.StatImpl
 
JoinTreeStats.StatsSource - Interface in il2.inf.structure
 
joints - Variable in class HuginPotential
 
JointWrapper - Class in edu.ucla.belief.inference
 
JTtoET - Class in edu.ucla.belief.inference
 
JTtoET(JoinTree, TableIndex[]) - Constructor for class JTtoET
Creates new JTtoET
JTUnifier - Interface in il2.inf.structure
il2.inf.structure.JTUnifier
JUNCTION_FOREST_LIT - Static variable in interface HuginLogReaderConstants
 
JUNCTION_TREE_DECL_LIT1 - Static variable in interface HuginLogReaderConstants
 
JUNCTION_TREE_DECL_LIT2 - Static variable in interface HuginLogReaderConstants
 
JVMProfiler - Class in edu.ucla.util
This code comes from Java Tip 92 on Javaworld.com (but was modified quite a bit) see http://www.javaworld.com/javaworld/javatips/jw-javatip92.html
JVMProfiler() - Constructor for class JVMProfiler
 
JVMTI - Class in edu.ucla.util
Access point for the Sun JVM Tool Interface (JVMTI).
JVMTI() - Constructor for class JVMTI
 

K

KB_SAT - Class in edu.ucla.belief.rc2.kb.sat
Class implements a knowledgebase using Prof.
kb_sat - Variable in class RC2
 
KB_UNSATISFIABLE - Static variable in class KnowledgeBase
 
KB_UNSATISFIABLE - Static variable in interface KnowledgeBase
 
kbCallAssertOnVar(int) - Method in interface KnowledgeBase.KnowledgeBaseListener
 
kbCallAssertOnVar(int) - Method in class RC
 
kbDontCallAssertOnVar(int) - Method in interface KnowledgeBase.KnowledgeBaseListener
 
kbDontCallAssertOnVar(int) - Method in class RC
 
KBMap - Class in edu.ucla.belief.rc2.kb
This interface defines functions required for mapping for multi-valued variables to binary variables.
KBMap() - Constructor for class KBMap
 
KBMap.Mapping - Class in edu.ucla.belief.rc2.kb
 
KBMap.Mapping(String, int[][], int, int) - Constructor for class KBMap.Mapping
 
keepBest(RCGenerator.EO, RCGenerator.EO) - Static method in class RCGenerator.EO
 
keepBest(RCGenerator.RC, RCGenerator.RC) - Static method in class RCGenerator.RC
 
KEEPNEW - Static variable in class RCComparator
 
KEY - Static variable in class EdgeDeletionEngineGenerator
 
KEY - Static variable in class RecoveryEngineGenerator
 
key(int) - Method in class IntMap
 
KEY_APPROXIMATED_PARENTS - Static variable in interface PropertySuperintendent
 
KEY_BKCOLOR - Static variable in class DSLConstants
 
KEY_CREATION_CREATED - Static variable in class DSLConstants
 
KEY_CREATION_CREATOR - Static variable in class DSLConstants
 
KEY_CREATION_MODIFIED - Static variable in class DSLConstants
 
KEY_DEFINITION_RESULTINGSTATES - Static variable in class DSLConstants
 
KEY_DOCUMENTATION - Static variable in class DSLConstants
 
KEY_EXCLUDEARRAY - Static variable in interface PropertySuperintendent
 
KEY_EXCLUDEPOLICY - Static variable in interface PropertySuperintendent
 
KEY_EXTRADEFINITION_DEFAULT_STATE - Static variable in class DSLConstants
 
KEY_EXTRADEFINITION_DIAGNOSIS_TYPE - Static variable in class DSLConstants
 
KEY_EXTRADEFINITION_DOCUMENTATIONS - Static variable in class DSLConstants
 
KEY_EXTRADEFINITION_FAULT_LABELS - Static variable in class DSLConstants
 
KEY_EXTRADEFINITION_FAULT_NAMES - Static variable in class DSLConstants
 
KEY_EXTRADEFINITION_FAULT_STATES - Static variable in class DSLConstants
 
KEY_EXTRADEFINITION_MANDATORY - Static variable in class DSLConstants
 
KEY_EXTRADEFINITION_QUESTION - Static variable in class DSLConstants
 
KEY_EXTRADEFINITION_RANKED - Static variable in class DSLConstants
 
KEY_EXTRADEFINITION_SETASDEFAULT - Static variable in class DSLConstants
 
KEY_EXTRADEFINITION_STATECOMMENTS - Static variable in class DSLConstants
 
KEY_EXTRADEFINITION_STATEREPAIRINFO - Static variable in class DSLConstants
 
KEY_HEADER_COMMENT - Static variable in class DSLConstants
 
KEY_HUGIN_ID - Static variable in interface PropertySuperintendent
 
KEY_HUGIN_LABEL - Static variable in interface PropertySuperintendent
 
KEY_HUGIN_NAME - Static variable in interface PropertySuperintendent
 
KEY_HUGIN_NODE_SIZE - Static variable in interface PropertySuperintendent
 
KEY_HUGIN_POSITION - Static variable in interface PropertySuperintendent
 
KEY_HUGIN_potential - Static variable in interface PropertySuperintendent
 
KEY_HUGIN_potential_data - Static variable in interface PropertySuperintendent
 
KEY_HUGIN_STATES - Static variable in interface PropertySuperintendent
 
KEY_HUGIN_SUBTYPE - Static variable in interface PropertySuperintendent
 
KEY_HUGINITY - Static variable in interface PropertySuperintendent
 
KEY_IDS_RECOVERABLE_PARENTS - Static variable in interface PropertySuperintendent
 
KEY_ISMAPVARIABLE - Static variable in interface PropertySuperintendent
 
KEY_NUMSAMPLES - Static variable in class DSLConstants
 
KEY_OBSERVATION_COST_NODECOSTSLIST - Static variable in class DSLConstants
 
KEY_OBSERVATION_COST_NODENAMESLIST - Static variable in class DSLConstants
 
KEY_OBSERVATION_COST_NODEPARENTSLIST - Static variable in class DSLConstants
 
KEY_POSITION_HEIGHT - Static variable in class DSLConstants
 
KEY_POSITION_WIDTH - Static variable in class DSLConstants
 
KEY_RECOVERABLES - Static variable in interface PropertySuperintendent
 
KEY_SCREEN_BORDERCOLOR - Static variable in class DSLConstants
 
KEY_SCREEN_BORDERTHICKNESS - Static variable in class DSLConstants
 
KEY_SCREEN_COLOR - Static variable in class DSLConstants
 
KEY_SCREEN_FONT - Static variable in class DSLConstants
 
KEY_SCREEN_FONTCOLOR - Static variable in class DSLConstants
 
KEY_SCREEN_SELCOLOR - Static variable in class DSLConstants
 
KEY_SCREENCOMMENT_COMMENT - Static variable in class DSLConstants
 
KEY_SCREENCOMMENT_COORDINATES - Static variable in class DSLConstants
 
KEY_SEENDEFAULTEVIDENCE - Static variable in interface PropertySuperintendent
 
KEY_SHOWAS - Static variable in class DSLConstants
 
KEY_SOFT_EVIDENCE_CHILDREN - Static variable in interface PropertySuperintendent
 
KEY_SUBALGORITHM - Static variable in class EdgeDeletionEngineGenerator
 
KEY_SUBALGORITHM - Static variable in class RecoveryEngineGenerator
 
KEY_SUBMODEL - Static variable in class DSLConstants
 
KEY_TARGET - Static variable in class DSLConstants
 
KEY_TEAM - Static variable in class EdgeDeletionEngineGenerator
 
KEY_TEAM - Static variable in class RecoveryEngineGenerator
 
KEY_TYPE - Static variable in class DSLConstants
 
KEY_USER_PROPERTIES - Static variable in class DSLConstants
 
KEY_USERPROPERTIES - Static variable in interface PropertySuperintendent
 
KEY_WINDOWPOSITION_CENTER_X - Static variable in class DSLConstants
 
KEY_WINDOWPOSITION_CENTER_Y - Static variable in class DSLConstants
 
KEY_WINDOWPOSITION_HEIGHT - Static variable in class DSLConstants
 
KEY_WINDOWPOSITION_WIDTH - Static variable in class DSLConstants
 
keyNOISYOR - Static variable in class DSLConstants
 
keys() - Method in class DoubleMap
 
keys() - Method in class IntMap
 
keySet() - Method in class LearningData
 
keySet() - Method in class IdentityArrayMap
 
keySubalgorithm() - Method in class ApproxEngineGenerator
 
keySubalgorithm() - Method in class EdgeDeletionEngineGenerator
 
keySubalgorithm() - Method in class RecoveryEngineGenerator
 
keyTeam() - Method in class ApproxEngineGenerator
 
keyTeam() - Method in class EdgeDeletionEngineGenerator
 
keyTeam() - Method in class RecoveryEngineGenerator
 
kill - Static variable in class BeliefNetwork.Auditor.Intention
 
kill(ThreadGroup) - Static method in class Interruptable
 
killInferenceEngineAndJoinTree(PropertySuperintendent) - Method in class DefaultGenerator
 
killRCInfo(PropertySuperintendent) - Method in class RCEngineGenerator
 
killState(PropertySuperintendent) - Method in class ApproxEngineGenerator
 
killState() - Method in class BeliefPropagationSettings
 
killState(PropertySuperintendent) - Method in class PropagationEngineGenerator
 
killState(PropertySuperintendent) - Method in class Dynamator
 
killState(PropertySuperintendent) - Method in class DefaultGenerator
 
killState(PropertySuperintendent) - Method in class RandomEngineGenerator
 
killState(PropertySuperintendent) - Method in class RCEngineGenerator
 
killState(PropertySuperintendent) - Method in class RCEngineGenerator
 
killState() - Method in interface Setting.Settings
 
killState() - Method in class SettingsImpl
 
kind - Variable in class Token
An integer that describes the kind of this token.
kl(double[], double[]) - Static method in class Prob
 
kl(double[], double[]) - Method in class EDAlgorithm
 
KnowledgeBase - Class in edu.ucla.belief
Define KnowledgeBase.
KnowledgeBase(MappedList, int[], int[], int[], boolean[], KnowledgeBase.KnowledgeBaseListener) - Constructor for class KnowledgeBase
 
KnowledgeBase - Interface in edu.ucla.belief.rc2.kb
Define KnowledgeBase.
knowledgeBase() - Method in class RC
 
KnowledgeBase.KBUnsatisfiableStateException - Exception in edu.ucla.belief
This Exception is thrown when the KnowledgeBase becomes inconsistent, or unsatisfiable.
KnowledgeBase.KBUnsatisfiableStateException(String) - Constructor for exception KnowledgeBase.KBUnsatisfiableStateException
 
KnowledgeBase.KnowledgeBaseListener - Interface in edu.ucla.belief
 
KnowledgeBase.KnowledgeBaseListener - Interface in edu.ucla.belief.rc2.kb
 
KnowledgeBaseImpl - Class in edu.ucla.belief.rc2.kb
Implement KnowledgeBase.

L

LabelComparator - Class in edu.ucla.belief
 
LabelComparator() - Constructor for class LabelComparator
 
lambdaLocations() - Method in class BeliefCompilation
 
largest() - Method in class IntSet
 
LARGEST_ACCEPTABLE_CACHE - Static variable in class RCNodeCache
 
largestAcceptableEOCluster - Static variable in class EOGenerator
 
largestAcceptableEOTSS - Static variable in class RCGenerator
 
largestAcceptableRCCache - Static variable in class EOGenerator
 
largestAcceptableRCCache - Static variable in class RCGenerator
 
largestAcceptableRCCost - Static variable in class EOGenerator
 
largestAcceptableRCCost - Static variable in class RCGenerator
 
largestClusterSize() - Method in class JoinTree
 
largestContextSize() - Method in class DGraph
 
largestCptClique(Collection) - Static method in class EliminationOrders
 
largestCutsetSize() - Method in class DGraph
 
largestSeparatorSize() - Method in class JoinTree
 
lastBucket() - Method in class Bucketer
 
lastIndex() - Method in class DoubleList
 
lastIndex() - Method in class IntList
 
lastIndexOf(Object) - Method in class MappedList
Returns the index in this list of the last occurrence of the specifed element, or -1 if this list does not contain this element.
lastIndexOf(Object) - Method in class WeakLinkedList
Returns the index in this list of the last occurrence of the specified element, or -1 if the list does not contain this element.
lastNodeGetsParentLastNode() - Method in interface Tree
 
lastValue() - Method in class DoubleList
 
lastValue() - Method in class IntList
 
leaf(Attributes) - Method in class Builder
 
LEAF - Static variable in class InOutDegreeProperty
 
LEAF_ADDITIONAL_EVID - Static variable in class Pedigree
 
LEAF_PRUNE - Static variable in class Pedigree
 
leafForID(String) - Method in class DecisionTreeImpl
interface Factory
leafForID(String) - Method in interface Factory
 
leafNeighbor(int) - Method in class JoinTree
 
Learning - Class in edu.ucla.belief.learn
A collection of static functions for performing learning on BeliefNetworks.
Learning() - Constructor for class Learning
 
LearningData - Class in edu.ucla.belief.learn
 
LearningData(List) - Constructor for class LearningData
 
LearningData() - Constructor for class LearningData
 
LearningData.Struct - Class in edu.ucla.belief.learn
 
LearningData.Struct(String, int) - Constructor for class LearningData.Struct
 
LearningDataOld - Class in edu.ucla.belief.learn
A structure that contains a list of evidence mappings.
LearningDataOld(Collection) - Constructor for class LearningDataOld
Creates an empty LearningDataOld list.
learnParamsEM(BeliefNetwork, LearningDataOld, double, int, Dynamator, boolean) - Static method in class Learning
Returns a new BeliefNetwork with CPTs learned from the EM learning algorithm.
learnParamsEM(BeliefNetwork, LearningData, double, int, Dynamator, boolean) - Static method in class Learning
 
learnParamsEM(BeliefNetwork, LearningDataOld, Dynamator, double, int, boolean, ProgressMonitor, EMThread.LearningListener) - Static method in class Learning
 
learnParamsEM(BeliefNetwork, LearningData, Dynamator, double, int, boolean, ProgressMonitor, EMThread.LearningListener) - Static method in class Learning
 
learnParamsEM(BeliefNetwork, LearningDataOld, Dynamator, boolean) - Static method in class Learning
Returns a new BeliefNetwork with CPTs learned from one interation of the EM learning algorithm.
learnParamsEM(BeliefNetwork, LearningData, Dynamator, boolean) - Static method in class Learning
Returns a new BeliefNetwork with CPTs learned from one interation of the EM learning algorithm.
LEAVES - Static variable in class Classifier
 
leaves - Variable in class Stats
 
leaves() - Method in class Graph
 
left() - Method in class DtreeNodeInternal
 
left - Variable in class RC2NodeInternal
 
left() - Method in class RCNodeInternalBinaryCache
 
length - Variable in class Optimizer.EquivalenceKey
 
length() - Method in class EOGenerator.EO
 
length - Variable in class CPTInfo
 
LEXICAL_ERROR - Static variable in error TokenMgrError
Lexical error occured.
lexStateNames - Static variable in class HuginLogReaderTokenManager
 
lexStateNames - Static variable in class HuginReaderTokenManager
 
lexStateNames - Static variable in class NeticaReaderTokenManager
 
librarySupports(FileType) - Static method in class SMILEReader
 
limitedContexts(boolean) - Method in class RC
 
limitsExceeded() - Method in class EDAlgorithm
 
LinearFunction - Class in edu.ucla.util
Represents a function c_0 + c_1 x_1 + ...
LinearFunction(String, Object[], double, double[]) - Constructor for class LinearFunction
 
linearSearch(Class<? extends JoinTreeAlgorithm>) - Static method in enum Flavor
find the factory method for a particular class using linear search
LINK_DECL_LIT1 - Static variable in interface HuginLogReaderConstants
 
LINK_DECL_LIT2 - Static variable in interface HuginLogReaderConstants
 
LINK_DECL_LIT3 - Static variable in interface HuginLogReaderConstants
 
list() - Method in class NeticaReader
 
list2array(List) - Static method in class Macros
 
listClassFileNames - Variable in class Test
 
ListConverter - Class in edu.ucla.belief.io
 
ListConverter() - Constructor for class ListConverter
 
listIterator() - Method in class MappedList
Returns a list iterator of the elements in this list (in proper sequence).
listIterator(int) - Method in class MappedList
Returns a list iterator of the elements in this list (in proper sequence) starting at the specified position in this list.
listIterator(int) - Method in class WeakLinkedList
Returns a list-iterator of the elements in this list (in proper sequence), starting at the specified position in the list.
listJavaFileNames - Variable in class Test
 
literalsPositive - Variable in class MultiValuedCNF
 
literalsStates - Variable in class MultiValuedCNF
 
literalsVars - Variable in class MultiValuedCNF
 
load(JFileChooser) - Static method in class FileType
 
loadBeliefNetwork(String) - Static method in class UaiEdgeCutter
 
loadBeliefNetwork(String) - Method in class UaiMain
 
loadCommandLineOptions(String[]) - Static method in class UaiMain
Load methods
loaded() - Static method in class Hmetis
 
loaded() - Static method in class KB_SAT
 
loaded() - Static method in class JVMProfiler
 
loadEvidence() - Method in class UaiMain
 
loadForSaveAs(JFileChooser, File) - Static method in class FileType
 
loadMap(Map, File) - Method in class InstantiationXmlizer
 
loadMap(Map, Map, File) - Method in class InstantiationXmlizer
 
loadMapVariables() - Method in class UaiMain
 
loadSMILE(File, FileType) - Method in class SMILEReader
 
LOCAL - Variable in class Optimizer
 
location(Map<Object, Object>, Object) - Static method in class Macros
 
Loci - Class in edu.ucla.belief.io.geneticlinkage
 
loci(int) - Method in class Loci
 
Loci.Footer - Class in edu.ucla.belief.io.geneticlinkage
 
Loci.Footer() - Constructor for class Loci.Footer
 
Loci.Footer.BinaryILink - Class in edu.ucla.belief.io.geneticlinkage
 
Loci.Footer.GH - Class in edu.ucla.belief.io.geneticlinkage
 
Loci.Footer.Linkmap - Class in edu.ucla.belief.io.geneticlinkage
 
Loci.Footer.Mlink - Class in edu.ucla.belief.io.geneticlinkage
 
Loci.Footer.ProgData - Class in edu.ucla.belief.io.geneticlinkage
 
Loci.Header - Class in edu.ucla.belief.io.geneticlinkage
 
Loci.Locus - Class in edu.ucla.belief.io.geneticlinkage
 
Loci.LocusData - Class in edu.ucla.belief.io.geneticlinkage
 
Loci.LocusDataAffectionStatus - Class in edu.ucla.belief.io.geneticlinkage
 
Loci.LocusDataComplexAffection1 - Class in edu.ucla.belief.io.geneticlinkage
 
Loci.LocusDataComplexAffection2 - Class in edu.ucla.belief.io.geneticlinkage
 
Loci.LocusDataNumberedAlleles - Class in edu.ucla.belief.io.geneticlinkage
 
lock() - Method in class DoubleList
 
lock() - Method in class DoubleMap
 
lock() - Method in class IntList
 
lock() - Method in class IntMap
 
lock() - Method in class IntSet
 
locusOrdering() - Method in class Pedigree.GeneticNetwork
 
locusVaried - Variable in class Loci.Footer.BinaryILink
 
locusVaried - Variable in class Loci.Footer.Linkmap
 
LOD(RC_Link.RC_Results, RC_Link.RC_Results) - Static method in class RC_Link.RC_Results
 
log(Map<Object, Object>, Object, Macros.Recoverable) - Static method in class Macros
 
log(int, FiniteVariable, FiniteVariable, FiniteVariable, FiniteVariable, Map<Object, Object>, Map<Object, Object>, BeliefNetwork) - Static method in class Macros
 
LOG10 - Static variable in class UaiMain
 
LOG_ODDS_CHANGE - Static variable in class SensitivitySuggestionComparator
 
log_probability - Variable in class UaiMapSolution
The computed mpe probability in log_e space or Double.NaN if computing P (e).
logBaseTwo(double) - Static method in class JoinTreeStats
 
logBaseTwo(BigInteger) - Static method in class JoinTreeStats
 
logCardinalities(int[]) - Static method in class Util
Returns a map from each variable to the log base 2 of its cardinality.
logCompMPE() - Method in class EDMPAlgorithm
This computes an approximation to log Pr(MPE).
logging() - Method in class EdgeDeletionInferenceEngine
 
logMaxClusterSize - Variable in class UaiPreprocessResult
The log max cluster size of the elimination order.
logMaxClusterSize(int[], int[], int[][]) - Static method in class Util
Returns the log base two of the maximum cluster size of the given elimination order when applied to the given graph.
logOdds(double) - Static method in class Prob
 
logOddsDiff(double, double) - Static method in class Prob
 
logOddsToProb(double) - Static method in class Prob
 
logPrEvidence() - Method in class BeliefPropagation
 
logPrEvidence() - Method in class MaxProduct
 
logPrEvidence() - Method in class EDAlgorithm
 
logPrEvidence() - Method in interface JointEngine
 
logPrEvidence() - Method in class JoinTreeAlgorithm
 
logPrEvidence() - Method in class NormalizedMaxSSAlgorithm
 
logPrEvidence() - Method in class NormalizedSSAlgorithm
 
logPrEvidence() - Method in class NormalizedZCAlgorithm
 
logPrEvidence() - Method in class RCEngine
 
logPrMPE() - Method in class MaxProduct
 
logPrMPE(int[]) - Method in class MaxProduct
 
logPrMPE() - Method in class EDMPAlgorithm
This computes an approximation to log Pr(MPE), where: = MPE is computed in simplified network = the value log Pr(MPE) is computed in original network
logPrMPE(int[]) - Method in class EDMPAlgorithm
This computes an approximation to log Pr(MPE), where: = MPE is given = the value log Pr(MPE) is computed in original network Use this if you call EDMPAlgorithm.mpe() yourself, as the method EDMPAlgorithm.logPrMPE() also calls EDMPAlgorithm.mpe(), which performs a non-trivial amount of work.
logPrMPE() - Method in class NormalizedMaxSSAlgorithm
 
logPrpMPE() - Method in class EDMPAlgorithm
This computes an approximation to log Pr(MPE), where: = MPE is given = the value log Pr'(MPE) is computed in simplfied network This gives another approximation to the value of the MPE in the original network.
logSize(int) - Method in class Domain
 
logSize(IntSet) - Method in class Domain
 
logsub(double, double) - Static method in class RC2Utils
Compute ln(a-b) from ln(a) and ln(b) using the log sub equation.
logsub(double, double) - Static method in class RCUtilities
Compute ln(a-b) from ln(a) and ln(b) using the log sub equation.
logsub2(double, double) - Static method in class RC2Utils
Compute ln(a-b) from ln(a) and ln(b) using the log sub equation.
logsub2(double, double) - Static method in class RCUtilities
Compute ln(a-b) from ln(a) and ln(b) using the log sub equation.
logsum(double, double) - Static method in class TableScaled
Copied from edu.ucla.belief.recursiveconditioning.RCUtilities
LONG_BYTE_KILO_THRESHOLD - Static variable in class RCSettings
 
LONG_BYTE_KILO_THRESHOLD - Static variable in class Settings
 
LONG_BYTES_PER_DOUBLE - Static variable in class RCSettings
 
LONG_BYTES_PER_DOUBLE - Static variable in class Settings
 
LONG_CEILING_CPT_SIZE - Static variable in class ModelCoder
 
LONG_KILO_MEGA_THRESHOLD - Static variable in class RCSettings
 
LONG_KILO_MEGA_THRESHOLD - Static variable in class Settings
 
LONG_PAUSE_GRACE_MILLIS - Static variable in class Interruptable
 
LONG_SLEEP_MILLIS - Static variable in class SystemGCThread
 
LONG_TIMEOUT_MILLIS_DEFAULT - Static variable in class BeliefPropagationSettings
 
LONG_TIMEOUT_MILLIS_DEFAULT - Static variable in class EDAlgorithm
 
LONG_TOO_OLD - Static variable in class ParanoidFileFinder
 
lookingAhead - Variable in class HuginReader
 
lookingAhead - Variable in class NeticaReader
 
LOOP_DETECTED - Static variable in error TokenMgrError
Detected (and bailed out of) an infinite loop in the token manager.

M

Macros - Class in edu.ucla.belief.approx
Helper class for approximation related tasks, for example ed-bp edge removal/recovery.
Macros() - Constructor for class Macros
 
Macros.Bridge - Class in edu.ucla.belief.approx
 
Macros.Bridge(BeliefNetwork, Converter, Macros.Recoverable[], FiniteVariable[][], int[][], EDAlgorithm, Map<FiniteVariable, Integer>, Map<FiniteVariable, Integer>, Map<FiniteVariable, Integer>, Map<FiniteVariable, Integer>, Map<FiniteVariable, Integer>) - Constructor for class Macros.Bridge
 
Macros.Category - Enum in edu.ucla.belief.approx
 
Macros.Doubler - Enum in edu.ucla.belief.approx
Convert arrays with various component types to individual primitive double values.
Macros.RankingArgs - Class in edu.ucla.belief.approx
 
Macros.RankingArgs(BeliefNetwork, EdgeDeletionInferenceEngine, EDAlgorithm.RankingHeuristic, int) - Constructor for class Macros.RankingArgs
 
Macros.Recoverable - Class in edu.ucla.belief.approx
 
Macros.Recoverable(int, FiniteVariable, FiniteVariable, FiniteVariable, FiniteVariable) - Constructor for class Macros.Recoverable
 
Macros.Recoverable(String, BeliefNetwork) - Constructor for class Macros.Recoverable
 
Macros.Recoverables - Class in edu.ucla.belief.approx
 
Macros.Recoverables() - Constructor for class Macros.Recoverables
 
Macros.Recoverables(Macros.Recoverable...) - Constructor for class Macros.Recoverables
 
Macros.RecoveryInfo - Class in edu.ucla.belief.approx
 
Macros.RecoveryInfo() - Constructor for class Macros.RecoveryInfo
 
Macros.RecoveryInfo(Macros.Recoverable...) - Constructor for class Macros.RecoveryInfo
 
main(String[]) - Static method in class Macros
 
main(String[]) - Static method in class XmlWriter
test/debug
main(String[]) - Static method in class RCInfo
 
MAIN - Variable in class DSLSubmodelFactory
 
main(String[]) - Static method in class SMILEReader
 
main(String[]) - Static method in class GraphvizIO
 
main(String[]) - Static method in class HuginLogReader
 
main(String[]) - Static method in class HuginReader
 
main(String[]) - Static method in class ListConverter
 
main(String[]) - Static method in class NeticaReader
 
main(String[]) - Static method in class UAI06Parser
test/debug
main(String[]) - Static method in class XmlbifParser
test/debug
main(String[]) - Static method in class LearningData
Test/debug
main(String[]) - Static method in class Compiled_MLink
 
main(String[]) - Static method in class NetworkDiff
 
main(String[]) - Static method in class RC_Link
 
main(String[]) - Static method in class RC_Link_UAI2006
 
main(String[]) - Static method in class TestClass
 
main(String[]) - Static method in class TimePeVsIl2
 
main(String[]) - Static method in class Xmlizer
test/debug
main(String[]) - Static method in class UaiEdgeCutter
 
main(String[]) - Static method in class UaiMpeMain
 
main(String[]) - Static method in class UaiPeMain
 
main(String[]) - Static method in class HashGraph
 
main(String[]) - Static method in class ProbabilityQueryCoder
Test/debug.
main(String[]) - Static method in class ScriptTest
 
main(String[]) - Static method in class Test
 
main(String[]) - Static method in class JVMProfiler
Test/debug
main(String[]) - Static method in class JVMTI
Test/debug
main(String[]) - Static method in enum Algorithm
test/debug
main(String[]) - Static method in enum Flavor
test/debug
mainImpl(String, XmlbifParser, XmlbifParser) - Static method in class XmlbifParser
 
maintainsAcyclicity(BeliefNetwork, Map<String, Set<String>>, Variable, Variable) - Method in class Macros.Recoverables
 
maintainsAcyclicity(Object, Object) - Method in class BeliefNetworkImpl
 
maintainsAcyclicity(Object, Object) - Method in class AbstractDirectedGraph
Check whether adding the proposed edge would keep the graph acyclic.
maintainsAcyclicity(Object, Object) - Method in interface DirectedGraph
Check whether adding the proposed edge would keep the graph acyclic.
makeCDF(int) - Method in class Table
 
makeClique(Graph, Set) - Static method in class Graphs
 
makeComposite(Function, Function) - Static method in class Maps
 
makeCPT(int) - Method in class Table
 
makeCumulative(Index) - Method in class Table
 
makeDate() - Method in class InstantiationXmlizer
 
makeDate() - Static method in class ModelCoder
 
makeDimension() - Method in class DSLNodeImpl
Convenience method.
makeDimensional(List, int[]) - Static method in class ListConverter
 
makeElement(RCNode, Document, String) - Method in class Xmlizer
 
makeExcludeArray(StandardNode) - Static method in class ExcludePolicy
 
makeExcludeString(FiniteVariable, boolean[]) - Static method in class ExcludePolicy
 
makeID(int) - Static method in class ParameterImpl
 
makeIDLinear(int) - Static method in class ParameterImpl
 
makeIDRec(int) - Static method in class ParameterImpl
 
makeIDRecursive(int) - Static method in class ParameterImpl
 
makeJoinTreeInferenceEngineImpl(BeliefNetwork, JoinTreeSettings) - Method in class JEngineGenerator
 
makeMapRootToVariableList(RC) - Static method in class Xmlizer
 
makeNetwork(NeticaObject) - Static method in class NeticaObject
 
makePotential(Map) - Method in class HuginPotential
 
makeShell(Map) - Method in class PotentialInfo
 
makeUniform() - Method in class DecisionLeaf
 
makeUniform() - Method in class Table
 
makeUniform() - Method in class TableScaled
 
makeUserEnumProperties(Map) - Method in interface BeliefNetwork
 
makeUserEnumProperties(Map) - Method in class BeliefNetworkImpl
 
manual_variance(BeliefNetwork, Map, PrintWriter) - Static method in class VEVariance
this method is intended for use with SamIam expecting evidence as Map of FiniteVariable to Object
manual_variance(BayesianNetwork, IntMap, PrintWriter) - Static method in class VEVariance
this method is intended for use with SamIam
manual_variance(BeliefNetwork, Map) - Static method in class VEVariance
 
manual_variance(BayesianNetwork, IntMap) - Static method in class VEVariance
 
manufactureInferenceEngine(BeliefNetwork) - Method in class Dynamator
 
manufactureInferenceEngine(BeliefNetwork, Dynamator) - Method in class Dynamator
 
manufactureInferenceEngine(BeliefNetwork, DefaultGenerator) - Method in class DefaultGenerator
 
manufactureInferenceEngine(BeliefNetwork, JoinTreeSettings) - Method in class DefaultGenerator
 
manufactureInferenceEngine(BeliefNetwork, DefaultGenerator) - Method in class HuginEngineGenerator
 
manufactureInferenceEngine(BeliefNetwork, DefaultGenerator) - Method in class JEngineGenerator
 
manufactureInferenceEngine(BeliefNetwork, DefaultGenerator) - Method in class SSEngineGenerator
 
manufactureInferenceEngine(BeliefNetwork, DefaultGenerator) - Method in class ZCEngineGenerator
 
manufactureInferenceEngineOrDie(BeliefNetwork, Dynamator, Setting.Settings<E>) - Method in class ApproxEngineGenerator
 
manufactureInferenceEngineOrDie(BeliefNetwork, Dynamator) - Method in class ApproxEngineGenerator
 
manufactureInferenceEngineOrDie(BeliefNetwork, Dynamator, Setting.Settings<EdgeDeletionBeliefPropagationSetting>) - Method in class EdgeDeletionEngineGenerator
 
manufactureInferenceEngineOrDie(BeliefNetwork, Dynamator) - Method in class PropagationEngineGenerator
 
manufactureInferenceEngineOrDie(BeliefNetwork, Dynamator, Setting.Settings<RecoverySetting>) - Method in class RecoveryEngineGenerator
 
manufactureInferenceEngineOrDie(BeliefNetwork, Dynamator) - Method in class Dynamator
 
manufactureInferenceEngineOrDie(BeliefNetwork, Dynamator) - Method in class DefaultGenerator
 
manufactureInferenceEngineOrDie(BeliefNetwork, Dynamator) - Method in class RandomEngineGenerator
 
manufactureInferenceEngineOrDie(BeliefNetwork, Dynamator) - Method in class RCEngineGenerator
 
manufactureInferenceEngineOrDie(BeliefNetwork, Dynamator) - Method in class RCEngineGenerator
 
manufactureJoinTree(BeliefNetwork, JoinTreeSettings) - Method in class DefaultGenerator
 
manufactureRC(Dtree, BeliefNetwork, CachingScheme, boolean) - Method in interface Settings.RCFactory
 
map(Attributes, Object) - Method in class Builder
 
map - Variable in class KBMap.Mapping
 
map(Map, Collection, Collection) - Static method in class Maps
 
map(Map, Set) - Static method in class Maps
 
MAP(Collection, IntSet) - Static method in class BasicInference
 
Map_EClause - Class in edu.ucla.belief.rc2.kb
This class creates a mapping using the new eclause (which handles the multivalued variables).
map_kb - Variable in class RC2
 
Map_L - Class in edu.ucla.belief.rc2.kb
This class creates a mapping using the L (logarithmic) mapping for multi-valued variables.
MAP_LIT - Static variable in interface HuginReaderConstants
 
MAPCoder - Class in edu.ucla.util.code
 
MAPCoder() - Constructor for class MAPCoder
 
MAPCoder.OptionPrune - Class in edu.ucla.util.code
 
MAPCoder.OptionPrune() - Constructor for class MAPCoder.OptionPrune
 
MAPCoder.OptionTimings - Class in edu.ucla.util.code
 
MAPCoder.OptionTimings() - Constructor for class MAPCoder.OptionTimings
 
MapEngine - Class in edu.ucla.belief.inference.map
 
MapEngine(BeliefNetwork, Set, Map) - Constructor for class MapEngine
 
MapEngine(BeliefNetwork, List, Set, Map) - Constructor for class MapEngine
 
MapInitializer - Class in il2.inf.map
 
MapInitializer.MapResult - Class in il2.inf.map
 
mapInstance(String, Object) - Method in class CPTImportColumnInfo
 
MapJoinTree - Class in il2.inf.map
 
MapJoinTree(EliminationOrders.JT, int, Collection, IntSet) - Constructor for class MapJoinTree
Creates a new instance of MapJoinTree
mapJoinTree(Collection, IntSet, IntList, double) - Static method in class MapOrderMaker
 
mapOrder(Collection, Set) - Static method in class EliminationOrders
 
mapOrdering() - Method in class MapTree
 
MapOrderMaker - Class in il2.inf.map
 
MappedHeap - Class in il2.util
 
MappedHeap() - Constructor for class MappedHeap
 
MappedList - Class in edu.ucla.structure
A List of unique values which can be indexed as a list and the index can be efficiently determined( O(1) time).
MappedList() - Constructor for class MappedList
Creates an empty MappedList.
MappedList(MappedList) - Constructor for class MappedList
 
MappedList(int) - Constructor for class MappedList
Creates an empty MappedList with specified capacity.
MappedList(int[]) - Constructor for class MappedList
Creates a MappedList containing Integers corresponding to the ints in values.
MappedList(Collection) - Constructor for class MappedList
Creates a mapped list containing the elements of collection in the order provided by the collections iterator.
mapping - Variable in class Graph.Compressed
 
mappings - Variable in class Partition
The partition that each of the initial members was assigned to
mappings - Variable in class Index.Partition
 
MapProperty - Class in edu.ucla.belief.inference.map
 
MapRunner - Class in edu.ucla.belief.inference.map
 
MapRunner() - Constructor for class MapRunner
 
MapRunner.MapResult - Class in edu.ucla.belief.inference.map
 
MapRunner.MapResult(long, long, long, long, Map, double) - Constructor for class MapRunner.MapResult
 
Maps - Class in edu.ucla.util
 
Maps() - Constructor for class Maps
 
MapSearch - Class in il2.inf.map
 
MapSearch.MapInfo - Class in il2.inf.map
2004-09-28: Changed result of map query from array list of map results to this object.
MapSearch.MapInfo(ArrayList, long, long, long, long, boolean, double, long) - Constructor for class MapSearch.MapInfo
 
MapSearch.MapResult - Class in il2.inf.map
 
mapToString(Map) - Method in class AbstractStringifier
 
mapToString(Map) - Method in interface Stringifier
 
MapTree - Class in il2.inf.map
 
MapTree(Table[], int, Random, IntSet, double) - Constructor for class MapTree
 
MapTree(JoinTree, Table[], IntSet, double) - Constructor for class MapTree
 
mapVars - Variable in class UaiMain
 
massageEpsilon(double) - Static method in class Optimizer
 
MATCHER_AUXILIARY_VAR - Static variable in class Macros
 
MATCHER_COMMENT - Static variable in class XmlbifParser
 
max() - Method in class AbstractInferenceEngine
 
max() - Method in class SynchronizedInferenceEngine
 
max() - Method in interface InferenceEngine
 
max() - Method in class Table
 
max(double[]) - Static method in class DblArrays
 
max(Collection) - Static method in class Maps
 
max(int[]) - Static method in class ArrayUtils
Returns the maximum of the values in the given array.
max(double[]) - Static method in class ArrayUtils
Returns the maximum of the values in the given array.
max - Variable in class IntStats
 
maxAssignment() - Method in class Table
returns assignment of variables to values with highest value
maxBpMarginals(BeliefNetwork) - Static method in class UaiEdgeCutter
 
maxCache - Static variable in class CachingDFBnB.OrderingAlgo
 
maxCluster - Variable in class Stats
 
maxCluster - Variable in class EOGenerator.RC
 
maxClusterSize() - Method in class RCInfo
 
maxContext - Variable in class Stats
 
maxContextSize() - Method in class RCInfo
 
maxCutset - Variable in class Stats
 
maxCutsetSize() - Method in class RCInfo
 
maxDeriv - Static variable in class CachingDFBnB.OrderingAlgo
 
maxError() - Method in class EdgeDeletionInferenceEngine
 
maximize(IntSet) - Method in class Table
 
maximize(int) - Method in class Table
 
maximizeInto(Table, int[][]) - Method in class Table
 
maximizeInto(double[], double[], int[][]) - Static method in class Table
 
maxInd() - Method in class Table
 
maxInd(int[]) - Static method in class ArrayUtils
Returns the index of the maximum value in the given array.
maxInd(double[]) - Static method in class ArrayUtils
Returns the index of the maximum value in the given array.
maxIndex() - Method in class Table
 
maxOut(Index, double[], int, double[]) - Static method in class Table
 
maxProduct(Collection) - Static method in class BasicInference
 
MaxProduct - Class in il2.inf.bp
 
MaxProduct(Table[], MessagePassingScheduler, int, long, double) - Constructor for class MaxProduct
 
MaxProduct(Table[], int, long, double) - Constructor for class MaxProduct
 
MaxProductLinearSmoothness - Class in il2.inf.bp
Max-Product BP with more efficient message updates as in "Efficient Belief Propagation for Early Vision" by Felzenszwalb and Huttenlocher CVPR 2004, IJCV 2006 this assumes smoothness cost: \rho_p(d_s,d_t) = min(\lambda |d_s-d_t|,T) as in "Symmetric Stereo Matching for Occlusion Handling" by Sun, Li, Kang, and Shum CVPR 2005
MaxProductLinearSmoothness(Table[], MessagePassingScheduler, double, double, double, int, long, double) - Constructor for class MaxProductLinearSmoothness
 
MaxProductLinearSmoothness(Table[], double, double, double, int, long, double) - Constructor for class MaxProductLinearSmoothness
 
maxReduce(Collection, double) - Static method in class BasicInference
 
maxScore() - Method in class Heap
Returns the maximum score in the heap.
mayContain(Object) - Method in interface BeliefNetwork
 
mayContain(Object) - Method in class BeliefNetworkImpl
 
mayContain(Object) - Method in class GenieNetImpl
 
mayContain(Object) - Method in class HuginNetImpl
 
MB - Static variable in class RC_Link.RC_Results
 
MB - Static variable in class RCNodeCache
 
mean - Variable in class IntStats
 
median - Variable in class IntStats
 
members - Variable in class HuginClique
 
membership(Macros.Bridge, Collection<FiniteVariable>) - Method in enum Macros.Category
 
memoryUsage() - Method in class RC2Index
 
memUsed() - Method in class RC2.ComputationStats
 
memUsedMB() - Method in class RC2.ComputationStats
 
mentioned - Variable in class CPTInfo.Parameter
 
merge(Instantiation) - Method in class Instantiation
 
merge(MPE, MPE) - Static method in class MPE
 
mergingTwoVars_OneIsChanging(FiniteVariable, FiniteVariable) - Method in class Pedigree.GeneticNetwork
 
MessagePassingScheduler - Class in edu.ucla.belief.approx
 
MessagePassingScheduler() - Constructor for class MessagePassingScheduler
 
MessagePassingScheduler - Class in il2.inf.bp.schedules
 
MessagePassingScheduler(Table[]) - Constructor for class MessagePassingScheduler
 
messagesIncoming(int) - Method in class MessagePassingScheduler
 
Messenger - Class in edu.ucla.belief.inference
 
Messenger(IntGraph) - Constructor for class Messenger
Creates new AbstractJoinTreeEngine
method - Variable in enum Flavor
the implementation class's factory method
METHOD_ONLY - Variable in class OptionBreadth
 
methodAlgorithmForClass() - Static method in class Dynamator
 
MethodEliminationOrder - Class in edu.ucla.belief.dtree
 
MethodEliminationOrder() - Constructor for class MethodEliminationOrder
 
methodForClass(Class<? extends JoinTreeAlgorithm>) - Static method in enum Flavor
find the factory method for a particular class, first using reflection, then linear search
methodForClassSafe(Class<? extends JoinTreeAlgorithm>) - Static method in enum Flavor
find the factory method for a particular class, but don't throw any exceptions if not found
MethodHmetis - Class in edu.ucla.belief.dtree
 
MethodHmetis() - Constructor for class MethodHmetis
 
MethodHmetis.Algorithm - Class in edu.ucla.belief.dtree
 
MethodHuginLog - Class in edu.ucla.belief.dtree
 
MethodHuginLog() - Constructor for class MethodHuginLog
 
MethodHuginLog.Style - Class in edu.ucla.belief.dtree
 
methodTigerToIL2() - Static method in class Dynamator
 
min() - Method in class Table
 
min(double[]) - Static method in class DblArrays
 
min(Collection) - Static method in class Maps
 
min(int[]) - Static method in class ArrayUtils
Returns the minimum of the values in the given array.
min(double[]) - Static method in class ArrayUtils
Returns the minimum of the values in the given array.
min - Variable in class IntStats
 
MIN_DEG - Static variable in class EliminationHeuristic
 
MIN_DEGREE - Static variable in class EliminationOrders
 
MIN_FILL - Static variable in class EliminationHeuristic
 
MIN_FILL - Static variable in class EliminationOrders
 
MIN_FILL_NO_SIZE - Static variable in class EliminationOrders
 
MIN_MEMORY - Static variable in class RCComparator
 
MIN_SIZE - Static variable in class EliminationHeuristic
 
MIN_SIZE - Static variable in class EliminationOrders
 
MIN_TIME - Static variable in class RCComparator
 
MINCACHE - Static variable in class MethodHuginLog
 
minCache - Static variable in class CachingDFBnB.OrderingAlgo
 
minDegree(BeliefNetwork) - Static method in class EliminationOrders
 
minDegree(Graph) - Static method in class EliminationOrders
 
minDegree(Graph, Set) - Static method in class EliminationOrders
 
minDegree(BeliefNetwork, Set) - Static method in class EliminationOrders
 
minDeriv - Static variable in class CachingDFBnB.OrderingAlgo
 
mindex(int, int[]) - Method in class TableIndex
Converts the linear index to the corresponding multidimensional index.
minFill(Set, int, Random) - Static method in class EliminationOrders
 
minFill(Collection, Set, int, Random) - Static method in class EliminationOrders
 
minFill(BeliefNetwork, int, Random) - Static method in class EliminationOrders
 
minFill(Graph, int, Random) - Static method in class EliminationOrders
 
minFill(BeliefNetwork, Set, int, Random) - Static method in class EliminationOrders
 
minFill(Graph, Set, int, Random) - Static method in class EliminationOrders
 
minFill(Collection, int, Random) - Static method in class EliminationOrders
 
minfill2(Collection, IntSet[], int, Random) - Static method in class EliminationOrders
Replacing JD's original minfill with a much faster version.
MinfillEoe - Class in il2.inf.structure.minfill2
An EliminationOrderEngine that uses minfill.
MinfillEoe() - Constructor for class MinfillEoe
 
MinFillOrderer - Class in il2.inf.structure
 
MinFillOrderer(int) - Constructor for class MinFillOrderer
 
MinFillOrderGenerator - Class in il2.inf.structure
 
MinFillOrderGenerator(Graph, Domain) - Constructor for class MinFillOrderGenerator
 
minimalProperties(Map) - Static method in class BeliefNetworkImpl
 
miniMAP(Collection, IntSet, int) - Static method in class BasicInference
 
miniMaxProduct(Collection, int) - Static method in class BasicInference
 
miniMultiplyAndForget(Collection, int, int) - Static method in class Table
 
miniMultiplyAndForget(Collection, int, int, boolean) - Static method in class Table
 
miniMultiplyAndMaximize(Collection, int, int) - Static method in class Table
 
minInd(int[]) - Static method in class ArrayUtils
Returns the index of the minimum value in the given array.
minInd(double[]) - Static method in class ArrayUtils
Returns the index of the minimum value in the given array.
miniPartition(List, double) - Static method in class Partition
 
miniPartition(Index[], double) - Static method in class Partition
 
miniPartition(Index[], int) - Static method in class Index
 
miniSumProduct(Collection, int, boolean) - Static method in class BasicInference
 
MiniTree - Class in il2.inf.mini
 
MiniTree(Table[], int, Random, double) - Constructor for class MiniTree
 
MinPairCostTreeGenerator - Class in edu.ucla.belief.tree
 
MinPairCostTreeGenerator(TableIndex[], List, CostFunction) - Constructor for class MinPairCostTreeGenerator
 
minSize(BeliefNetwork) - Static method in class EliminationOrders
 
minSize(Graph) - Static method in class EliminationOrders
 
minSize(Graph, Set) - Static method in class EliminationOrders
 
minSize(BeliefNetwork, Set) - Static method in class EliminationOrders
 
minSize(Collection) - Static method in class EliminationOrders
 
MinSizeOrderer - Class in il2.inf.structure
 
MinSizeOrderer(Domain) - Constructor for class MinSizeOrderer
 
ML - Static variable in class InitializationMethod
 
mode - Variable in class IntStats
 
modefrequency - Variable in class IntStats
 
ModelCoder - Class in edu.ucla.util.code
 
ModelCoder(BeliefNetwork, String) - Constructor for class ModelCoder
 
ModelCoder(BayesianNetwork, String) - Constructor for class ModelCoder
 
ModelCoder.LibraryVersionOption - Class in edu.ucla.util.code
 
ModelCoder.LibraryVersionOption() - Constructor for class ModelCoder.LibraryVersionOption
 
modelToJavaCodeIL1(BeliefNetwork, boolean, PrintStream) - Method in class ModelCoder
 
modelToJavaCodeIL2(BayesianNetwork, boolean, PrintStream) - Method in class ModelCoder
 
MODIFIERS() - Static method in enum Flavor
modifiers of factory methods
MONITOR - Variable in class ProbabilityQueryCoder.MarginalScopeOption
 
MORAL_LIT1 - Static variable in interface HuginLogReaderConstants
 
MORAL_LIT2 - Static variable in interface HuginLogReaderConstants
 
moralBlock() - Method in class HuginLogReader
 
moralGraph(Collection) - Static method in class EliminationOrders
 
moralGraph(DirectedGraph) - Static method in class Graphs
Returns the moral graph of dg.
moralGraph(DirectedGraph, Collection, PrintStream) - Static method in class Graphs
 
MPE - Static variable in class InitializationMethod
 
mpe() - Method in class MaxProduct
 
mpe() - Method in class EDMPAlgorithm
 
mpe() - Method in class NormalizedMaxSSAlgorithm
 
MPE - Class in il2.util
 
MPE() - Constructor for class MPE
 
MPE(ArrayList) - Constructor for class MPE
 
MPE(IntSet, int[]) - Constructor for class MPE
 
MPEAlgorithm - Class in il2.inf.jointree
 
MPECoder - Class in edu.ucla.util.code
 
MPECoder() - Constructor for class MPECoder
 
mpeInstantiations() - Method in class MPETable
 
MPETable - Class in il2.model
 
MPETable(Domain, IntSet) - Constructor for class MPETable
 
MPETable(Index, double[]) - Constructor for class MPETable
 
MPETable(Index, double[], MPE[]) - Constructor for class MPETable
 
MULTIPLICATION - Static variable in interface ArithmeticExpression
 
MULTIPLICATION - Static variable in class EliminationTree
 
multiply(Table, Table) - Static method in class Table
 
multiply(Table) - Method in class Table
 
multiply(TableIndex) - Method in class TableIndex
Returns the Index which corresponds to basically the cartesian product of the two arrays.
multiply(Table) - Method in class TableScaled
 
multiply(double[], double) - Static method in class DblArrays
 
multiply(double) - Method in class LinearFunction
 
multiply(Table) - Method in class Table
 
multiplyAll(Set) - Static method in class Table
 
multiplyAll(Set) - Static method in class TableScaled
 
multiplyAll(Collection) - Static method in class Table
 
multiplyAndProjectInto(Table[]) - Method in class MPETable
 
multiplyAndProjectInto(Table[]) - Method in class Table
 
multiplyAndProjectMaxInto(Table[]) - Method in class Table
 
multiplyByConstant(double) - Method in class Table
 
multiplyInto(Table) - Method in interface CPTShell
 
multiplyInto(Table) - Method in class DecisionShell
 
multiplyInto(Table) - Method in class NoisyOrShellHenrion
 
multiplyInto(Table) - Method in class NoisyOrShellPearl
 
multiplyInto(Table) - Method in class Table
 
multiplyInto(Table) - Method in class TableScaled
 
multiplyInto(Table) - Method in class TableShell
 
multiplyInto(double[], double[], int[][]) - Static method in class Table
 
multiplyInto(Table) - Method in class Table
 
multiplyInto(Table, int[][]) - Method in class Table
 
multiplyInto2(Table) - Method in class Table
 
multiplyVarIndicators(int, int) - Method in class Table
 
multiplyVarIndicators(int, double[]) - Method in class Table
 
MultiValuedCNF - Class in edu.ucla.belief.rc2.kb
Class representing Multi-Valued CNFs.
my_decide(int, int) - Method in class KB_SAT
 
my_decide(int) - Method in class KB_SAT
 
myArray - Variable in class CSITypeProperty
 
myArray - Variable in class FlagProperty
 
myArray - Static variable in class InOutDegreeProperty
 
myBeliefNetwork - Static variable in class UaiEdgeCutter
 
myConverter - Static variable in class UaiEdgeCutter
 
myCreationMethod - Variable in class Dtree
 
myJoinTree - Variable in class BeliefCompilation
 
myList - Variable in class CSITypeProperty
 
myList - Variable in class FlagProperty
 
myList - Static variable in class InOutDegreeProperty
 
myLog(double) - Static method in class Table
 
myName - Variable in class NamedObject
 
myShell - Variable in class PotentialInfo
 

N

name() - Method in class Dtree.Create
 
name() - Method in class DtreeCreateEO
 
name() - Method in class DtreeCreateHMetis
 
name() - Method in class DtreeCreateHMetis1
 
name() - Method in class DtreeCreateHMetis1wn
 
name() - Method in class DtreeCreateJT
 
name() - Method in class DtreeCreateString
 
name - Variable in class HuginFunction
 
name - Variable in class RC2CachingScheme_Collection
 
name - Variable in class CPTShells
 
name - Variable in enum EDAlgorithm.RankingHeuristic
 
name() - Method in class DgraphCreateHMetis
 
name() - Method in class DgraphCreateHMetis1
 
name() - Method in class DgraphCreateHMetis1wn
 
name(int) - Method in class Domain
 
NamedObject - Class in edu.ucla.util
 
NamedObject(String) - Constructor for class NamedObject
 
namesToString() - Method in class Domain
 
nanosPerMilli - Static variable in class JVMProfiler
 
narrows(FileType) - Method in class FileType
a.k.a.: distinguishes()
NEGATIVE_ONE - Static variable in class Macros
 
negl - Static variable in class ApproxEngine
 
neighborIndex(int, int) - Method in class IntGraph
 
neighboringEdges(Object) - Method in interface Graph
 
neighboringEdges(Object) - Method in class HashGraph
 
neighbors(Object) - Method in interface Graph
Construct an Iterator over the vertices adjacent to vertex.
neighbors(Object) - Method in class HashGraph
Construct an Iterator over the vertices adjacent to vertex.
neighbors(int) - Method in class IntGraph
 
neighbors(int) - Method in class Graph
 
NET - Static variable in interface HuginReaderConstants
 
netBlock() - Method in class HuginReader
 
NETICA - Static variable in class FileType
 
neticaFile() - Method in class NeticaReader
 
NeticaObject - Class in edu.ucla.belief.io.netica
 
NeticaObject() - Constructor for class NeticaObject
 
neticaObject() - Method in class NeticaReader
 
NeticaReader - Class in edu.ucla.belief.io.netica
 
NeticaReader(InputStream) - Constructor for class NeticaReader
 
NeticaReader(Reader) - Constructor for class NeticaReader
 
NeticaReader(NeticaReaderTokenManager) - Constructor for class NeticaReader
 
NeticaReaderConstants - Interface in edu.ucla.belief.io.netica
 
NeticaReaderTokenManager - Class in edu.ucla.belief.io.netica
 
NeticaReaderTokenManager(SimpleCharStream) - Constructor for class NeticaReaderTokenManager
 
NeticaReaderTokenManager(SimpleCharStream, int) - Constructor for class NeticaReaderTokenManager
 
network() - Method in class RCInfo
 
network - Variable in class EliminationOrders.JT
 
NetworkDiff - Class in edu.ucla.belief.rc2.tools
 
NetworkDiff(File, File) - Constructor for class NetworkDiff
 
NetworkIO - Class in edu.ucla.belief.io
 
NetworkIO() - Constructor for class NetworkIO
 
NetworkIO.BeliefNetworkIOListener - Interface in edu.ucla.belief.io
 
networkName - Variable in class FileInfo
 
newDomain() - Method in class EDNetwork
 
newFiniteVariable(Map) - Method in interface BeliefNetwork
 
newFiniteVariable(Map) - Method in class BeliefNetworkImpl
 
newFiniteVariable(Map) - Method in class GenieNetImpl
 
newFiniteVariable(Map) - Method in class HuginNetImpl
 
newInternal(FiniteVariable) - Method in class DecisionTreeImpl
interface Factory
newInternal(FiniteVariable) - Method in interface Factory
 
newInternal(Factory, FiniteVariable) - Method in class Optimizer.EquivalenceKey
 
newLeaf(FiniteVariable) - Method in class DecisionTreeImpl
interface Factory
newLeaf(FiniteVariable, Parameter[]) - Method in class DecisionTreeImpl
interface Factory
newLeaf(FiniteVariable) - Method in interface Factory
 
newLeaf(FiniteVariable, Parameter[]) - Method in interface Factory
 
newLeaf(Factory, FiniteVariable) - Method in class Optimizer.EquivalenceKey
 
newNode - Variable in class PotentialInfo
 
newParameter(double) - Method in class DecisionTreeImpl
interface Factory
newParameter(String, double) - Method in class DecisionTreeImpl
interface Factory
newParameter(double) - Method in interface Factory
 
newParameter(String, double) - Method in interface Factory
 
newPotential - Variable in class PotentialInfo
 
newTables() - Method in class EDNetwork
 
newTableToOldTable(Table) - Method in class EDNetwork
this converts a table of the new network into a table of the old network.
newToken(int) - Static method in class Token
Returns a new Token object, by default.
newToOldVar(int) - Method in class EDNetwork
 
newVarOfEdge(int) - Method in class EDNetwork
 
next - Variable in class Token
A reference to the next regular (non-special) token from the input stream.
next() - Method in class RCIterator
Does not guarantee any particular ordering of the nodes returned.
next() - Method in class RCNodeInternalBinaryCache.ChildIterator
 
next() - Method in class TableIndex.Iterator
returns the next linear index.
next() - Method in class DepthFirstIterator
 
next() - Method in class RecursiveDepthFirstIterator
 
next() - Method in interface IntIterator
 
next() - Method in class InstanceIterator
 
next(int[]) - Method in class Index
 
nextIteration() - Method in class MessagePassingScheduler
This returns an array of message indices to be passed at the next iteration.
nextIteration() - Method in class ParallelSchedule
 
nextIteration() - Method in class SequentialSchedule
 
nextIteration() - Method in class TreeSchedule
 
nextNode() - Method in class RCIterator
Does not guarantee any particular ordering of the nodes returned.
nextNode() - Method in class RCIteratorArray
Does not guarantee any particular ordering of the nodes returned.
nextNode() - Method in class RCIteratorTraversal
Does not guarantee any particular ordering of the nodes returned.
nextNode() - Method in class RCNodeInternalBinaryCache.ChildIterator
 
nextSafe(int[]) - Method in class Index
 
node - Static variable in class BeliefNetwork.Auditor.Unit
 
node - Variable in class DecisionEvent
 
NODE - Static variable in interface HuginReaderConstants
 
nodeBlock() - Method in class HuginReader
 
nodeCount() - Method in interface ArithmeticExpression
 
nodeCount() - Method in class BeliefCompilation
Deprecated.  
nodeCount() - Method in class S4DoubleExpression
 
nodeForID(String) - Method in class DecisionTreeImpl
interface Factory
nodeForID(String) - Method in interface Factory
 
nodeID - Variable in class RC2Node
 
NodeLinearTask - Class in edu.ucla.belief.io
A task that we expect to run in time roughly linear in the number of nodes a model contains.
NodeLinearTask(String, Estimate, int, String[]) - Constructor for class NodeLinearTask
 
nodes() - Method in class CachingDFBnB.SearchGraph
 
nodeSet(Object) - Method in class Hypergraph
 
NOISY_OR - Static variable in class DSLNodeType
 
NoisyOrShell - Interface in edu.ucla.belief
An interface for noisy-or
NoisyOrShellHenrion - Class in edu.ucla.belief
 
NoisyOrShellHenrion(List, double[]) - Constructor for class NoisyOrShellHenrion
 
NoisyOrShellPearl - Class in edu.ucla.belief
 
NoisyOrShellPearl(List, FiniteVariable, double[], int[]) - Constructor for class NoisyOrShellPearl
 
NONE - Variable in class Optimizer
 
NONE - Static variable in class Pedigree
 
none - Static variable in class CachingDFBnB.HeurFunct
 
NONE - Variable in class ProbabilityQueryCoder.MarginalScopeOption
 
noNullElements(Object[]) - Static method in class Assert
 
normalize() - Method in interface CPTShell
 
normalize(boolean) - Method in class DecisionLeaf
 
normalize() - Method in interface DecisionTree
 
normalize() - Method in class DecisionTreeImpl
interface DecisionTree
normalize() - Method in class DecisionShell
 
normalize(Map) - Method in class GraphvizIO
 
normalize() - Method in class NoisyOrShellHenrion
 
normalize() - Method in class NoisyOrShellPearl
 
normalize() - Method in class Table
 
normalize(int) - Method in class Table
 
normalize(Table) - Static method in class Table
 
normalize(int) - Method in class TableScaled
 
normalize() - Method in class TableShell
 
normalize - Static variable in class UaiMain
 
normalize() - Method in class Table
 
normalizeAllNew() - Method in class CPTInfo
 
normalized - Variable in enum Flavor
computes the log of answers to avoid underflow
normalized() - Static method in enum Flavor
the flavors that compute the log of answers to avoid underflow
NormalizedMaxSSAlgorithm - Class in il2.inf.jointree
 
NormalizedSSAlgorithm - Class in il2.inf.jointree
this class should be checked (AC): = double check sendMessage = define the semantics of partial and joint methods (only their relative values are correct) = there implements a faster way to do log Pr(e) by accumulating the normalizing constants during message passing
NormalizedSSAlgorithm(EliminationOrders.JT, Table[]) - Constructor for class NormalizedSSAlgorithm
 
NormalizedZCAlgorithm - Class in il2.inf.jointree
this class should be checked (AC): = double check sendMessage = define the semantics of partial and joint methods (only their relative values are correct) = there is a faster way to do log Pr(e) by accumulating the normalizing constants during message passing
NormalizedZCAlgorithm(EliminationOrders.JT, Table[]) - Constructor for class NormalizedZCAlgorithm
 
normalizeEnumProperties(BeliefNetwork) - Static method in class NetworkIO
 
normalizeInPlace() - Method in class Table
 
normalizeSuperimposed() - Method in class CPTInfo
 
NOT_COMPUTED_dbl - Static variable in class RC.RCStats
 
NOT_COMPUTED_int - Static variable in class RC.RCStats
 
noteOptimizationEpsilon(double) - Method in class DecisionTreeImpl
 
notifyNonPriorityListeners() - Method in class EvidenceController
Fire evidenceChanged() event when evidence has not actually changed, usually when the computed query answer has changed for some other reason, and you want registered listeners to know about it.
notNull(Object) - Static method in class Assert
 
notNull(Object, String) - Static method in class Assert
 
notoriousEdges() - Method in class AbstractInferenceEngine
 
notoriousEdges() - Method in class RecoveryInferenceEngine
 
notoriousEdges() - Method in class SynchronizedInferenceEngine
 
notoriousEdges() - Method in interface InferenceEngine
 
noun - Variable in class BeliefNetwork.Auditor.Unit
 
now() - Static method in class EdgeDeletionInferenceEngine.DateFormatFilename
 
now() - Static method in class AbstractStringifier.DateFormatFilename
 
nthElement(int) - Method in class IntPriorityQueue
Returns the nth element in the priority queue, where n indicates how the elements are stored not their priority.
nthKey(int) - Method in class IntPriorityQueue
Returns the nth key in the priority queue, where n indicates how the elements are stored not their priority.
NuclearFamily - Class in edu.ucla.belief.io.geneticlinkage
 
NuclearFamily(Person, Person, Person[]) - Constructor for class NuclearFamily
 
NUM - Static variable in interface HuginLogReaderConstants
 
NUM - Static variable in interface HuginReaderConstants
 
NUM - Static variable in interface NeticaReaderConstants
 
numCacheEntries() - Method in class RC.RCStats
 
numCacheEntries_local_total() - Method in class RCNode
 
numCacheEntries_local_total() - Method in class RCNodeInternalBinaryCache
 
numCacheEntries_local_used() - Method in class RCNode
 
numCacheEntries_local_used() - Method in class RCNodeInternalBinaryCache
 
numCacheEntries_MPE() - Method in class RC
Number of Caches being used by this RC object.
numCacheEntriesMB() - Method in class RC.RCStats
 
numCacheEntriesMpe_local_total() - Method in class RCNode
 
numCacheEntriesMpe_local_total() - Method in class RCNodeInternalBinaryCache
 
numCacheEntriesMpe_local_used() - Method in class RCNode
 
numCacheEntriesMpe_local_used() - Method in class RCNodeInternalBinaryCache
 
numCachingFull() - Method in class CachingDFBnB.SearchGraph
 
numCachingFullMinusWorthless() - Method in class CachingDFBnB.SearchGraph
 
numChildren() - Method in class Person
 
numChildren() - Method in class RCNodeInternalBinaryCache
 
numClauses() - Method in class KnowledgeBase
 
numClauses - Variable in class KBMap.Mapping
 
numClauses() - Method in interface KnowledgeBase
 
numClauses() - Method in class KnowledgeBaseImpl
 
numClauses() - Method in class MultiValuedCNF
 
numClauses() - Method in class KB_SAT
 
numComplexAffection - Variable in class Loci.Header
 
numCond() - Method in class EOGenerator.EO
 
numCond - Variable in class EOGenerator.RC
 
numCond() - Method in class RCGenerator.EO
 
numCutsetInstantiations() - Method in class RC2NodeInternal
 
numEdges() - Method in class BeliefNetworkImpl
 
numEdges() - Method in class Hypergraph
 
numEdges() - Method in class AbstractDirectedGraph
 
numEdges() - Method in interface DirectedGraph
 
numEdges() - Method in class HashDirectedGraph
 
numEvals - Variable in class Loci.Footer.Linkmap
 
numInternalNodes(TableIndex) - Static method in class Stats
 
numInternalNodes() - Method in class RC.RCStats
 
numLeafNodes() - Method in class RC.RCStats
 
numLiterals() - Method in class KnowledgeBase
 
numLiterals() - Method in interface KnowledgeBase
 
numLiterals() - Method in class KnowledgeBaseImpl
 
numLiterals() - Method in class MultiValuedCNF
 
numLiterals() - Method in class KB_SAT
 
numLoci - Variable in class Loci.Header
 
numNodes() - Method in class Hypergraph
 
numNodes() - Method in class RC.RCStats
 
numNodesCached() - Method in class RC2.ComputationStats
 
numNodesCached() - Method in class RC.RCStats
 
numNodesNotCached() - Method in class RC.RCStats
 
numOutcomes() - Method in class DecisionInternal
 
numOutcomes() - Method in class DecisionLeaf
 
numOutcomes() - Method in interface DecisionNode
 
numOutcomes() - Method in class DecisionNodeAbstract
 
numParentNodes() - Method in class RC2Node
 
numPossibleStates(FiniteVariable) - Method in interface KnowledgeBase
 
numPossibleStates(FiniteVariable) - Method in class KnowledgeBaseImpl
 
numRecords() - Method in class LearningData
Returns the number of evidence Maps in list.
numRecords() - Method in class LearningDataOld
Returns the number of evidence Maps in list.
numRoots() - Method in class RC
 
numSearchCalls() - Method in class CachingDFBnB.DFBnB_TmpVars
 
numSearchNodesVisited - Variable in class MapSearch.MapInfo
 
numVars - Variable in class KBMap.Mapping
 
numVars() - Method in class RC2Index
 
numVarsAppearingInCNF() - Method in class MultiValuedCNF
 

O

ObjArrays - Class in edu.ucla.util
A class consisting of static utility functions dealing with Object arrays.
ObjArrays() - Constructor for class ObjArrays
 
OBJECT - Static variable in class SensitivitySuggestionComparator
 
object - Variable in class Reference
 
objectToString(Object) - Method in class AbstractStringifier
 
objectToString(Object) - Method in interface Stringifier
 
OBSERVATION - Static variable in class DiagnosisType
 
OBSERVATION - Static variable in class SMILEReader
 
OBSERVE - Static variable in class BeliefNetwork.Auditor.Deed
 
observe(FiniteVariable, Object) - Method in class EvidenceController
Add var=value to the list of observations.
observe(Map) - Method in class EvidenceController
Adds the observations listed to the set of current observations
observe(FiniteVariable, Object) - Method in class RC2
 
observe(int, int) - Method in class RC2NodeLeaf
 
observe(int, int) - Method in class RC2NodeLeafEvidInd
 
observe(FiniteVariable, Object) - Method in class RC
Add var=value to the list of observations.
observeNotifyOnlyPriorityListeners(FiniteVariable, Object) - Method in class EvidenceController
 
offset(IntMap) - Method in class Index
 
offsetIndex(Index) - Method in class Index
 
OK - Static variable in class Macros
 
oldConstrainedMinFill(Collection, IntSet) - Static method in class EliminationOrders
The old version of minfill which should not be used any more unless there is a very good reason.
oldDomain() - Method in class EDNetwork
 
oldEliminateForMinFill(Graph, Set) - Static method in class EliminationOrders
 
oldEvidenceToNewEvidence(Map, Map<FiniteVariable, FiniteVariable>) - Static method in class UaiEdgeCutter
 
oldMinFill(Set) - Static method in class EliminationOrders
 
oldMinFill(Collection, Set) - Static method in class EliminationOrders
 
oldMinFill(BeliefNetwork) - Static method in class EliminationOrders
 
oldMinFill(Graph) - Static method in class EliminationOrders
 
oldMinFill(BeliefNetwork, Set) - Static method in class EliminationOrders
 
oldMinFill(Graph, Set) - Static method in class EliminationOrders
 
oldMinFill(Collection) - Static method in class EliminationOrders
The old version of minfill which should not be used any more unless there is a very good reason.
oldTableOfEdge(int) - Method in class EDNetwork
 
oldTables() - Method in class EDNetwork
 
oldToNewEvidence(IntMap) - Method in class EDNetwork
 
oldToNewVar(int) - Method in class EDNetwork
Helper functions
oldVarOfEdge(int) - Method in class EDNetwork
 
onClone() - Method in class BeliefPropagationSettings
interface UserObject
onClone() - Method in class JoinTreeSettings
interface UserObject
onClone() - Method in class RCSettings
interface UserObject
onClone() - Method in class Settings
interface UserObject
onClone() - Method in class SettingsImpl
interface UserObject
onClone() - Method in interface UserObject
 
ONE - Static variable in class Table
 
oneMoreIteration(boolean) - Method in class BeliefPropagation
 
oneMoreIteration(boolean) - Method in class EDAlgorithm
 
open(PrintStream) - Method in enum XmlbifWriter.Element
 
openFile(File, NetworkIO.BeliefNetworkIOListener) - Method in class FileType
 
openSamiamDtree(String, BeliefNetwork) - Static method in class Settings
 
OPERATOR_EQUALS - Static variable in class SensitivityConstraint
 
OPERATOR_EQUALS - Static variable in class SensitivityEngine
 
OPERATOR_GTE - Static variable in class SensitivityConstraint
 
OPERATOR_GTE - Static variable in class SensitivityEngine
 
OPERATOR_LTE - Static variable in class SensitivityConstraint
 
OPERATOR_LTE - Static variable in class SensitivityEngine
 
optimize(CPTShell) - Method in class Optimizer
 
optimize(DecisionNode[], FiniteVariable, Factory) - Method in class Optimizer
 
optimize(Parameter[], FiniteVariable, Factory) - Method in class Optimizer
 
optimize(double[], FiniteVariable, Factory) - Method in class Optimizer
 
optimize(double[], FiniteVariable, Factory) - Method in class Optimizer.ParameterOptimizationLevel
 
optimize(double[], FiniteVariable, Factory) - Method in class Optimizer.ParameterOptimizationOn
 
Optimizer - Class in edu.ucla.belief.decision
 
Optimizer(double) - Constructor for class Optimizer
 
Optimizer.EquivalenceKey - Class in edu.ucla.belief.decision
 
Optimizer.EquivalenceKey(Object[], FiniteVariable) - Constructor for class Optimizer.EquivalenceKey
 
Optimizer.ParameterOptimizationLevel - Class in edu.ucla.belief.decision
 
Optimizer.ParameterOptimizationLevel(String) - Constructor for class Optimizer.ParameterOptimizationLevel
 
Optimizer.ParameterOptimizationOn - Class in edu.ucla.belief.decision
 
Optimizer.ParameterOptimizationOn(String) - Constructor for class Optimizer.ParameterOptimizationOn
 
Optimizer.Unsortable - Class in edu.ucla.belief.decision
 
Optimizer.Unsortable(double, int) - Constructor for class Optimizer.Unsortable
 
OPTION_AMOUNT - Static variable in class CPTCoder
 
OPTION_AMOUNT - Static variable in class EMCoder
 
OPTION_AMOUNT - Static variable in class MAPCoder
 
OPTION_AMOUNT - Static variable in class ModelCoder
 
OPTION_AMOUNT - Static variable in class MPECoder
 
OPTION_AMOUNT - Static variable in class SensitivityCoder
 
OPTION_BREADTH - Static variable in class ProbabilityQueryCoder
 
OPTION_LIBRARY_VERSION - Static variable in class ModelCoder
 
OPTION_MARGINALSCOPE - Static variable in class ProbabilityQueryCoder
 
OPTION_PRUNE - Static variable in class MAPCoder
 
OPTION_TIMINGS - Static variable in class MAPCoder
 
OPTION_WITH_COMMENTS - Static variable in class CPTCoder
 
OPTION_WITH_COMMENTS - Static variable in class EMCoder
 
OPTION_WITH_COMMENTS - Static variable in class MAPCoder
 
OPTION_WITH_COMMENTS - Static variable in class ModelCoder
 
OPTION_WITH_COMMENTS - Static variable in class MPECoder
 
OPTION_WITH_COMMENTS - Static variable in class ProbabilityQueryCoder
 
OPTION_WITH_COMMENTS - Static variable in class SensitivityCoder
 
OptionBreadth - Class in edu.ucla.util.code
 
OptionBreadth(String) - Constructor for class OptionBreadth
 
OptionWithComments - Class in edu.ucla.util.code
 
OR - Variable in class CSITypeProperty
 
order - Variable in class ExactMap.SizedOrder
 
order() - Method in class CachingDFBnB.SearchGraph
 
order - Variable in class UaiEdgeCutter.MyRecord
 
order(BayesianNetwork, int) - Method in enum Algorithm.EliminationOrderHeuristic
 
order(BayesianNetwork, Map<Algorithm.Setting, ?>) - Static method in enum Algorithm
elimination order
order(Collection, IntSet, IntList) - Static method in class MapOrderMaker
 
order(Collection, IntSet, double, IntList) - Static method in class MapOrderMaker
 
order - Variable in class EliminationOrders.JT
 
order - Variable in class EliminationOrders.Record
 
order(Random, int[], int[][], int[][]) - Method in class EliminationOrderEngine
Computes a "restricted" elimination order for a subset of nodes.
orderAlgo - Variable in class CachingDFBnB
 
orderedInstances(FiniteVariable, Table) - Static method in class UaiEdgeCutter
 
Orderer - Interface in il2.inf.structure
 
orderVars(List, Collection) - Static method in class RCNodeInternalBinaryCache
 
orient(RC2Node, Map) - Static method in class RC2CreatorDtToDg
Cannot be called if rt has already been added to the RC object in rt.rc.
original - Variable in class Macros.Bridge
 
outcomes - Variable in class XmlbifParser.Variable
 
outcomeStrings - Variable in class XmlbifParser.Variable
 
outDegree(Object) - Method in class BeliefNetworkImpl
 
outDegree(Object) - Method in class AbstractDirectedGraph
 
outDegree(Object) - Method in interface DirectedGraph
Returns the number of edges leaving the vertex.
outDegree(Object) - Method in class HashDirectedGraph
Returns the number of edges leaving the vertex.
outDegree(int) - Method in class IntDirectedGraph
 
outGoing(Object) - Method in class BeliefNetworkImpl
 
outGoing(Object) - Method in class DecisionTreeImpl
interface DirectedGraph
outGoing(Object) - Method in interface DirectedGraph
Constructs an Iterator over the vertices adjacent to edges leaving the specified vertex.
outGoing(Object) - Method in class HashDirectedGraph
Constructs an Iterator over the vertices adjacent to edges leaving the specified vertex.
outGoing(int) - Method in class IntDirectedGraph
 
output(double[]) - Method in class LinearFunction
 
outputChangingVariables(PrintStream) - Method in class Pedigree.GeneticNetwork
 
outputConsole - Variable in class RC2
 
outputConsole - Variable in class RC2.RCCreationParams
 
outputConsole - Variable in class RC
 
outputInfo(String) - Method in class RC2
 
outputSolution(UaiMapSolution) - Method in class UaiMain
 

P

Pair - Class in il2.util
An ordered pair of ints.
Pair(Integer, Integer) - Constructor for class Pair
Initializes the pair.
Pair(int, int) - Constructor for class Pair
Initializes the pair.
PARALLEL - Static variable in class MessagePassingScheduler
 
ParallelSchedule - Class in il2.inf.bp.schedules
 
ParallelSchedule(Table[]) - Constructor for class ParallelSchedule
 
parameter(Attributes) - Method in class Builder
 
Parameter - Interface in edu.ucla.belief.decision
 
PARAMETER_TYPES() - Static method in enum Flavor
parameter types of factory methods
parameterForID(String) - Method in class DecisionTreeImpl
interface Factory
parameterForID(String) - Method in interface Factory
 
ParameterImpl - Class in edu.ucla.belief.decision
 
ParameterImpl(String, double) - Constructor for class ParameterImpl
 
ParameterImpl(int, double) - Constructor for class ParameterImpl
 
parameters - Variable in class Stats
 
ParanoidFileFinder - Class in edu.ucla.util.code
 
ParanoidFileFinder() - Constructor for class ParanoidFileFinder
 
paranoidFindAll(File, Collection) - Method in class ParanoidFileFinder
 
parent - Variable in class DecisionEvent
 
parent(int) - Method in class EliminationTree
 
parent(int) - Method in class JoinTree
 
PARENT_INSERTED - Static variable in class DecisionEvent
 
parentChildOrdering() - Method in class RC
Guarantees a parent before a child.
parentIDs - Variable in class PotentialInfo
 
parentNodes() - Method in class RC2Node
 
parentNodes() - Method in class RCNode
 
parents(Pair) - Method in class JoinTree
 
parentStateInserted(FiniteVariable, int) - Method in interface CPTShell
 
parentStateInserted(FiniteVariable, int) - Method in class DecisionShell
 
parentStateInserted(FiniteVariable, int) - Method in class NoisyOrShellHenrion
 
parentStateInserted(FiniteVariable, int) - Method in class NoisyOrShellPearl
 
parentStateInserted(FiniteVariable, int) - Method in class Table
 
parentStateInserted(FiniteVariable, int) - Method in class TableShell
 
parentStateRemoved(FiniteVariable, int) - Method in interface CPTShell
 
parentStateRemoved(FiniteVariable, int) - Method in class DecisionShell
 
parentStateRemoved(FiniteVariable, int) - Method in class NoisyOrShellHenrion
 
parentStateRemoved(FiniteVariable, int) - Method in class NoisyOrShellPearl
 
parentStateRemoved(FiniteVariable, int) - Method in class Table
 
parentStateRemoved(FiniteVariable, int) - Method in class TableShell
 
parse(File) - Method in class AbstractSaxHandler
 
parse(InputStream) - Method in class AbstractSaxHandler
 
parse(InputSource) - Method in class AbstractSaxHandler
 
parse() - Method in class HuginLogReader
 
parseArgs(String[], String[], Map) - Static method in class NetworkIO
 
parseArgs(Set, String[], Map) - Static method in class NetworkIO
 
parseData() - Method in class XmlbifParser.Definition
 
ParseException - Exception in edu.ucla.belief.io
This exception is thrown when parse errors are encountered.
ParseException(Token, int[][], String[]) - Constructor for exception ParseException
This constructor is used by the method "generateParseException" in the generated parser.
ParseException() - Constructor for exception ParseException
The following constructors are for use by you for whatever purpose you can think of.
ParseException(String) - Constructor for exception ParseException
 
partial(FiniteVariable) - Method in class PropagationInferenceEngineImpl
interface PartialDerivativeEngine
partial(FiniteVariable) - Method in class JoinTreeInferenceEngineImpl
Returns the partial derivatives of the probability function with respect to the variable var.
partial(FiniteVariable) - Method in class PartialDerivativeWrapperEngine
 
partial(FiniteVariable) - Method in class RandomInferenceEngine
 
partial(FiniteVariable) - Method in class SynchronizedInferenceEngine.SynchronizedPartialDerivativeEngine
 
partial(FiniteVariable) - Method in interface PartialDerivativeEngine
Returns the partial derivatives of the probability function with respect to the variable var.
partial - Variable in enum Algorithm
supports compiling a partial derivative engine ??
partial - Variable in enum Flavor
supports compiling a partial derivative engine ??
partial(BayesianNetwork, EliminationOrders.JT) - Method in enum Flavor
compile a partial derivative engine, if supported
PartialDerivativeEngine - Interface in edu.ucla.belief
 
PartialDerivativeEngine - Interface in il2.inf
 
PartialDerivativeWrapper - Class in edu.ucla.belief.inference
 
PartialDerivativeWrapperEngine - Class in edu.ucla.belief.inference
 
partials() - Static method in enum Algorithm
the flavors that support compiling a partial derivative engine
partials() - Static method in enum Flavor
the flavors that support compiling a partial derivative engine
Partition - Class in il2.inf.mini
 
Partition(Index[], int[]) - Constructor for class Partition
 
partitionOrder(IntList, IntSet, int) - Method in class VEVariance
 
PATTERN_COMMENT - Static variable in class XmlbifParser
 
PATTERN_DATA_DELIMITER - Static variable in class XmlbifParser
 
PATTERN_POSITION - Static variable in class XmlbifParser
 
pauseRecCondAsThread() - Method in class RC
 
ped - Variable in class Pedigree.GeneticNetwork
 
Pedigree - Class in edu.ucla.belief.io.geneticlinkage
This class reads in and stores pedigrees.
Pedigree.GeneticNetwork - Class in edu.ucla.belief.io.geneticlinkage
 
Pedigree.GeneticNetwork(int, Pedigree) - Constructor for class Pedigree.GeneticNetwork
 
Pedigree.PseudoLoci - Class in edu.ucla.belief.io.geneticlinkage
 
Pedigree.PseudoLoci() - Constructor for class Pedigree.PseudoLoci
 
peekTimer() - Method in class VEVariance
 
PerlScriptGenius - Class in edu.ucla.util.code
 
PerlScriptGenius() - Constructor for class PerlScriptGenius
 
permute(FiniteVariable[]) - Method in class Table
 
Person - Class in edu.ucla.belief.io.geneticlinkage
 
Person(int, int, int, int, int, int, int, int, boolean, Pedigree.PseudoLoci) - Constructor for class Person
 
pipe(PrintWriter) - Method in class ScriptExecution
 
pipe(Process, PrintWriter) - Static method in class ScriptExecution
 
placeInBucket(SubDomain) - Method in class Bucketer
 
placeInBucket(SubDomain, int) - Method in class Bucketer
 
placeInBucket2(SubDomain, int) - Method in class Bucketer
same as placeInBucket, except that it returns the index of the bucket the table is placed into.
placeInBuckets(Collection) - Method in class Bucketer
 
placeInBuckets(Collection, int) - Method in class Bucketer
 
pole() - Method in class ParanoidFileFinder
 
populate() - Method in class Dtree
 
populate(Collection) - Method in class DtreeNodeLeaf
 
postProcess(BeliefNetwork) - Static method in class Macros.Recoverables
 
POTENTIAL - Static variable in interface HuginReaderConstants
 
Potential - Interface in edu.ucla.belief
 
potentialBlock() - Method in class HuginReader
 
PotentialInfo - Class in edu.ucla.belief.io.dsl
 
PotentialInfo(DSLNode, String[], double[], int[], int) - Constructor for class PotentialInfo
 
PotentialInfo(HuginPotential) - Constructor for class PotentialInfo
 
PREFIX - Static variable in enum EdgeDeletionInferenceEngine.CPTPolicy
 
prefix() - Static method in enum EdgeDeletionInferenceEngine.CPTPolicy
 
prepareForUpdate(int[][], int[], int, boolean[], boolean[][]) - Static method in class Util
 
prePrepareToStartComputation() - Method in class RC2
Attempt to do some preparation steps before computations are actually run.
PREPROCESS - Static variable in class Pedigree
 
preprocessNet(Random, BeliefNetwork, Map<FiniteVariable, Object>, boolean) - Method in interface UaiUtilsIf
Preprocess the given network according to the given evidence and returns the result.
prEvidence() - Method in class Macros.Bridge
 
prEvidence() - Method in class JointWrapper
 
prEvidence() - Method in class BeliefPropagation
 
prEvidence() - Method in class MaxProduct
 
prEvidence() - Method in class EDAlgorithm
 
prEvidence() - Method in interface JointEngine
 
prEvidence() - Method in class JoinTreeAlgorithm
 
prEvidence() - Method in class RCEngine
 
print(Graph, PrintStream) - Static method in class Graphs
 
print(DirectedGraph, PrintStream) - Static method in class Graphs
 
print(double[], PrintStream) - Static method in class DblArrays
displays the double array on System.stream
print(int[], PrintStream) - Static method in class IntArrays
displays the integer array on System.stream
print(Object[], PrintStream) - Static method in class ObjArrays
displays the object array on System.stream
printAll(Throwable, PrintStream) - Static method in class AbstractSaxHandler
 
printArr(double[], PrintWriter) - Static method in class Table
 
printArr(double[], PrintStream) - Static method in class Table
 
printArr(Table, PrintWriter) - Static method in class Table
 
printArr(Table, PrintStream) - Static method in class Table
 
printArrScaled(double[], double) - Static method in class Table
Calls TableScaled.toScaled on each value.
printArrUnScaled(double[], double) - Static method in class Table
Calls TableScaled.toRealPr on each value.
printCollectionOfIDs(Collection, PrintStream) - Static method in class MAPCoder
 
printDoubleArray(double[], PrintStream) - Static method in class ModelCoder
 
printEdges(int[][]) - Static method in class EDEdgeDeleter
 
printEdges(int[][], String, PrintStream) - Static method in class EDEdgeDeleter
 
printFamily(int, int) - Method in class Pedigree
 
printInfo(UaiPreprocessResult, UaiMapSolution) - Method in class UaiMain
Query methods
printInfoCompilation(PrintWriter) - Method in class AbstractInferenceEngine
 
printInfoCompilation(PrintWriter) - Method in class JoinTreeInferenceEngineImpl
 
printInfoCompilation(PrintWriter) - Method in class RandomInferenceEngine
 
printInfoCompilation(PrintWriter) - Method in class SynchronizedInferenceEngine
 
printInfoCompilation(PrintWriter) - Method in class WrapperInferenceEngine
 
printInfoCompilation(PrintWriter) - Method in interface InferenceEngine
 
printInfoPropagation(PrintWriter) - Method in class AbstractInferenceEngine
 
printInfoPropagation(PrintWriter) - Method in class JoinTreeInferenceEngineImpl
 
printInfoPropagation(PrintWriter) - Method in class RandomInferenceEngine
 
printInfoPropagation(PrintWriter) - Method in class SynchronizedInferenceEngine
 
printInfoPropagation(PrintWriter) - Method in class WrapperInferenceEngine
 
printInfoPropagation(PrintWriter) - Method in interface InferenceEngine
 
printInformation(IntSet, int, IntList) - Method in class VEVariance
 
printInstanceNames(Domain, int, PrintStream) - Static method in class ModelCoder
 
printIntSetValues(IntSet, Map, PrintStream) - Static method in class ModelCoder
 
printListOfStrings(List, PrintStream) - Static method in class ModelCoder
 
println(double[], PrintStream) - Static method in class DblArrays
displays the double array on System.stream
println(int[], PrintStream) - Static method in class IntArrays
displays the integer array on System.stream
println(Object[], PrintStream) - Static method in class ObjArrays
displays the object array on System.stream
printMethodStackTraceElement(Throwable, String, PrintStream, boolean) - Static method in class Interruptable
 
printOptimizedStats(BeliefNetwork, PrintWriter) - Method in class Optimizer
 
printPerson(int, int) - Method in class Pedigree
 
printRC2(PrintStream, RC2) - Static method in class RC2Utils
 
printRC2(PrintWriter, RC2) - Static method in class RC2Utils
 
printRepeat(String, int, String[], PrintStream) - Static method in class ModelCoder
 
printStack() - Method in class ApproxReport
 
printSubDomains(List) - Method in class UaiEdgeCutter.MyIndex
 
printSubDomains(Index, List) - Static method in class UaiEdgeCutter
 
printSubDomains(List, List) - Static method in class UaiEdgeCutter
 
printTables(Table[], PrintWriter) - Method in class AbstractInferenceEngine
 
printTables(PrintWriter) - Method in class EdgeDeletionInferenceEngine
 
printTables(PrintWriter) - Method in class PropagationInferenceEngineImpl
 
printTables(PrintWriter) - Method in class RecoveryInferenceEngine
 
printTables(PrintWriter) - Method in class JoinTreeInferenceEngineImpl
 
printTables(PrintWriter) - Method in class RandomInferenceEngine
 
printTables(PrintWriter) - Method in class SynchronizedInferenceEngine
 
printTables(PrintWriter) - Method in class WrapperInferenceEngine
 
printTables(PrintWriter) - Method in interface InferenceEngine
 
printTables(PrintWriter) - Method in class RCInferenceEngine
 
printTimes(Collection, PrintStream) - Static method in class ParanoidFileFinder
 
printToWriter(String) - Method in class ApproxEngine
 
printToWriter(String) - Method in class SensitivityEngine
 
printVarianceInformation(VarianceInfo) - Method in class VEVariance
 
PriorityQueue - Class in il2.inf.structure.minfill2
A base class for priority queues.
PriorityQueue() - Constructor for class PriorityQueue
 
Prob - Class in edu.ucla.util
 
Prob() - Constructor for class Prob
 
probabilities - Variable in class PotentialInfo
 
probability() - Method in class EdgeDeletionInferenceEngine
 
probability() - Method in class PropagationInferenceEngineImpl
 
probability() - Method in class RecoveryInferenceEngine
 
probability() - Method in class JoinTreeInferenceEngineImpl
 
probability() - Method in class MapEngine
 
probability() - Method in class RandomInferenceEngine
 
probability() - Method in class SynchronizedInferenceEngine
 
probability() - Method in class WrapperInferenceEngine
 
probability() - Method in interface InferenceEngine
 
probability() - Method in class RCInferenceEngine
Returns P(e).
probability - Variable in class UaiMapSolution
The computed P (e) or null if computing MPE.
probability() - Method in class JoinTreeInference
 
probability() - Method in class ShenoyShaferAlgorithm
 
probabilityDisplayOperatorUnicode() - Method in class AbstractInferenceEngine
 
probabilityDisplayOperatorUnicode() - Method in class EdgeDeletionInferenceEngine
 
probabilityDisplayOperatorUnicode() - Method in class PropagationInferenceEngineImpl
 
probabilityDisplayOperatorUnicode() - Method in class RecoveryInferenceEngine
 
probabilityDisplayOperatorUnicode() - Method in class SynchronizedInferenceEngine
 
probabilityDisplayOperatorUnicode() - Method in interface InferenceEngine
 
probabilityInterval(int) - Method in class SensitivityTable
 
ProbabilityInterval - Class in edu.ucla.util
Class for probability interval.
ProbabilityInterval() - Constructor for class ProbabilityInterval
 
ProbabilityInterval(double) - Constructor for class ProbabilityInterval
 
ProbabilityInterval(double, double) - Constructor for class ProbabilityInterval
 
ProbabilityInterval(Interval, double) - Constructor for class ProbabilityInterval
 
probabilityIntervals() - Method in class SensitivityTable
 
ProbabilityQueryCoder - Class in edu.ucla.util.code
 
ProbabilityQueryCoder() - Constructor for class ProbabilityQueryCoder
 
ProbabilityQueryCoder.MarginalScopeOption - Class in edu.ucla.util.code
 
ProbabilityQueryCoder.MarginalScopeOption() - Constructor for class ProbabilityQueryCoder.MarginalScopeOption
 
probabilitySupported() - Method in class AbstractInferenceEngine
 
probabilitySupported() - Method in class PropagationEngineGenerator
If you change the return value, you must consider changing the return value of PropagationInferenceEngineImpl.probabilitySupported()
probabilitySupported() - Method in class PropagationInferenceEngineImpl
 
probabilitySupported() - Method in class Dynamator
 
probabilitySupported() - Method in class SynchronizedInferenceEngine
 
probabilitySupported() - Method in interface InferenceEngine
 
probOfEvidence - Variable in class MapSearch.MapInfo
 
processOutcome(ScriptExecution) - Method in interface ScriptExecution.ProcessCustodian
 
profilerRunning() - Static method in class JVMProfiler
Will return true if the command line to start the profiler was set, otherwise will return false.
profilerRunning_native() - Static method in class JVMProfiler
Will return true if the command line to start the profiler was set, otherwise will return false.
progData - Variable in class Loci.Footer
 
program - Variable in class Loci.Header
 
ProgressMonitorable - Interface in edu.ucla.util
A task that estimates how much total work it must do and reports on how much it has completed so far.
project(Set) - Method in class Table
 
project(Set) - Method in class TableIndex
Returns a new index formed from limiting the current index to the variables contained in variables.
project(LinearFunction, List) - Method in class LinearFunction
Projects onto a subset of arguments
projectInto(Table) - Method in class Table
 
projectInto(Table, int[][]) - Method in class Table
 
projectInto(double[], double[], int[][]) - Static method in class Table
 
projectInto2(Table) - Method in class Table
 
projectOnto(int) - Method in class Table
 
PropagationEngineGenerator - Class in edu.ucla.belief.approx
 
PropagationEngineGenerator() - Constructor for class PropagationEngineGenerator
 
PropagationInferenceEngine - Interface in edu.ucla.belief.approx
 
PropagationInferenceEngineImpl - Class in edu.ucla.belief.approx
 
PropagationInferenceEngineImpl(BeliefNetwork, BeliefPropagationSettings, Dynamator) - Constructor for class PropagationInferenceEngineImpl
 
properties - Variable in enum EdgeDeletionBeliefPropagationSetting
 
properties() - Method in enum EdgeDeletionBeliefPropagationSetting
 
properties(PropertySuperintendent) - Static method in class Macros
suppress unchecked caste warning
properties - Variable in enum RecoverySetting
 
properties() - Method in enum RecoverySetting
 
properties - Variable in class XmlbifParser.Definition
 
properties - Variable in class XmlbifParser.Variable
 
properties() - Method in interface Setting
 
properties - Variable in enum Algorithm.Setting
 
propertiesArrayCopy(EnumProperty[]) - Static method in class VariableImpl
 
propertiesAsArray() - Method in interface BeliefNetwork
 
propertiesAsArray() - Method in class BeliefNetworkImpl
 
PROPERTY - Static variable in class MapProperty
 
PROPERTY - Static variable in class DiagnosisType
 
property() - Method in class DiagnosisType
 
PROPERTY - Static variable in class DSLNodeType
 
property() - Method in class DSLNodeType
 
PROPERTY - Static variable in class ExcludePolicy
 
property() - Method in class ExcludePolicy
 
PROPERTY - Static variable in class CSITypeProperty
 
property() - Method in interface EnumValue
 
PROPERTY - Static variable in class EvidenceAssertedProperty
 
property() - Method in class FlagProperty.FlagValue
 
PROPERTY - Static variable in class HiddenProperty
 
PROPERTY - Static variable in class ImpactProperty
 
PROPERTY - Static variable in class InferenceValidProperty
 
PROPERTY - Static variable in class InOutDegreeProperty
 
PROPERTY - Static variable in class QueryParticipantProperty
 
property() - Method in class UserEnumValue
 
PropertyKey - Enum in edu.ucla.util
general properties of something editable
PropertySuperintendent - Interface in edu.ucla.belief.io
 
proportionalChanges(int, double, double[], boolean[]) - Static method in class Prob
 
proportionalSchemes(FiniteVariable) - Static method in class CovaryingScheme
 
Prune - Class in edu.ucla.belief
A class containing utility methods that assist code that wants to work with a pruned network.
Prune() - Constructor for class Prune
 
prune(BeliefNetwork, Set, Map, Map, Map, Set, Map) - Static method in class Prune
Returns a copy of the given network pruned according to the given query variables and the given evidence.
prunedEngine(BeliefNetwork, Collection, Map) - Method in class DefaultGenerator
 
prunedEngine(BeliefNetwork, Collection, Map) - Method in class HuginEngineGenerator
 
prunedEngine(BeliefNetwork, Collection, Map) - Method in class JEngineGenerator
 
prunedEngine(BeliefNetwork, Collection, Map) - Method in class SSEngineGenerator
 
prunedEngine(BeliefNetwork, Collection, Map) - Method in class ZCEngineGenerator
 
pruneDurationMillisElapsed - Variable in class MapRunner.MapResult
 
pruneDurationMillisElapsed - Variable in class MapSearch.MapInfo
 
pruneDurationMillisProfiled - Variable in class MapRunner.MapResult
 
pruneDurationMillisProfiled - Variable in class MapSearch.MapInfo
 
put(Object, Object) - Method in class LearningData
 
put(Object, Object) - Method in class IdentityArrayMap
 
put(E, Object) - Method in interface Setting.Settings
 
put(E, PropertyKey, Object) - Method in interface Setting.Settings
 
put(E, Object) - Method in class SettingsImpl
 
put(E, PropertyKey, Object) - Method in class SettingsImpl
 
put(int, double) - Method in class DoubleMap
 
put(int, int) - Method in class IntMap
 
putAll(Map, Map) - Static method in class BeliefNetworkImpl
 
putAll(Map) - Method in class LearningData
 
putAll(Map) - Method in class IdentityArrayMap
 
putAtEnd(int, int) - Method in class IntMap
 
putHyperedge(Object, Collection) - Method in class Hypergraph
 
putTree(FiniteVariable, DecisionTree) - Method in class XmlDocumentHandler
 

Q

QuantitativeDependencyHandler - Interface in edu.ucla.belief
 
QueryParticipantProperty - Class in edu.ucla.util
Built in property to designate variables of interest before pruning.
QuickSort - Class in il2.util
 
QuickSort(int) - Constructor for class QuickSort
 
quote(String) - Method in class AbstractScriptGenius
 
quote(String) - Method in interface ScriptGenius
 

R

random(FiniteVariable) - Method in class AbstractInferenceEngine
 
RANDOM - Static variable in class InitializationMethod
 
random(FiniteVariable) - Method in class SynchronizedInferenceEngine
 
random(FiniteVariable) - Method in interface InferenceEngine
 
random(Map) - Method in class Table
 
RANDOM - Static variable in class Test
 
random - Variable in class Test
 
random(int) - Static method in class Prob
 
random(double, double) - Static method in class Prob
 
randomCPT(Collection, FiniteVariable) - Static method in class BeliefNetworks
Returns a cpt where the values in the table are random numbers consistent with it being a CPT.
randomCPT(Collection, FiniteVariable) - Static method in class RandomNetworks
Returns a cpt where the values in the table are random numbers consistent with it being a CPT.
randomCPT(Collection, FiniteVariable, double) - Static method in class RandomNetworks
 
randomDAG(Object[], double) - Static method in class Graphs
Generates a Dag, where there is an edge from (nodes[i],nodes[j]) with probability prob, where irandomElement(Collection) - Static method in class Test
 
randomElement(Object[]) - Static method in class Test
 
RandomEngineGenerator - Class in edu.ucla.belief.inference
Generates instances of RandomInferenceEngine, an inference engine that does no computation, instead returns random answers, for the purpose of testing.
RandomEngineGenerator() - Constructor for class RandomEngineGenerator
 
randomEvidence() - Method in class Test
 
randomGraph(Object[], int) - Static method in class BeliefNetworks
Generates a random directed graph using nodes as the vertices.
randomGraph(Object[], int) - Static method in class RandomNetworks
Generates a random directed graph using nodes as the vertices.
randomGraph(Object[], double) - Static method in class Graphs
Generates a graph generated by adding edge {nodes[i],nodes[j]) with probability prob.
RandomInferenceEngine - Class in edu.ucla.belief.inference
An inference engine that does no computation, instead returns random answers, for the purpose of testing.
RandomInferenceEngine(BeliefNetwork, Dynamator) - Constructor for class RandomInferenceEngine
 
randomJointValueIndex(Map) - Method in interface CPTShell
 
randomJointValueIndex(Map) - Method in class DecisionShell
 
randomJointValueIndex(Map) - Method in class NoisyOrShellHenrion
 
randomJointValueIndex(Map) - Method in class NoisyOrShellPearl
 
randomJointValueIndex(Map) - Method in class TableShell
 
randomNetwork(DirectedGraph) - Static method in class BeliefNetworks
returns a belief network with random CPTs.
randomNetwork(int, double) - Static method in class BeliefNetworks
Creates a random network where each edge has probability edgeProbability of being included.
randomNetwork(int, int) - Static method in class BeliefNetworks
Generates a random network consisting of boolean variables.
randomNetwork(DirectedGraph, double) - Static method in class RandomNetworks
Returns a belief network with biased CPTs.
randomNetwork(DirectedGraph) - Static method in class RandomNetworks
returns a belief network with uniformly random CPTs.
randomNetwork(int, double) - Static method in class RandomNetworks
Creates a random network where each edge has probability edgeProbability of being included.
randomNetwork(int, double, double) - Static method in class RandomNetworks
 
randomNetwork(int, int) - Static method in class RandomNetworks
Generates a random network consisting of boolean variables.
randomNetwork(int, int, double) - Static method in class RandomNetworks
 
RandomNetworks - Class in edu.ucla.belief
Contains a collection of static methods relating to generating random networks
RandomNetworks - Class in il2.model
 
RandomNetworks() - Constructor for class RandomNetworks
 
randomSubset(Collection, double) - Static method in class Test
 
randomSubset(int) - Method in class IntSet
 
rank(EDAlgorithm) - Method in enum EDAlgorithm.RankingHeuristic
 
ranked - Variable in class Macros.RankingArgs
 
rankEdgesByConvergence() - Method in class EDAlgorithm
 
rankEdgesByCorrelation() - Method in class EDAlgorithm
 
rankEdgesByMi() - Method in class EDAlgorithm
 
rankEdgesByScore(double[]) - Method in class EDAlgorithm
 
rankEdgesByTargetMi(int) - Method in class EDAlgorithm
 
rankEdgesRandomly(Random) - Method in class EDAlgorithm
 
RATIO - Static variable in class SensitivityConstraint
 
RATIO - Static variable in class SensitivityEngine
 
rc - Variable in class RC2Node
 
RC - Class in edu.ucla.belief.recursiveconditioning
This abstract class helps with removing code from the RCDgraph and RCDtree classes.
RC(RC.RCCreationParams) - Constructor for class RC
RC Object constructor.
RC - Class in il2.inf.rc
 
RC(DGraph, Table[]) - Constructor for class RC
 
RC.RCCounters - Class in edu.ucla.belief.recursiveconditioning
 
RC.RCCounters() - Constructor for class RC.RCCounters
 
RC.RCCreationException - Exception in edu.ucla.belief.recursiveconditioning
 
RC.RCCreationException(String) - Constructor for exception RC.RCCreationException
 
RC.RCCreationParams - Class in edu.ucla.belief.recursiveconditioning
 
RC.RCCreationParams() - Constructor for class RC.RCCreationParams
 
RC.RCStats - Class in edu.ucla.belief.recursiveconditioning
 
RC.RCStats() - Constructor for class RC.RCStats
Create an RCStats object without doing any computations yet.
RC.RCStats(int, double, double) - Constructor for class RC.RCStats
Warning: If you don't know the value of one of the parameters, you must pass in NOT_COMPUTED_int or NOT_COMPUTED_dbl, otherwise these classes will not work.
RC.RCStats_All - Class in edu.ucla.belief.recursiveconditioning
Handle storing and computing computational statistics based on doing All computations (on graphs it would be for all marginals, and for trees it would be the same as Pe).
RC.RCStats_All() - Constructor for class RC.RCStats_All
Create an RCStats object without doing any computations yet.
RC.RCStats_All(int, double, double) - Constructor for class RC.RCStats_All
Warning: If you don't know the value of one of the parameters, you must pass in NOT_COMPUTED_int or NOT_COMPUTED_dbl, otherwise the classes will not work.
RC.RCStats_Pe - Class in edu.ucla.belief.recursiveconditioning
Handle storing and computing computational statistics based on doing Pe computations.
RC.RCStats_Pe() - Constructor for class RC.RCStats_Pe
Create an RCStats object without doing any computations yet.
RC.RCStats_Pe(int, double, double) - Constructor for class RC.RCStats_Pe
Warning: If you don't know the value of one of the parameters, you must pass in NOT_COMPUTED_int or NOT_COMPUTED_dbl, otherwise the classes will not work.
RC.RecCondThreadListener - Interface in edu.ucla.belief.recursiveconditioning
 
RC2 - Class in edu.ucla.belief.rc2.structure
This class represents Dtrees and Dgraphs.
RC2(RC2.RCCreationParams) - Constructor for class RC2
An RC2 object should be created before any nodes are created, as it has to be passed into the node constructors.
RC2.CachingScheme - Interface in edu.ucla.belief.rc2.structure
 
RC2.ComputationStats - Class in edu.ucla.belief.rc2.structure
 
RC2.ComputationStats(String, double, int, double, double) - Constructor for class RC2.ComputationStats
 
RC2.RCCreationParams - Class in edu.ucla.belief.rc2.structure
 
RC2.RCCreationParams(BeliefNetwork) - Constructor for class RC2.RCCreationParams
 
RC2.StoredComputationStats - Class in edu.ucla.belief.rc2.structure
 
RC2.StoredComputationStats() - Constructor for class RC2.StoredComputationStats
 
RC2CachingScheme_Collection - Class in edu.ucla.belief.rc2.caching
This class generates caching schemes from Collections for RC2 Objects.
RC2CachingScheme_Collection(String, Collection) - Constructor for class RC2CachingScheme_Collection
This constructor saves the collection nodesToCache and uses it directly, it does not make a copy of it or ever modify it.
RC2CachingScheme_DFBnB - Class in edu.ucla.belief.rc2.caching
This class generates DFBnB caching schemes for RC2 Objects.
RC2CachingScheme_DFBnB(double, double) - Constructor for class RC2CachingScheme_DFBnB
 
RC2CachingScheme_Full - Class in edu.ucla.belief.rc2.caching
This class generates full caching schemes for RC2 Objects.
RC2CachingScheme_Full() - Constructor for class RC2CachingScheme_Full
 
RC2CachingScheme_Greedy - Class in edu.ucla.belief.rc2.caching
This class generates greedy caching schemes for RC2 Objects.
RC2CachingScheme_Greedy(double) - Constructor for class RC2CachingScheme_Greedy
 
RC2CachingScheme_Greedy(long) - Constructor for class RC2CachingScheme_Greedy
 
RC2CachingScheme_None - Class in edu.ucla.belief.rc2.caching
This class generates empty caching schemes for RC2 Objects.
RC2CachingScheme_None() - Constructor for class RC2CachingScheme_None
 
RC2CachingSchemeUtils - Class in edu.ucla.belief.rc2.caching
Utility functions for Caching Scheme objects.
RC2Creator - Class in edu.ucla.belief.rc2.creation
This class generates RC2 objects for a BeliefNetwork.
RC2Creator() - Constructor for class RC2Creator
 
RC2Creator.Params - Class in edu.ucla.belief.rc2.creation
 
RC2Creator.Params(BeliefNetwork) - Constructor for class RC2Creator.Params
 
RC2CreatorDtToDg - Class in edu.ucla.belief.rc2.creation
This class orients Dtrees into Dgraphs.
RC2CreatorDtToDg.ReducedRootSet - Class in edu.ucla.belief.rc2.creation
 
RC2CreatorDtToDg.ReducedRootSet(RC2Node[], HashMap) - Constructor for class RC2CreatorDtToDg.ReducedRootSet
 
RC2CreatorEO - Class in edu.ucla.belief.rc2.creation
This class generates RC2 objects for a BeliefNetwork from an elimination order.
RC2CreatorEO.Params - Class in edu.ucla.belief.rc2.creation
 
RC2CreatorEO.Params(BeliefNetwork, boolean, int, List, RC2.CachingScheme) - Constructor for class RC2CreatorEO.Params
 
RC2CreatorFile - Class in edu.ucla.belief.rc2.creation
This class generates RC2 objects for a BeliefNetwork from a file.
RC2CreatorFile.Params - Class in edu.ucla.belief.rc2.creation
 
RC2CreatorFile.Params(BeliefNetwork, String) - Constructor for class RC2CreatorFile.Params
 
RC2CreatorHM - Class in edu.ucla.belief.rc2.creation
This class generates RC2 objects for a BeliefNetwork.
RC2CreatorHM() - Constructor for class RC2CreatorHM
 
RC2Index - Class in edu.ucla.belief.rc2.structure
This class represent an Index for RC2.
RC2Index(RC2, Collection) - Constructor for class RC2Index
 
RC2Index(RC2, List, long[]) - Constructor for class RC2Index
 
RC2Node - Class in edu.ucla.belief.rc2.structure
This class represents RCNode objects.
RC2Node(int, RC2, int, Collection) - Constructor for class RC2Node
 
RC2NodeInternal - Class in edu.ucla.belief.rc2.structure
This class represents Internal RCNode objects.
RC2NodeInternal(int, RC2, RC2Node, RC2Node, Map) - Constructor for class RC2NodeInternal
 
RC2NodeLeaf - Class in edu.ucla.belief.rc2.structure
This class represents Leaf RCNode objects.
RC2NodeLeaf(int, RC2, FiniteVariable, Map) - Constructor for class RC2NodeLeaf
 
RC2NodeLeafEvidInd - Class in edu.ucla.belief.rc2.structure
This class represents Leaf RCNode objects which are evidence indicators..
RC2NodeLeafEvidInd(int, RC2, FiniteVariable) - Constructor for class RC2NodeLeafEvidInd
 
RC2Utils - Class in edu.ucla.belief.rc2.structure
This class contains utility functions for RC2 objects.
RC2Utils.MiscStats - Class in edu.ucla.belief.rc2.structure
 
RC2Utils.MiscStats() - Constructor for class RC2Utils.MiscStats
 
RC2WriteToFile - Class in edu.ucla.belief.rc2.io
This class writes RC2 objects to a file.
RC_Link - Class in edu.ucla.belief.rc2.tools
 
RC_Link(RC_Link.CmdLn) - Constructor for class RC_Link
 
RC_Link.RC_Results - Class in edu.ucla.belief.rc2.tools
 
RC_Link.RC_Results(double, RC2, double) - Constructor for class RC_Link.RC_Results
 
RC_Link2PeEngine - Class in edu.ucla.belief.uai2006
An interface for an algorithm that computes MAP for the 2006 UAI evaluation.
RC_Link2PeEngine() - Constructor for class RC_Link2PeEngine
 
RC_Link_UAI2006 - Class in edu.ucla.belief.rc2.tools
 
RC_Link_UAI2006() - Constructor for class RC_Link_UAI2006
 
rcCalls_all() - Method in class RC2.ComputationStats
 
rcCalls_pe() - Method in class RC2.ComputationStats
 
rcCallsCounter - Variable in class RC2
 
RCComparator - Class in edu.ucla.belief.recursiveconditioning
 
RCComparator(String, String) - Constructor for class RCComparator
 
rcComputationError(String) - Method in interface RC.RecCondThreadListener
 
rcConstructionDone() - Method in interface CachingScheme.RCCreateListener
 
rcCore() - Method in class RCEngine
 
rcCore() - Method in class RCEngine
 
rcCreateDone(double, boolean) - Method in interface CachingScheme.RCCreateListener
 
rcCreateDone(RC) - Method in interface CachingScheme.RCCreateListener
 
rcCreateError(String) - Method in interface CachingScheme.RCCreateListener
 
rcCreateStopRequested() - Method in interface CachingScheme.RCCreateListener
 
rcCreateUpdate(double) - Method in interface CachingScheme.RCCreateListener
 
rcCreateUpdateThreshold() - Method in interface CachingScheme.RCCreateListener
 
RCDgraph - Class in edu.ucla.belief.recursiveconditioning
This class represents "compiled" dgraph objects used in recursive conditioning (it is a set of dtree objects which can share structure).
RCDgraph(RC.RCCreationParams) - Constructor for class RCDgraph
Warning: Using this constructor will not create the complete structure.
RCDgraph(RC.RCCreationParams, CachingScheme, CachingScheme.RCCreateListener, DecompositionStructureUtils.ParamsGraph) - Constructor for class RCDgraph
Creates a new RCDgraph based on the parameters.
RCDtree - Class in edu.ucla.belief.recursiveconditioning
This class represents "compiled" dtree objects used in recursive conditioning.
RCDtree(RC.RCCreationParams) - Constructor for class RCDtree
Warning: Using this constructor will not create the complete structure.
RCDtree(RC.RCCreationParams, CachingScheme, CachingScheme.RCCreateListener, DecompositionStructureUtils.ParamsTree) - Constructor for class RCDtree
Creates a new RCDtree based on the parameters.
RCEngine - Class in edu.ucla.belief.inference
 
RCEngine(RCSettings, Dynamator) - Constructor for class RCEngine
 
rcEngine() - Method in class RCWrapper
 
RCEngine - Class in il2.inf.rc
 
RCEngine(DGraph, Table[], IntMap) - Constructor for class RCEngine
 
RCEngineGenerator - Class in edu.ucla.belief.inference
 
RCEngineGenerator() - Constructor for class RCEngineGenerator
 
RCEngineGenerator - Class in edu.ucla.belief.recursiveconditioning
 
RCEngineGenerator() - Constructor for class RCEngineGenerator
 
rcFinished(double, long) - Method in interface RC.RecCondThreadListener
 
rcFinishedMPE(double, Map, long) - Method in interface RC.RecCondThreadListener
 
rcFromJT2(BeliefNetwork, BeliefCompilation) - Method in class Settings
 
RCGenerator - Class in edu.ucla.belief
 
RCGenerator.EO - Class in edu.ucla.belief
 
RCGenerator.EO(int) - Constructor for class RCGenerator.EO
 
RCGenerator.RC - Class in edu.ucla.belief
 
RCGenerator.RC(int) - Constructor for class RCGenerator.RC
 
RCGenerator.Util - Class in edu.ucla.belief
 
RCInferenceEngine - Class in edu.ucla.belief.recursiveconditioning
 
RCInferenceEngine(RCDgraph, Dynamator, BeliefNetwork) - Constructor for class RCInferenceEngine
Constructs a new RCInferenceEngine that wraps a RCDgraph.
RCInfo - Class in edu.ucla.belief.inference
 
RCInfo(BeliefNetwork, boolean, EliminationHeuristic) - Constructor for class RCInfo
 
RCInstanceIterator - Class in edu.ucla.belief.recursiveconditioning
This class represents an Instance Iterator and will only work if RC does not use a KB.
RCInstanceIterator(RC, Collection) - Constructor for class RCInstanceIterator
 
RCInstanceIterator(RC, Collection, int[]) - Constructor for class RCInstanceIterator
Normally the constructor (RC, Collection) is used, but sometimes a non-standard instantiation array is desired.
RCInstanceIteratorKB - Class in edu.ucla.belief.recursiveconditioning
This class represents an Instance Iterator and will work with or without a KB.
RCInstanceIteratorKB(RC, Collection) - Constructor for class RCInstanceIteratorKB
 
RCIterator - Class in edu.ucla.belief.recursiveconditioning
This abstract class iterates through trees & graphs but does not guarantee any particular node ordering.
RCIterator() - Constructor for class RCIterator
 
RCIteratorArray - Class in edu.ucla.belief.recursiveconditioning
This class iterates through trees & graphs but does not guarantee any particular node ordering.
RCIteratorArray(RCNode) - Constructor for class RCIteratorArray
 
RCIteratorArray(RCNode[]) - Constructor for class RCIteratorArray
 
RCIteratorArray(Collection) - Constructor for class RCIteratorArray
 
RCIteratorArray(RCIterator) - Constructor for class RCIteratorArray
 
RCIteratorArray(RCNode[], Object) - Constructor for class RCIteratorArray
Will iterate using nodesToIterate (no copies are made).
RCIteratorTraversal - Class in edu.ucla.belief.recursiveconditioning
This class iterates/traverses through trees & graphs visiting each node once.
RCIteratorTraversal(RCNode) - Constructor for class RCIteratorTraversal
 
RCIteratorTraversal(RCNode[]) - Constructor for class RCIteratorTraversal
 
RCIteratorTraversal(Collection) - Constructor for class RCIteratorTraversal
 
rclink2Mode - Static variable in class UaiMain
 
rclinkMode - Static variable in class UaiMain
 
rcMode - Static variable in class UaiMain
 
RCNode - Class in edu.ucla.belief.recursiveconditioning
 
RCNode(RC) - Constructor for class RCNode
Warning: by using this constructor you must later call init.
RCNode(RC, long, long) - Constructor for class RCNode
 
RCNodeCache - Class in edu.ucla.belief.recursiveconditioning
This class represents Caches for RCNodes.
RCNodeCache(RCNode, ArrayList, double) - Constructor for class RCNodeCache
 
rcNodeComparator_Size - Static variable in class CachingDFBnB
 
rcNodeComparator_Size - Static variable in class CachingNonOptimalSize
 
RCNodeInternalBinaryCache - Class in edu.ucla.belief.recursiveconditioning
This class represents Internal RCNode objects which always have two children and a cache.
RCNodeInternalBinaryCache(RC, RCNode, RCNode) - Constructor for class RCNodeInternalBinaryCache
Warning: by using this constructor you must later call init.
RCNodeInternalBinaryCache(RC, Collection, Collection, RCNode, RCNode, double, Collection) - Constructor for class RCNodeInternalBinaryCache
Warning: by using this constructor you must later call initCacheOrder.
RCNodeInternalBinaryCache(RC, Collection, List, RCNode, RCNode, double, Collection, ArrayList) - Constructor for class RCNodeInternalBinaryCache
Creates a new RCNodeInternalCache.
RCNodeInternalBinaryCache.ChildIterator - Class in edu.ucla.belief.recursiveconditioning
 
RCNodeInternalBinaryCache.ChildIterator() - Constructor for class RCNodeInternalBinaryCache.ChildIterator
 
RCNodeLeaf - Class in edu.ucla.belief.recursiveconditioning
This class represents Leaf RCNode objects.
RCNodeLeaf(RC, FiniteVariable) - Constructor for class RCNodeLeaf
Warning: by using this constructor you must later call init.
RCNodeLeaf(RC, FiniteVariable, Collection) - Constructor for class RCNodeLeaf
Creates a new RCNodeLeaf.
rcScore() - Method in class EOGenerator.RC
 
rcScore() - Method in class RCGenerator.RC
 
RCSettings - Class in edu.ucla.belief.inference
 
RCSettings() - Constructor for class RCSettings
 
rcType - Variable in class FileInfo
 
RCUtilities - Class in edu.ucla.belief.recursiveconditioning
This class contains utility functions for RC objects.
RCUtilitiesIO - Class in edu.ucla.belief.recursiveconditioning
This class contains utility functions for input and output of RC objects.
RCWrapper - Class in edu.ucla.belief.inference
 
RCWrapper(RCInfo) - Constructor for class RCWrapper
 
RCWrapper(RCInfo, QuantitativeDependencyHandler) - Constructor for class RCWrapper
 
read(String) - Static method in class NetworkIO
 
read(File) - Static method in class NetworkIO
 
readChar() - Method in class SimpleCharStream
 
readData(File, BeliefNetwork) - Method in class LearningData
Reads data from a Hugin-style plain text "case" file.
readData(BufferedReader, BeliefNetwork) - Method in class LearningData
 
readData(File, BeliefNetwork) - Method in class LearningDataOld
Reads data from a Hugin-style plain text "case" file.
readDbl(StringBuffer) - Static method in class UtilGeneReader
 
readDblExpected(StringBuffer) - Static method in class UtilGeneReader
 
readDtree(BeliefNetwork, File, MethodHuginLog.Style) - Static method in class MethodHuginLog
 
readEvidenceCases(String, Domain) - Static method in class IO
 
readHeader(BufferedReader) - Static method in class Loci.Header
 
readHuginNet(File) - Static method in class NetworkIO
Reads a hugin description.
readHuginNet(Reader) - Static method in class NetworkIO
 
readHuginNet(InputStream) - Static method in class NetworkIO
Does not try to estimate the network size for the purposes of progress monitoring.
readHuginNet(File, NetworkIO.BeliefNetworkIOListener) - Static method in class NetworkIO
Skims the file once before actually parsing it in order to estimate network size for the purposes of progress monitoring.
readHuginNet(InputStream, String, NetworkIO.BeliefNetworkIOListener) - Static method in class NetworkIO
Skims the file once before actually parsing it in order to estimate network size for the purposes of progress monitoring.
readHuginNet(Reader, String, NetworkIO.BeliefNetworkIOListener) - Static method in class NetworkIO
 
readInt(StringBuffer) - Static method in class UtilGeneReader
 
readIntExpected(StringBuffer) - Static method in class UtilGeneReader
 
readLoci(String) - Static method in class Loci
 
readLoci(File) - Static method in class Loci
 
readLoci(BufferedReader) - Static method in class Loci
 
readLocus(BufferedReader, Loci.Header, int) - Static method in class Loci.Locus
 
readNetwork(String) - Static method in class IO
 
readRC(RC2.RCCreationParams, RC2CreatorFile.Params) - Static method in class RC2CreatorFile
 
readRC(RC2.RCCreationParams, RC2CreatorFile.Params, Collection) - Static method in class RC2CreatorFile
Reads in the RC, but sets up no Caching and fills cachedNodes (if null, it attempts to setup caching).
readRCFromFile(BufferedReader, BeliefNetwork, double) - Static method in class RCUtilitiesIO
 
readSMILE(File) - Static method in class NetworkIO
 
readSMILE(File, FileType) - Static method in class NetworkIO
 
readSMILE(File, NetworkIO.BeliefNetworkIOListener) - Static method in class NetworkIO
 
readSMILE(File, FileType, NetworkIO.BeliefNetworkIOListener) - Static method in class NetworkIO
 
readxml(File, BeliefNetwork, Settings, boolean) - Method in class Xmlizer
 
readxml(File) - Static method in class Xmlizer
 
readxmldtree(Element, BeliefNetwork) - Method in class Xmlizer
 
readxmlrcdgraph(Element, BeliefNetwork, Settings, boolean, File) - Method in class Xmlizer
 
readxmlrcdtree(BeliefNetwork, Settings, double, boolean, File) - Method in class Xmlizer
 
readxmlrcdtree(Element, BeliefNetwork, Settings, double, boolean, File) - Method in class Xmlizer
 
recallOptimizationEpsilon() - Method in class DecisionTreeImpl
 
recCond_All() - Method in class RC
Run Recursive conditioning P(e) for each root node (special for testing & output of timing/memory...).
recCond_All() - Method in class RCDgraph
 
recCond_All(boolean, boolean, boolean) - Method in class RCDgraph
Run Recursive conditioning P(e) for each root node.
recCond_All() - Method in class RCDtree
 
recCond_MPE(Map) - Method in class RC
Run Recursive conditioning MPE.
recCond_MPE3(double) - Method in class RC
Run Recursive conditioning MPE3.
recCond_MPE4(double) - Method in class RC
Run Recursive conditioning MPE4.
recCond_MPEAsThread(RC.RecCondThreadListener) - Method in class RC
Run rEccond_Mpe In A Separate Thread, And Call Finished.Rcfinishedmpe( Double, Map) When Done.
recCond_Pe() - Method in class RC
Run Recursive conditioning P(e).
recCond_Pe_Scaled() - Method in class RC
Run Recursive conditioning P(e).
recCond_Pe_ScaledAsThread(RC.RecCondThreadListener) - Method in class RC
Run recCond_Pe_Scaled in a separate thread, and call finished.rcFinished( double) when done.
recCond_PeAsThread(RC.RecCondThreadListener) - Method in class RC
Run recCond_Pe in a separate thread, and call finished.rcFinished( double) when done.
recCond_PreCompute() - Method in class RC
Run RC for each root node to "precompute" the marginals.
recCond_PreCompute() - Method in class RCDgraph
 
recCond_PreCompute() - Method in class RCDtree
 
recentEvidenceChangeVariables - Variable in class EvidenceChangeEvent
 
recombinationValues_female - Variable in class Loci.Footer
 
recombinationValues_male - Variable in class Loci.Footer
 
recomVaried - Variable in class Loci.Footer.Mlink
 
record(FiniteVariable, int) - Method in class CPTImport.CompleteParameterRecorder
 
record(FiniteVariable, int) - Method in class CPTImport.IncompleteParameterRecorder
 
record(FiniteVariable, int) - Method in interface CPTImport.ParameterRecorder
 
recover(BeliefNetwork) - Method in class Macros.Recoverable
 
recoverables - Variable in class Macros.Bridge
 
recoverables(Map<Object, Object>, Object) - Static method in class Macros
suppress unchecked caste warning
recovered - Variable in class Macros.Bridge
 
recoverEdge(BeliefNetwork, FiniteVariable, FiniteVariable, Collection<FiniteVariable>) - Static method in class Macros
 
RecoveryEngineGenerator - Class in edu.ucla.belief.approx
 
RecoveryEngineGenerator() - Constructor for class RecoveryEngineGenerator
 
RecoveryInferenceEngine - Class in edu.ucla.belief.approx
 
RecoveryInferenceEngine(BeliefNetwork, Converter, Setting.Settings<RecoverySetting>, Map<CrouchingTiger.DynamatorImpl, Dynamator>, Dynamator) - Constructor for class RecoveryInferenceEngine
 
RecoverySetting - Enum in edu.ucla.belief.approx
 
recursiveCalls() - Method in class RCInfo
 
recursiveCalls() - Method in class CachingScheme
 
recursiveCallsFullCaching() - Method in class RCInfo
 
recursiveCallsFullCaching() - Method in class CachingScheme
 
RecursiveDepthFirstIterator - Class in edu.ucla.structure
 
RecursiveDepthFirstIterator(DirectedGraph) - Constructor for class RecursiveDepthFirstIterator
 
RecursiveDepthFirstIterator(DirectedGraph, Collection) - Constructor for class RecursiveDepthFirstIterator
 
recursiveEliminationTree(TableIndex[], List) - Static method in class Trees
 
RecursiveEliminationTreeGenerator - Class in edu.ucla.belief.tree
 
RecursiveEliminationTreeGenerator(TableIndex[], List) - Constructor for class RecursiveEliminationTreeGenerator
Creates new RecursiveEliminationTreeGenerator
recXmlize(RCNode, String, Document, Element, Map) - Method in class Xmlizer
 
recXmlize(RCNode, Document, Element, Map) - Method in class Xmlizer
 
reduceToOnlyMarginals(RC2Node[], Collection, BeliefNetwork) - Static method in class RC2CreatorDtToDg
If the roots is not from a complete dgraph, it is possible for the preprocessing to produce incorrect results.
reduceToOnlyMarginals(Collection) - Method in class RCDgraph
Reduce this graph to one which (possibly) has fewer roots, but can only compute variable marginals instead of being able to compute family marginals.
redundant - Variable in class CPTInfo.Parameter
 
Reference - Class in edu.ucla.util
A simple class to ease call by reference type implementations.
Reference() - Constructor for class Reference
Creates new Reference
Reference(Object) - Constructor for class Reference
 
reflect(Class, String, String, Class[], Object, Object[], Object) - Static method in class AbstractStringifier
 
reflectY(HuginNode) - Static method in class HuginCopier
 
refresh() - Method in class Bundle
 
refresh() - Method in class Computation
 
refresh(RC) - Method in class Settings
 
REGEX_COMMENT - Static variable in class XmlbifParser
 
REGEX_DATA_DELIMITER - Static variable in class XmlbifParser
 
REGEX_JAVA_SOURCE_PATH - Static variable in class JDKRun
 
REGEX_POSITION - Static variable in class XmlbifParser
 
regexOrEnd(String) - Static method in class ParanoidFileFinder
 
register(BeliefNetwork, Map<Object, Object>, Macros.Recoverables) - Static method in class Macros
 
ReInit(InputStream) - Method in class HuginLogReader
 
ReInit(Reader) - Method in class HuginLogReader
 
ReInit(HuginLogReaderTokenManager) - Method in class HuginLogReader
 
ReInit(SimpleCharStream) - Method in class HuginLogReaderTokenManager
 
ReInit(SimpleCharStream, int) - Method in class HuginLogReaderTokenManager
 
ReInit(InputStream) - Method in class HuginReader
 
ReInit(InputStream, String) - Method in class HuginReader
 
ReInit(Reader) - Method in class HuginReader
 
ReInit(HuginReaderTokenManager) - Method in class HuginReader
 
ReInit(SimpleCharStream) - Method in class HuginReaderTokenManager
 
ReInit(SimpleCharStream, int) - Method in class HuginReaderTokenManager
 
ReInit(InputStream) - Method in class NeticaReader
 
ReInit(Reader) - Method in class NeticaReader
 
ReInit(NeticaReaderTokenManager) - Method in class NeticaReader
 
ReInit(SimpleCharStream) - Method in class NeticaReaderTokenManager
 
ReInit(SimpleCharStream, int) - Method in class NeticaReaderTokenManager
 
ReInit(Reader, int, int, int) - Method in class SimpleCharStream
 
ReInit(Reader, int, int) - Method in class SimpleCharStream
 
ReInit(Reader) - Method in class SimpleCharStream
 
ReInit(InputStream, String, int, int, int) - Method in class SimpleCharStream
 
ReInit(InputStream, int, int, int) - Method in class SimpleCharStream
 
ReInit(InputStream, String) - Method in class SimpleCharStream
 
ReInit(InputStream) - Method in class SimpleCharStream
 
ReInit(InputStream, String, int, int) - Method in class SimpleCharStream
 
ReInit(InputStream, int, int) - Method in class SimpleCharStream
 
relabelNodes(Map) - Method in class JoinTree
 
relaxed - Variable in class HuginPotential
 
releaseKB() - Method in class KB_SAT
 
remove(Macros.Recoverable...) - Method in class Macros.RecoveryInfo
 
remove(Object) - Method in class BeliefNetworkImpl
 
remove(int) - Method in interface FiniteVariable
 
remove(int) - Method in class FiniteVariableImpl
 
remove(Object) - Method in class LearningData
 
remove() - Method in class RCIterator
 
remove(Object) - Method in class AbstractDirectedGraph
 
remove() - Method in class DepthFirstIterator
 
remove(Object) - Method in interface Graph
Removes vertex from the graph(Optional operation).
remove(Object) - Method in class HashGraph
Removes vertex from the graph(Optional operation).
remove(Object) - Method in class IdentityArrayMap
 
remove(int) - Method in class MappedList
 
remove(Object) - Method in class MappedList
Not supported.
remove() - Method in class RecursiveDepthFirstIterator
 
remove(Object) - Method in class WeakLinkedList
Removes the first occurrence of the specified element in this list.
remove(int) - Method in class WeakLinkedList
Removes the element at the specified position in this list.
remove() - Method in class IntPriorityQueue
Removes and returns the highest priority element.
remove(int) - Method in class DoubleList
 
remove(int) - Method in class DoubleMap
 
remove(int) - Method in class Graph
 
remove(int) - Method in class IntList
 
remove(int) - Method in class IntMap
 
remove(int) - Method in class IntSet
 
removeAll(Collection) - Method in class BeliefNetworkImpl
 
removeAll(Collection) - Method in class AbstractDirectedGraph
 
removeAll(Collection) - Method in class HashGraph
 
removeAll(Collection) - Method in class MappedList
Not supported.
removeAndConnect(Graph, Object) - Static method in class Graphs
Removes node n and connects all of its neighbors.
removeAndConnect(int) - Method in class Graph
 
removeAuditor(BeliefNetwork.Auditor) - Method in interface BeliefNetwork
 
removeAuditor(BeliefNetwork.Auditor) - Method in class BeliefNetworkImpl
 
removeBest() - Method in class ConnectivityOrderer
 
removeBest() - Method in interface Orderer
 
removeBest() - Method in class IndexedHeap
 
removeBest() - Method in class MappedHeap
 
removeBestGroup() - Method in class DynamicEliminator
 
removeChangeListener(ChangeListener) - Method in class BeliefPropagationSettings
interface ChangeBroadcaster
removeChangeListener(ChangeListener) - Method in class JoinTreeSettings
interface ChangeBroadcaster
removeChangeListener(ChangeListener) - Method in class RCSettings
interface ChangeBroadcaster
removeChangeListener(ChangeListener) - Method in class Settings
interface ChangeBroadcaster
removeChangeListener(ChangeListener) - Method in interface ChangeBroadcaster
 
removeChangeListener(ChangeListener) - Method in class AbstractCodeGenius
interface ChangeBroadcaster
removeChangeListener(ChangeListener) - Method in class SettingsImpl
interface ChangeBroadcaster
removeChild(DecisionNode) - Method in class DecisionInternal
 
removeChild(DecisionNode) - Method in interface DecisionNode
 
removeChild(DecisionNode) - Method in class DecisionNodeAbstract
 
removeDataPoint(double) - Method in class DataSetStatistic
 
removedLabel() - Method in class DynamicEliminator
 
removeEdge(Variable, Variable, boolean) - Method in interface BeliefNetwork
Removes an edge from the network.
removeEdge(Object, Object) - Method in class BeliefNetworkImpl
 
removeEdge(Variable, Variable) - Method in class BeliefNetworkImpl
Removes an edge from the network.
removeEdge(Variable, Variable, boolean) - Method in class BeliefNetworkImpl
 
removeEdge(Object, Object) - Method in class AbstractDirectedGraph
 
removeEdge(Object, Object) - Method in interface DirectedGraph
Removes the directed edge from the graph(Optional operation).
removeEdge(Object, Object) - Method in interface Graph
Removes edge from the graph(Optional operation).
removeEdge(Object, Object) - Method in class HashDirectedGraph
Removes the directed edge from the graph(Optional operation).
removeEdge(Object, Object) - Method in class HashGraph
Removes edge from the graph(Optional operation).
removeEdge(int, int) - Method in class Graph
 
removeEdgeNoCPTChanges(Variable, Variable) - Method in class BeliefNetworkImpl
Removes an edge from the network.
removeEntryAt(int) - Method in class IntSet
 
removeEvidence(FiniteVariable) - Method in class JointWrapper
 
removeEvidenceChangeListener(EvidenceChangeListener) - Method in class EvidenceController
 
removeFirst() - Method in class WeakLinkedList
Removes and returns the first element from this list.
removeHistory(DecisionLeaf) - Method in class DecisionTreeImpl
interface Factory
removeHistory(DecisionLeaf) - Method in interface Factory
 
removeHistoryAllDescendants(DecisionNode) - Method in class DecisionTreeImpl
 
removeIncomplete() - Method in class LearningDataOld
Removes all records that do not contain a complete instantiation of the variables.
removeIncomplete(Set) - Method in class LearningDataOld
Removes all records that do not contain a complete instantiation of the subset "vars".
removeItemsContaining(int) - Method in class Binner
 
removeIterationListener(EvidenceChangeListener) - Method in class EdgeDeletionInferenceEngine
 
removeLargeCaches(RC2, Collection) - Static method in class RC2CachingSchemeUtils
Remove nodes which have caches which are too large for a cache to be created.
removeLast() - Method in class WeakLinkedList
Removes and returns the last element from this list.
removeLast() - Method in class IntList
 
removeListener(DecisionListener) - Method in interface DecisionNode
 
removeListener(DecisionListener) - Method in class DecisionNodeAbstract
 
removeListener(DecisionListener) - Method in interface DecisionTree
 
removeListener(DecisionListener) - Method in class DecisionTreeImpl
interface DecisionTree
removeNewDtreeListener(ChangeListener) - Method in class Settings
 
removeNoVarGroup() - Method in class DynamicEliminator
 
removeNoVarItems() - Method in class Binner
 
removePriorityEvidenceChangeListener(EvidenceChangeListener) - Method in class EvidenceController
 
removeState(FiniteVariable, int) - Method in interface BeliefNetwork
 
removeState(FiniteVariable, int) - Method in class BeliefNetworkImpl
 
removeState(int) - Method in interface CPTShell
 
removeState(int) - Method in class DecisionShell
 
removeState(int) - Method in class NoisyOrShellHenrion
 
removeState(int) - Method in class NoisyOrShellPearl
 
removeState(int) - Method in class Table
 
removeState(int) - Method in class TableShell
 
removeVariable(Variable) - Method in interface BeliefNetwork
Removes a variable from the network.
removeVariable(Variable) - Method in class BeliefNetworkImpl
Removes a variable from the network.
removeVariable(Variable) - Method in class EvidenceController
 
removeVariable(Variable) - Method in class GenieNetImpl
 
removeVertex(Object) - Method in class BeliefNetworkImpl
 
removeVertex(Object) - Method in class AbstractDirectedGraph
 
removeVertex(Object) - Method in interface DirectedGraph
Removes vertex from the graph(Optional operation).
removeVertex(Object) - Method in class HashDirectedGraph
Removes vertex from the graph(Optional operation).
removeWorthlessCaches(RC2, Collection) - Static method in class RC2CachingSchemeUtils
Will traverse all nodes in rc and attempt to remove any worthless caches from cachedNodes (will recognize when a state space is too large and won't be cached and will adjust usefulness based on them).
RENAME - Static variable in class DecisionEvent
 
renameInstantiation(Map, Map) - Static method in class Prune
Renames the variables in the given instantiation.
renamePathForEmOutput(String) - Static method in class Learning
 
RepetitionThread - Class in edu.ucla.util
 
RepetitionThread(Runnable, long, int) - Constructor for class RepetitionThread
 
RepetitionThread(Runnable, Runnable, long, int) - Constructor for class RepetitionThread
 
replaceAllPotentials(Map) - Method in interface BeliefNetwork
 
replaceAllPotentials(Map) - Method in class BeliefNetworkImpl
 
replacedEdges(BeliefNetwork) - Method in class Macros.Recoverables
 
replaceEdge(BeliefNetwork, FiniteVariable, FiniteVariable, Collection<FiniteVariable>) - Static method in class Macros
 
replaceVariables(Map, NodeLinearTask) - Method in interface BeliefNetwork
 
replaceVariables(Map) - Method in class BeliefNetworkImpl
 
replaceVariables(Map, NodeLinearTask) - Method in class BeliefNetworkImpl
 
replaceVariables(Map, boolean) - Method in interface CPTShell
 
replaceVariables(Map, boolean) - Method in class DecisionShell
 
replaceVariables(Map) - Method in class EvidenceController
 
replaceVariables(Map, NodeLinearTask) - Method in class GenieNetImpl
 
replaceVariables(Map, boolean) - Method in class NoisyOrShellHenrion
 
replaceVariables(Map, boolean) - Method in class NoisyOrShellPearl
 
replaceVariables(Map) - Method in class Table
 
replaceVariables(Map, boolean) - Method in class Table
 
replaceVariables(Map, boolean) - Method in class TableShell
 
replaceVertex(Object, Object) - Method in class BeliefNetworkImpl
 
replaceVertex(Object, Object) - Method in class AbstractDirectedGraph
 
replaceVertex(Object, Object) - Method in interface DirectedGraph
 
replaceVertex(Object, Object) - Method in class HashDirectedGraph
 
replaceVertices(Map, NodeLinearTask) - Method in class BeliefNetworkImpl
 
replaceVertices(Map, NodeLinearTask) - Method in class AbstractDirectedGraph
 
replaceVertices(Map, NodeLinearTask) - Method in interface DirectedGraph
 
replaceVertices(Map, NodeLinearTask) - Method in class HashDirectedGraph
 
report(LinkedList<Throwable>, String) - Static method in class Macros
 
report(PrintStream) - Method in class CPTShells
 
report(Appendable) - Method in class DataSetStatistic
 
report(Appendable, NumberFormat) - Method in class DataSetStatistic
 
reset() - Method in class ApproxEngine
 
reset() - Method in class Stats
 
reset() - Method in class Stats.Stat
 
reset(String, Attributes) - Method in class XmlElementHandler
 
reset() - Method in class RC.RCStats
 
resetEquations() - Method in class SensitivityEngine
 
resetEvidence() - Method in class EvidenceController
Restores the evidence to the state of no observations.
resetEvidence() - Method in class RC
Returns the evidence to the state of no observations.
resetLocal() - Method in class RCNode
 
resetLocal() - Method in class RCNodeInternalBinaryCache
 
resetOptions() - Method in class AbstractCodeGenius
 
resetOptions() - Method in interface CodeGenius
 
resetParamsAndLeaks() - Method in class NoisyOrShellHenrion
 
resetParamsAndLeaks() - Method in class NoisyOrShellPearl
 
resetRC() - Method in class RC
 
resetSpecifiedDimension() - Method in interface HuginNode
 
resetSpecifiedDimension() - Method in class HuginNodeImpl
 
resetStatistics() - Method in class RC
 
resetTables() - Method in class EDNetwork
 
resetTiming() - Method in class DtreeCreateHMetis
 
resetTiming() - Method in class DgraphCreateHMetis
 
resetXmlElementHandler(String, Attributes) - Method in class XmlDocumentHandler
 
residual() - Method in class BeliefPropagation
 
restart() - Method in class RCIterator
 
restart() - Method in class RCIteratorArray
 
restart() - Method in class RCIteratorTraversal
 
restart() - Method in class RCNodeInternalBinaryCache.ChildIterator
 
restoreEdges(ApproxReport) - Method in class ApproxEngine
 
restoreSnapshot() - Method in interface DecisionTree
 
restoreSnapshot() - Method in class DecisionTreeImpl
interface DecisionTree
result() - Method in class Builder
 
result - Variable in class MapInitializer.MapResult
 
result - Variable in class MapSearch.MapResult
 
results - Variable in class MapSearch.MapInfo
 
resumeKB() - Method in class RC
Warning: This function should not really be public and should not be called from outside of the package unless you are sure it will not lead to computation errors!
resumeRecCondAsThread() - Method in class RC
 
reSynchEvidWithBN(boolean) - Method in class RC
Should not normally be called from outside the package, usually it should be handled by the inference engine.
retainAll(Collection) - Method in class BeliefNetworkImpl
 
retainAll(Collection) - Method in class AbstractDirectedGraph
 
retainAll(Collection) - Method in class HashGraph
 
retainAll(Collection) - Method in class MappedList
Not supported.
RETRACT - Static variable in class BeliefNetwork.Auditor.Deed
 
retract(int) - Method in class KnowledgeBase
 
retract(int) - Method in interface KnowledgeBase
The parameter state should be the returned value from either an assertPositive call or from a currentState call.
retract(int) - Method in class KnowledgeBaseImpl
 
retrieveState(PropertySuperintendent) - Method in class ApproxEngineGenerator
 
retrieveState(PropertySuperintendent) - Method in class PropagationEngineGenerator
 
retrieveState(PropertySuperintendent) - Method in class Dynamator
 
retrieveState(PropertySuperintendent) - Method in class DefaultGenerator
 
retrieveState(PropertySuperintendent) - Method in class RandomEngineGenerator
 
retrieveState(PropertySuperintendent) - Method in class RCEngineGenerator
 
retrieveState(PropertySuperintendent) - Method in class RCEngineGenerator
 
RETURN_TYPE() - Static method in enum Flavor
return type of factory methods
reversed(int[]) - Static method in class ArrayUtils
Returns an array that contains the same values as the given array but reversed.
reverseLocusOrdering() - Method in class Pedigree.GeneticNetwork
 
right() - Method in class DtreeNodeInternal
 
right - Variable in class RC2NodeInternal
 
right() - Method in class RCNodeInternalBinaryCache
 
riskLoci - Variable in class Loci.Header
 
root() - Method in class Dtree
 
root(int) - Method in class RC
 
ROOT - Static variable in class InOutDegreeProperty
 
root() - Method in class DGraph
 
roots - Variable in class RC2CreatorDtToDg.ReducedRootSet
 
roots() - Method in class Graph
 
rotate(EnumProperty, EnumValue) - Static method in class AbstractEnumProperty
 
run(EdgeDeletionInferenceEngine, ThreadGroup, Thread.UncaughtExceptionHandler, boolean) - Method in enum EdgeDeletionInferenceEngine.Command
 
run() - Method in class Dynamator.RunCompile
 
run() - Method in class RunReadNetwork
 
run() - Method in class RunWriteBIF
 
run() - Method in class EMThread
 
run() - Method in class ScriptExecution.Pipe
 
run() - Method in class ScriptExecution.ProcessSitter
 
run() - Method in class Interruptable
Run the task in the current Thread, ie bypass the normal functioning of this class.
run(Object) - Method in class Interruptable
Run the task in the current Thread, ie bypass the normal functioning of this class.
run(boolean) - Method in class Interruptable
Run threaded or not.
run(boolean, Object) - Method in class Interruptable
Run threaded or not.
run() - Method in class RepetitionThread
 
runImpl(Object) - Method in class Interruptable
Implement this method to perform a expensive task.
RunReadBIF - Class in edu.ucla.belief.io.xmlbif
Support for reading the XML BIF format.
RunReadBIF(File, NetworkIO.BeliefNetworkIOListener) - Constructor for class RunReadBIF
 
RunReadBIF.MonitorableReusableParser - Interface in edu.ucla.belief.io.xmlbif
 
RunReadHugin - Class in edu.ucla.belief.io.hugin
 
RunReadHugin(File, NetworkIO.BeliefNetworkIOListener, boolean) - Constructor for class RunReadHugin
 
RunReadHugin(InputStream, String, NetworkIO.BeliefNetworkIOListener, boolean) - Constructor for class RunReadHugin
 
RunReadHugin(Reader, String, NetworkIO.BeliefNetworkIOListener) - Constructor for class RunReadHugin
 
RunReadNetwork - Class in edu.ucla.belief.io
 
RunReadNetwork(String, NetworkIO.BeliefNetworkIOListener) - Constructor for class RunReadNetwork
 
RunReadSMILE - Class in edu.ucla.belief.io.dsl
 
RunReadSMILE(File, FileType, NetworkIO.BeliefNetworkIOListener) - Constructor for class RunReadSMILE
 
runSynchronous(BeliefNetwork, DynaListener) - Method in class Dynamator
 
runtimeSupports(String) - Static method in class BourneScriptGenius
 
RunWriteBIF - Class in edu.ucla.belief.io.xmlbif
Support for writing the XML BIF format.
RunWriteBIF(File, BeliefNetwork) - Constructor for class RunWriteBIF
 
RunWriteBIF.BeliefNetworkWriter - Interface in edu.ucla.belief.io.xmlbif
 

S

s1 - Variable in class Pair
The first int.
s1 - Variable in class UPair
The smaller int.
s2 - Variable in class Pair
The second int.
s2 - Variable in class UPair
The larger int.
S4Compiler - Class in edu.ucla.belief.inference
 
S4Compiler() - Constructor for class S4Compiler
 
S4DoubleExpression - Class in edu.ucla.belief.inference
 
S4DoubleExpression.CircuitWriter - Class in edu.ucla.belief.inference
 
S4DoubleExpression.CircuitWriter() - Constructor for class S4DoubleExpression.CircuitWriter
 
safe(EdgeDeletionInferenceEngine, Thread.UncaughtExceptionHandler) - Method in enum EdgeDeletionInferenceEngine.Command
 
safeKL(double) - Method in class ApproxEngine
 
safeOrder(int[], int[][], int[][], double) - Method in class EliminationOrderEngine
 
safePrefix(Collection) - Static method in class EliminationOrders
 
safeProb(double) - Method in class ApproxEngine
 
sanityCheck() - Method in class JoinTree
 
sanityCheck() - Method in class MapTree
 
sanityCheck() - Method in class BayesianNetwork
 
sanityCheck() - Method in class Graph
 
sanityCheck() - Method in class Heap
 
sanityCheck() - Method in class IntSet
 
satisfied(InferenceEngine) - Method in class SensitivityConstraint
 
satisfiesCPTProperty(Table, FiniteVariable, double) - Static method in class BeliefNetworks
 
satisfiesCPTProperty(FiniteVariable, double) - Method in class Table
 
save(File, BeliefNetwork) - Method in class FileType
 
save(Map, File) - Method in class InstantiationXmlizer
 
save(Map, Map, File) - Method in class InstantiationXmlizer
 
save(Map, Map, Map, File) - Method in class InstantiationXmlizer
 
saveFileAs(BeliefNetwork, File) - Static method in class NetworkIO
 
saveFileAs(BeliefNetwork, File, File) - Static method in class NetworkIO
 
saveToSMILEType(GenieNet, File, File, FileType) - Static method in class NetworkIO
 
scalar() - Method in interface CPTShell
 
scalar() - Method in class DecisionShell
 
scalar - Variable in class Pedigree.GeneticNetwork
 
scalar() - Method in class NoisyOrShellHenrion
 
scalar() - Method in class NoisyOrShellPearl
 
scalar - Variable in class RC2.RCCreationParams
 
scalar - Variable in class RC2
 
scalar - Variable in class RC.RCCreationParams
 
scalar - Variable in class RC
 
scalar() - Method in class Table
 
scalar() - Method in class TableScaled
 
scalar() - Method in class TableShell
 
scalarMultiply(SensitivityEquation, double) - Static method in class SensitivityEquation
 
scale(int) - Static method in class GraphvizIO
 
scale(double) - Method in class Table
 
scanColumnNames(File) - Method in class CPTImport
 
scanRows() - Method in class CPTImport
 
score(Object, Graph) - Method in interface EliminationOrders.ScoreFunction
 
score - Variable in class MapRunner.MapResult
 
score() - Method in class Heap.HeapElement
returns the priority associated with the element.
score - Variable in class MapInitializer.MapResult
 
score - Variable in class MapSearch.MapResult
 
Script - Interface in edu.ucla.util.code
 
ScriptExecution - Class in edu.ucla.util.code
 
ScriptExecution(Process, Script, String, String, String[], File, ScriptGenius, SystemSoftwareSource) - Constructor for class ScriptExecution
 
ScriptExecution.Pipe - Class in edu.ucla.util.code
 
ScriptExecution.Pipe(InputStream, PrintWriter) - Constructor for class ScriptExecution.Pipe
 
ScriptExecution.ProcessCustodian - Interface in edu.ucla.util.code
 
ScriptExecution.ProcessSitter - Class in edu.ucla.util.code
 
ScriptExecution.ProcessSitter(ScriptExecution, ScriptExecution.ProcessCustodian, long) - Constructor for class ScriptExecution.ProcessSitter
 
ScriptGenius - Interface in edu.ucla.util.code
 
ScriptTest - Class in edu.ucla.util.code
Tests each of the ScriptGenius sub classes by writing scripts.
ScriptTest(String[]) - Constructor for class ScriptTest
 
searchDurationMillisElapsed - Variable in class MapRunner.MapResult
 
searchDurationMillisElapsed - Variable in class MapSearch.MapInfo
 
searchDurationMillisProfiled - Variable in class MapRunner.MapResult
 
searchDurationMillisProfiled - Variable in class MapSearch.MapInfo
 
searchJavaExecutable(String) - Method in class ParanoidFileFinder
 
searchJavaExecutable(String, File) - Method in class ParanoidFileFinder
 
SearchMethod - Class in edu.ucla.belief.inference.map
 
SearchMethod() - Constructor for class SearchMethod
 
seededClone(Map) - Method in interface BeliefNetwork
 
seededClone(Map) - Method in class BeliefNetworkImpl
Call this method to clone a BeliefNetworkImpl when for whatever reason you have already cloned all the Variables it contains, and you have a mapping from the Variables it contains to Variables that you would like the cloned BeliefNetworkImpl to contain.
seededClone(Map) - Method in class GenieNetImpl
GenieNet's primary responsibility as of 061002 is to keep track of which variables belong to which submodels.
seededClone(Map) - Method in class HuginNetImpl
 
seenDefaultEvidence(PropertySuperintendent, BeliefNetwork) - Static method in class StandardNodeImpl
 
segment - Variable in class Optimizer.EquivalenceKey
 
select(int[], int[]) - Static method in class ArrayUtils
Returns an array that contains selected values from the given array.
select(double[], int[]) - Static method in class ArrayUtils
Returns an array that contains selected values from the given array.
select(long[], int[]) - Static method in class ArrayUtils
 
select(int[]) - Method in class DoubleList
 
select(int[]) - Method in class IntList
 
selectBestDtree(Dtree, Dtree) - Static method in class Dtree
Will determine which dtree is better and return it.
selectBetterDtree(Dtree, Dtree, Stats) - Method in class Settings
 
selectBetterRCInfo(RCInfo, RCInfo) - Static method in class RCSettings
 
selectOut(Index, double[], int, int, double[]) - Static method in class Table
 
selectRandomly(double) - Method in class IntSet
 
selectStringifier() - Method in interface Stringifier.Selector
 
selectWithOffset(double[], int[], int, double[]) - Static method in class ArrayUtils
Fills an array with selected values from the given array.
selectWithOffset(double[], int[], int) - Static method in class ArrayUtils
Returns an array that contains selected values from the given array.
SensitivityCoder - Class in edu.ucla.util.code
 
SensitivityCoder() - Constructor for class SensitivityCoder
 
SensitivityConstraint - Class in edu.ucla.belief.sensitivity
 
SensitivityConstraint(FiniteVariable, Object, FiniteVariable, Object, Object, Object, double) - Constructor for class SensitivityConstraint
 
SensitivityConstraint(FiniteVariable, Object, FiniteVariable, Object, Object, Object, double, boolean, boolean) - Constructor for class SensitivityConstraint
 
SensitivityEngine - Class in edu.ucla.belief.sensitivity
 
SensitivityEngine(BeliefNetwork, InferenceEngine, PartialDerivativeEngine) - Constructor for class SensitivityEngine
 
SensitivityEngine(BeliefNetwork, InferenceEngine, PartialDerivativeEngine, PrintWriter) - Constructor for class SensitivityEngine
 
SensitivityEquation - Class in edu.ucla.belief.sensitivity
 
SensitivityEquation(PartialDerivativeEngine, double, Map, Map) - Constructor for class SensitivityEquation
 
SensitivityEquation(List, InferenceEngine, PartialDerivativeEngine) - Constructor for class SensitivityEquation
 
SensitivityReport - Class in edu.ucla.belief.sensitivity
 
SensitivityReport(Map, Map) - Constructor for class SensitivityReport
 
SensitivitySuggestion - Interface in edu.ucla.belief.sensitivity
 
SensitivitySuggestionComparator - Class in edu.ucla.belief.sensitivity
 
SensitivitySuggestionComparator(int) - Constructor for class SensitivitySuggestionComparator
 
SensitivityTable - Class in edu.ucla.belief.sensitivity
 
SensitivityTable(CPTShell, Interval[], boolean[]) - Constructor for class SensitivityTable
 
SensMPEEngine - Class in edu.ucla.belief.sensitivity
 
SensMPEEngine(BeliefNetwork, EliminationHeuristic) - Constructor for class SensMPEEngine
 
SensMPEReport - Class in edu.ucla.belief.sensitivity
 
SensMPEReport(Map[], Map) - Constructor for class SensMPEReport
 
SEP - Static variable in class JDKRun
 
separator(int, int) - Method in class JoinTree
 
separator(int, int) - Method in class JoinTree
 
separator(UPair) - Method in class JoinTree
 
separatorIndex(Index) - Method in class Index
 
separators() - Method in class JoinTree
 
separatorStats - Variable in class EliminationOrders.JT
 
SEQ - Static variable in class InitializationMethod
 
sequence(int) - Static method in class ArrayUtils
Returns an array of ints [0, 1, 2, ..., L - 1], where L is the given length.
SequentialSchedule - Class in il2.inf.bp.schedules
 
SequentialSchedule(Table[]) - Constructor for class SequentialSchedule
 
SequentialSchedule(Table[], Pair[]) - Constructor for class SequentialSchedule
 
serialVersionUID - Static variable in class EdgeDeletionEngineGenerator
 
serialVersionUID - Static variable in class RecoveryEngineGenerator
 
set(int, Object) - Method in interface FiniteVariable
 
set(int, Object) - Method in class FiniteVariableImpl
 
set(Table) - Method in class Table
Copies the values from another compatible array.
set(Table) - Method in class TableScaled
Copies the values from another compatible array.
set(int, Object) - Method in class MappedList
Replaces the element at the specified position in this list with the specified element.
set(double, int, boolean) - Method in class EMCoder
 
set(int, Object) - Method in class WeakLinkedList
Replaces the element at the specified position in this list with the specified element.
set(int, double) - Method in class DoubleList
 
set(int, int) - Method in class IntList
 
setAllValues(Collection, BeliefNetwork) - Static method in class CSITypeProperty
 
setAllValues(Collection, EvidenceController) - Static method in class EvidenceAssertedProperty
 
setAllValues(Collection, BeliefNetwork) - Static method in class InOutDegreeProperty
 
setApproximationParameters(SearchMethod, InitializationMethod, int) - Method in class MAPCoder
 
setAutoCPTInvalidation(boolean) - Method in interface BeliefNetwork
 
setAutoCPTInvalidation(boolean) - Method in class BeliefNetworkImpl
 
setBalanceFactor(Object) - Method in class Settings
 
setBeliefNetwork(BeliefNetwork) - Method in class EvidenceController
 
setBeliefNetwork(BeliefNetwork) - Method in interface EMThread.LearningListener
 
setBeliefNetwork(BeliefNetwork) - Method in class JoinTree
 
setBeliefNetwork(BeliefNetwork) - Method in class ProbabilityQueryCoder
 
setBeliefNetwork(BeliefNetwork) - Method in class SensitivityCoder
 
setBundle(Bundle) - Method in class Settings
 
setCacheFactor(double) - Method in class CachingFull
 
setCacheFactor(double) - Method in class CachingNone
 
setCacheFactor(double) - Method in class CachingScheme
Fraction of maximum possible cache to use.
setCachingScheme(RC2.CachingScheme) - Method in class RC2
This function will set the caching in the RC2 object based on the caching scheme passed in, and will compute the current memory usage and expected RC calls based on the changes.
setCachingScheme(CachingScheme) - Method in class Bundle
 
setCachingScheme(CachingScheme) - Method in class Settings
 
setCaseSensitive(boolean) - Method in class InflibFileFilter
 
setCharactersHandler(CharactersHandler) - Method in class AbstractSaxHandler
 
setClasspath(ClassModule, File) - Method in class GuessingSource
 
setCompose(Map, Map, Map) - Static method in class Maps
 
setCompose(Map, Map) - Static method in class Maps
 
setConstraint(FiniteVariable, Object, FiniteVariable, Object, Object, Object, double) - Method in class SensitivityCoder
 
setConstructionTask(NodeLinearTask) - Method in class HuginReader
 
setControlPanel(Component) - Method in class AbstractInferenceEngine
 
setControlPanel(Component) - Method in class SynchronizedInferenceEngine
 
setControlPanel(Component) - Method in interface InferenceEngine
 
setConvergenceThreshold(double) - Method in class BeliefPropagationSettings
 
setConvergenceThreshold(double) - Method in class PropagationInferenceEngineImpl
 
setConverter(Converter) - Method in class ModelCoder
 
setConvThreshold(double) - Method in class EDAlgorithm
 
setCP(int, double) - Method in interface CPTInfo.ReadableWritableTable
 
setCP(int, double) - Method in class Table
 
setCP(int, double) - Method in class TableScaled
 
setCPT(FiniteVariable) - Method in class EdgeDeletionInferenceEngine
 
setCPT(FiniteVariable) - Method in class PropagationInferenceEngineImpl
 
setCPT(FiniteVariable) - Method in class RecoveryInferenceEngine
 
setCPT(FiniteVariable) - Method in class JoinTreeInferenceEngineImpl
Sets the CPT associated with var to the values in vals.
setCPT(FiniteVariable, double[]) - Method in class JointWrapper
 
setCPT(FiniteVariable) - Method in class RandomInferenceEngine
 
setCPT(FiniteVariable) - Method in class SynchronizedInferenceEngine
 
setCPT(FiniteVariable) - Method in class WrapperInferenceEngine
Sets the CPT associated with var to the values in vals.
setCPT(FiniteVariable) - Method in interface InferenceEngine
Sets the CPT associated with var to the values in vals.
setCPT(FiniteVariable, boolean) - Method in class RC2
Call this function after updating the CPTShell object for a FiniteVariable, however, RC2 can only handle parameter changes, the variables and their indexing must remain the same.
setCPT(int) - Method in class RC2NodeLeaf
 
setCPT(int) - Method in class RC2NodeLeafEvidInd
 
setCPT(FiniteVariable) - Method in class RC
 
setCPT(FiniteVariable) - Method in class RCInferenceEngine
This function tells the dgraph to clear all caches above where var's leaf node is.
setCPTShell(CPTShell) - Method in interface FiniteVariable
Deprecated.  
setCPTShell(DSLNodeType, CPTShell) - Method in interface FiniteVariable
 
setCPTShell(CPTShell) - Method in class FiniteVariableImpl
Deprecated.  
setCPTShell(DSLNodeType, CPTShell) - Method in class FiniteVariableImpl
 
setCurrentRecord(int) - Method in class LearningData
 
setData(FiniteVariable, Object) - Method in class VariableInstance
 
setDebugID(String) - Method in class JoinTreeSettings
 
setDebugID(String) - Method in class RCSettings
 
setDebugID(String) - Method in class Settings
 
setDebugID(String) - Method in class UserEnumProperty
 
setDebugStream(PrintStream) - Method in class HuginLogReaderTokenManager
 
setDebugStream(PrintStream) - Method in class HuginReaderTokenManager
 
setDebugStream(PrintStream) - Method in class NeticaReaderTokenManager
 
setDefault(EnumValue) - Method in class UserEnumProperty
 
setDefaultEvidence(EvidenceController) - Static method in class StandardNodeImpl
 
setDefaultStateIndex(Integer) - Method in interface DSLNode
 
setDefaultStateIndex(Integer) - Method in class DSLNodeImpl
Convenience method.
setDepth(int) - Method in class ParanoidFileFinder
 
setDiagnosisType(DiagnosisType) - Method in interface StandardNode
originally in DSLNode
setDiagnosisType(DiagnosisType) - Method in class StandardNodeImpl
 
setDimension(Dimension) - Method in interface StandardNode
 
setDimension(Dimension) - Method in class StandardNodeImpl
 
setDSLNodeType(DSLNodeType) - Method in interface FiniteVariable
moved from DSLNode 010905
setDSLNodeType(DSLNodeType) - Method in class FiniteVariableImpl
 
setDSLNodeType(DSLNodeType) - Method in class DSLNodeImpl
Convenience method.
setDSLSubmodel(DSLSubmodel) - Method in interface DSLNode
 
setDSLSubmodel(DSLSubmodel) - Method in class DSLNodeImpl
 
setDtree(Dtree) - Method in class Bundle
 
setDtree(Dtree) - Method in class Settings
 
setDtreeMethod(CreationMethod) - Method in class Settings
 
setDtreeRequired(boolean) - Method in class Settings
 
setDtreeStyle(MethodHuginLog.Style) - Method in class Settings
 
setDynamator(Dynamator) - Method in class AbstractInferenceEngine
 
setDynamator(Dynamator) - Method in class SynchronizedInferenceEngine
 
setDynamator(Dynamator) - Method in interface InferenceEngine
 
setDynamator(Dynamator) - Method in class EMCoder
 
setDynamator(Dynamator) - Method in class ProbabilityQueryCoder
 
setDynamator(Dynamator) - Method in class SensitivityCoder
 
setEdgeWeight(Object, Integer) - Method in class Hypergraph
Sets the weight of the edge to wt.
setEditable(boolean) - Method in interface DecisionNode
 
setEditable(boolean) - Method in class DecisionNodeAbstract
 
setElementHandler(ElementHandler) - Method in class AbstractSaxHandler
 
setElimAlgo(EliminationHeuristic) - Method in class Settings
 
setEliminationHeuristic(EliminationHeuristic) - Method in class JoinTreeSettings
 
setEliminationHeuristic(EliminationHeuristic) - Method in class RCSettings
 
setEngine(JoinTreeInferenceEngine) - Method in class JoinTreeSettings
 
setEpsilon(double) - Method in class Optimizer
 
setEstimator(SkimmerEstimator) - Method in class HuginReader
 
setEvidence(Map<FiniteVariable, Object>) - Method in class Macros.Bridge
 
setEvidence(Map) - Method in class MAPCoder
 
setEvidence(Map) - Method in class MPECoder
 
setEvidence(Map) - Method in class ProbabilityQueryCoder
 
setEvidence(Map) - Method in class SensitivityCoder
 
setEvidence(IntMap) - Method in class BeliefPropagation
 
setEvidence(IntMap) - Method in class EDAlgorithm
 
setEvidence(IntMap) - Method in interface JointEngine
 
setEvidence(IntMap) - Method in class JoinTreeAlgorithm
 
setEvidence(int, int) - Method in class JoinTreeInference
 
setEvidence(IntMap) - Method in class RCEngine
 
setEvidenceController(EvidenceController) - Method in interface BeliefNetwork
 
setEvidenceController(EvidenceController) - Method in class BeliefNetworkImpl
 
setExactOrNot(boolean) - Method in class MAPCoder
 
setExactParameters(int, int, boolean, double) - Method in class MAPCoder
 
setExcludeArray(boolean[]) - Method in interface StandardNode
 
setExcludeArray(boolean[]) - Method in class StandardNodeImpl
 
setExcludePolicy(ExcludePolicy) - Method in interface StandardNode
 
setExcludePolicy(ExcludePolicy) - Method in class StandardNodeImpl
 
setExecutablePath(JDKTool, File) - Method in class GuessingSource
 
setExpectedNumberOfRCCalls(double) - Method in class RCSettings
 
setExpectedNumberOfRCCalls(double) - Method in class Computation
 
setFamily(FiniteVariable, double[]) - Method in class BeliefCompilation
Sets the family parameters for the variable supplied.
setFileInfo(FileInfo) - Method in class StatsHandler
 
setFileNameQuoted(String) - Method in class ParanoidFileFinder
 
setFinished(boolean) - Method in class NodeLinearTask
It is preferable for the code that creates this task to call setFinished(true) when the task is certainly completed.
setFlag(CodeOption, boolean) - Method in class AbstractCodeGenius
 
setFlag(CodeOption, boolean) - Method in interface CodeGenius
 
setFrozen(boolean) - Method in class EvidenceController
Freeze evidence.
setFullInstanceFromIndex(int, int[]) - Method in class Index
 
setHealthString(String) - Method in class VEVariance
 
setHeuristicAndValidateOrRollback(EliminationHeuristic, BeliefNetwork) - Method in class RCSettings
 
setHighPerformance(boolean) - Method in interface RunReadBIF.MonitorableReusableParser
 
setHighPerformance(boolean) - Method in class UAI06Parser
interface RunReadBIF.MonitorableReusableParser
setHighPerformance(boolean) - Method in class XmlbifParser
interface RunReadBIF.MonitorableReusableParser
setHMeTiSAlgo(MethodHmetis.Algorithm) - Method in class Settings
 
setHuginLogFile(File) - Method in interface CreationMethod.Settings
 
setHuginLogFile(File) - Method in class Settings
 
setID(String) - Method in interface DecisionNode
 
setID(String) - Method in class DecisionNodeAbstract
 
setID(String) - Method in interface Parameter
 
setID(String) - Method in class ParameterImpl
 
setID(String) - Method in class DSLNodeImpl
Convenience method.
setID(String) - Method in interface Variable
 
setID(String) - Method in class VariableImpl
 
setID(String) - Method in class UserEnumProperty
 
setInferenceEngine(InferenceEngine) - Method in class SensitivityEngine
 
setInferenceEngine(InferenceEngine) - Method in class ProbabilityQueryCoder
 
setInferenceEngine(InferenceEngine) - Method in class SensitivityCoder
 
setInfo(RCInfo) - Method in class RCSettings
 
setInputNetwork(BeliefNetwork, String) - Method in class EMCoder
 
setInst(int, int) - Method in class RC
When using KnowledgeBase, be careful about how algorithms will react to KB making changes.
setInstance(Object) - Method in class VariableInstance
 
setIsFlag(boolean) - Method in class UserEnumProperty
 
setJoint(FiniteVariable) - Method in class Stats
 
setJoinTree(JTUnifier) - Method in class JoinTreeSettings
 
setKeepBest(boolean) - Method in class Settings
 
setKey(int, double) - Method in class IntPriorityQueue
Sets the key of the given element to the given value.
setLabel(String) - Method in class DSLNodeImpl
Convenience method.
setLabel(String) - Method in class HuginNodeImpl
 
setLabel(String) - Method in interface StandardNode
 
setLabel(String) - Method in class XmlbifParser.BifNode
 
setLast(int) - Method in class IntList
 
setLeaf(int, Table) - Method in class ShenoyShaferAlgorithm
 
setLikelihood(FiniteVariable, double[]) - Method in class BeliefCompilation
Sets the likelihood parameters for the variable supplied.
setLikelihood(int, double[]) - Method in class MapJoinTree
 
setListener(EdgeDeletionInferenceEngine.CPTPolicy.Listener) - Method in class EdgeDeletionInferenceEngine
 
setListeners(Collection) - Method in class DecisionBackup
 
setLocation(Point) - Method in class DSLSubmodel
 
setLocation(Point) - Method in interface StandardNode
 
setLocation(Point) - Method in class StandardNodeImpl
 
setMain(DSLSubmodel) - Method in class DSLSubmodelFactory
 
setMandatory(Boolean) - Method in interface DSLNode
 
setMandatory(Boolean) - Method in class DSLNodeImpl
Convenience method.
setMAPVariable(boolean) - Method in interface StandardNode
 
setMAPVariable(boolean) - Method in class StandardNodeImpl
Moved from HuginNodeImpl 062204 @since 071603
setMaxIterations(int) - Method in class BeliefPropagationSettings
 
setMaxIterations(int) - Method in class PropagationInferenceEngineImpl
 
setMaxIterations(int) - Method in class EDAlgorithm
 
setMillisPerRCCall(double) - Static method in class RCSettings
 
setMillisPerRCCall(double) - Static method in class Settings
 
setModified(boolean) - Method in class UserEnumProperty
 
setName(String) - Method in class DSLSubmodel
 
setName(String) - Method in class NeticaObject
 
setName(String) - Method in class Interruptable
Set a descriptive name to identify this task
setName(String) - Method in class UserEnumProperty
 
setName(Object) - Method in class UserEnumValue
 
setNext(int, DecisionNode) - Method in class DecisionInternal
 
setNext(Object, DecisionNode) - Method in class DecisionInternal
 
setNext(DecisionNode) - Method in class DecisionInternal
 
setNext(int, DecisionNode) - Method in interface DecisionNode
 
setNext(Object, DecisionNode) - Method in interface DecisionNode
 
setNext(int, DecisionNode) - Method in class DecisionNodeAbstract
 
setNext(Object, DecisionNode) - Method in class DecisionNodeAbstract
 
setNotifyEnabled(boolean) - Method in class EvidenceController
Use this method to disable/re-enable evidence change events.
setNumDtrees(int) - Method in class Settings
 
setNumPartitions(int) - Method in class Settings
 
setObservations(Map) - Method in class EvidenceController
This differs from observe(Map evidence) in that the old observations are completely removed, and replaced by the current evidence.
setOpenAttr(String) - Method in enum XmlbifWriter.Element
 
SetOperation - Class in edu.ucla.structure
 
SetOperation(String) - Constructor for class SetOperation
 
setOption(CodeOption, CodeOptionValue) - Method in class AbstractCodeGenius
 
setOption(CodeOption, CodeOptionValue) - Method in interface CodeGenius
 
setOutcome(int, boolean, boolean) - Method in class ScriptExecution
 
setOutputClassName(String) - Method in class AbstractCodeGenius
 
setOutputClassName(String) - Method in interface CodeGenius
 
setOutStream(PrintWriter) - Method in class Settings
 
setParameter(int, Parameter) - Method in class DecisionLeaf
 
setParameter(Object, Parameter) - Method in class DecisionLeaf
 
setParameter(int, double[]) - Method in interface ArithmeticExpression
 
setParameter(int, double[]) - Method in class S4DoubleExpression
 
setParameter(String) - Method in class CPTImport.CompleteParameterRecorder
 
setParameter(String) - Method in class CPTImport.IncompleteParameterRecorder
 
setParameter(String) - Method in interface CPTImport.ParameterRecorder
 
setParameter(Map, String) - Method in class CPTInfo
 
setParameter(int[], String) - Method in class CPTInfo
 
setParameterOptimizationLevel(Optimizer.ParameterOptimizationLevel) - Method in class Optimizer
 
setParams(Map) - Method in interface GenieNet
 
setParams(Map) - Method in class GenieNetImpl
Sets the net parameters to the name value pairs contained in params.
setParams(Map) - Method in interface HuginNet
Sets the net parameters to the name value pairs contained in params.
setParams(Map) - Method in class HuginNetImpl
Sets the net parameters to the name value pairs contained in params.
setParent(ThreadGroup) - Method in class Interruptable
 
setPath(SoftwareEntity, File) - Method in class GuessingSource
 
setPath(File) - Method in class SoftwareEntity
 
setPathDataFile(String) - Method in class EMCoder
 
setPathInputFile(String) - Method in class MAPCoder
 
setPathInputFile(String) - Method in class MPECoder
 
setPathInputFile(String) - Method in class ProbabilityQueryCoder
 
setPathInputFile(String) - Method in class SensitivityCoder
 
setPathOutputNetworkFile(String) - Method in class EMCoder
 
setPmTable(int, Table) - Method in class EDNetwork
 
setPrEOnly(boolean) - Method in class RCSettings
 
setPrintWriter(PrintWriter) - Method in class ApproxEngine
 
setPrintWriter(PrintWriter) - Method in class SensitivityEngine
 
setProperty(EnumProperty, EnumValue) - Method in class DSLNodeImpl
 
setProperty(EnumProperty, EnumValue) - Method in class StandardNodeImpl
 
setProperty(EnumProperty, EnumValue) - Method in interface Variable
 
setProperty(EnumProperty, EnumValue) - Method in class VariableImpl
 
setQuantitativeDependencyHandler(QuantitativeDependencyHandler) - Method in class AbstractInferenceEngine
 
setQuantitativeDependencyHandler(QuantitativeDependencyHandler) - Method in class SynchronizedInferenceEngine
 
setQuantitativeDependencyHandler(QuantitativeDependencyHandler) - Method in interface InferenceEngine
 
setRanked(Boolean) - Method in interface DSLNode
 
setRanked(Boolean) - Method in class DSLNodeImpl
Convenience method.
setRC(RC) - Method in class Bundle
 
setRC(RC, File) - Method in class Bundle
 
setRC(RC) - Method in class Settings
 
setRC(RC, File) - Method in class Settings
 
setRCComparator(RCComparator) - Method in class Settings
 
setRCCreateListener(CachingScheme.RCCreateListener) - Method in class Settings
 
setRCFactory(Settings.RCFactory) - Method in class Settings
 
setRegexFileName(String) - Method in class ParanoidFileFinder
 
setRegexFilePath(String) - Method in class ParanoidFileFinder
 
setRegexSecurityName(String) - Method in class ParanoidFileFinder
 
setRegexSecurityPath(String) - Method in class ParanoidFileFinder
 
setRelaxed(boolean) - Method in class HuginReader
 
setRepetitions(int) - Method in class EliminationHeuristic.RandomizedBestOfNStrategy
 
setRoot(RCNode, boolean) - Method in class RCDtree
 
setRoots(RC2Node, RC2Node[], RC2Node[], RC2.CachingScheme) - Method in class RC2
Will set this objects root(s).
setRoots(Collection, boolean, Map, boolean) - Method in class RCDgraph
 
setRunnable(Runnable) - Method in class RepetitionThread
 
setScalars(double) - Method in interface BeliefNetwork
 
setScalars(double) - Method in class BeliefNetworkImpl
 
setScheduler(MessagePassingScheduler) - Method in class BeliefPropagationSettings
 
setSecondsPerRCCall(double) - Static method in class RCSettings
 
setSecondsPerRCCall(double) - Static method in class Settings
 
setSeed(Random) - Method in class EliminationHeuristic.RandomizedBestOfNStrategy
 
setSegment(int) - Method in class Optimizer.EquivalenceKey
 
setSelectedValue(int, int) - Method in class MapTree
 
setSeTable(int, Table) - Method in class EDNetwork
 
setSnapshot(DecisionBackup) - Method in interface DecisionTree
 
setSnapshot(DecisionBackup) - Method in class DecisionTreeImpl
interface DecisionTree
setStale(boolean) - Method in class Bundle
 
setStats(Stats) - Method in class Bundle
 
setStringifier(VariableStringifier) - Static method in class VariableImpl
 
setSupers(List) - Method in class NeticaObject
 
setTable(int, Table) - Method in class BeliefPropagation
 
setTable(int, Table) - Method in class EDAlgorithm
 
setTable(int, Table) - Method in interface JointEngine
 
setTable(int, Table) - Method in class JoinTreeAlgorithm
 
setTable(int, Table) - Method in class RC
 
setTable(int, Table) - Method in class RCEngine
 
setTargetList(List) - Method in interface DSLNode
 
setTargetList(List) - Method in class DSLNodeImpl
Convenience method.
setTargetState(int) - Method in class VEVariance
 
setTargetString(String) - Method in class VEVariance
 
setTentativeHuginLogFilePath(String) - Method in class Settings
 
setThreadGroup(ThreadGroup) - Method in class EdgeDeletionInferenceEngine
 
setThreadGroup(ThreadGroup) - Method in class RecoveryInferenceEngine
 
setTimeoutMillis(long) - Method in class BeliefPropagationSettings
 
setTimeoutMillis(long) - Method in class PropagationInferenceEngineImpl
 
setTimeoutMillis(long) - Method in class EDAlgorithm
 
setting - Variable in enum EdgeDeletionInferenceEngine.Attribute
 
Setting - Interface in edu.ucla.util
A Setting is key identifying a single configurable value.
Setting.Settings<E extends Enum<E> & Setting> - Interface in edu.ucla.util
A map of Setting keys to arbitrary values.
settingChanged(ChangeEvent) - Method in class AbstractInferenceEngine
interface ChangeListener
settings() - Method in class EdgeDeletionInferenceEngine
 
settings() - Method in class RecoveryInferenceEngine
 
Settings - Class in edu.ucla.belief.recursiveconditioning
 
Settings() - Constructor for class Settings
 
Settings.RCFactory - Interface in edu.ucla.belief.recursiveconditioning
 
SettingsImpl<E extends Enum<E> & Setting> - Class in edu.ucla.util
Reference implementation of Setting.Settings.
SettingsImpl(Class<E>) - Constructor for class SettingsImpl
 
setToProduct(Table[]) - Method in class Table
 
setToProduct(Table, Table) - Method in class Table
 
setType(String) - Method in class NeticaObject
 
setUseKB(boolean) - Method in class Settings
 
setUserEnumProperties(Collection) - Method in interface BeliefNetwork
 
setUserEnumProperties(Collection) - Method in class BeliefNetworkImpl
 
setUserEnumPropertiesModified(boolean) - Method in interface BeliefNetwork
 
setUserEnumPropertiesModified(boolean) - Method in class BeliefNetworkImpl
 
setUserMemoryProportion(double) - Method in class RCSettings
 
setUserMemoryProportion(double, boolean) - Method in class RCSettings
 
setUserMemoryProportion(double) - Method in class Settings
 
setUserMemoryProportion(double, boolean) - Method in class Settings
 
setUserObject(UserObject) - Method in class BeliefNetworkImpl
 
setUserObject(Object) - Method in interface Variable
 
setUserObject(Object) - Method in class VariableImpl
 
setUserObject2(UserObject) - Method in class BeliefNetworkImpl
 
setValid(boolean) - Method in class AbstractInferenceEngine
 
setValid(boolean) - Method in class SynchronizedInferenceEngine
 
setValid(boolean) - Method in interface InferenceEngine
 
setValue(double) - Method in interface Parameter
 
setValue(double) - Method in class ParameterImpl
 
setValue(int[], double) - Method in class Table
Sets the value of the table entry referenced by ind.
setValue(Object, double) - Method in class Heap
Modifies the priority of one of the heap elements.
setValue(Variable, BeliefNetwork) - Static method in class CSITypeProperty
 
setValue(Variable, EvidenceController) - Static method in class EvidenceAssertedProperty
 
setValue(Variable, BeliefNetwork) - Static method in class InOutDegreeProperty
 
setValues(double[]) - Method in class Table
 
setValues(double[]) - Method in class TableShell
 
setValues(EnumValue[]) - Method in class UserEnumProperty
 
setValues(List) - Method in class UserEnumProperty
 
setVariable(FiniteVariable) - Method in class CPTImportColumnInfo
 
setVariables(Collection) - Method in class MAPCoder
 
setVariables(Collection) - Method in class ProbabilityQueryCoder
 
setVersion(HuginFileVersion) - Method in interface HuginNet
 
setVersion(HuginFileVersion) - Method in class HuginNetImpl
 
setVertices(Object, Object) - Method in class Edge
 
setVeto(Interruptable.Veto) - Method in class Interruptable
Set a callback.
setWeights(List) - Method in interface NoisyOrShell
 
setWeights(double[]) - Method in interface NoisyOrShell
 
setWeights(List) - Method in class NoisyOrShellHenrion
 
setWeights(double[]) - Method in class NoisyOrShellHenrion
 
setWeights(List) - Method in class NoisyOrShellPearl
 
setWeights(double[]) - Method in class NoisyOrShellPearl
 
severNonTreeNodes(DecisionNodeAbstract) - Static method in class DecisionNodeAbstract
 
sexDiffConstant - Variable in class Loci.Footer
 
sexDifference - Variable in class Loci.Footer
 
sexLinked - Variable in class Loci.Header
 
sexLinked() - Method in class Pedigree.PseudoLoci
 
sg() - Method in class CachingDFBnB.DFBnB_TmpVars
 
shallowClone() - Method in interface BeliefNetwork
 
shallowClone() - Method in class BeliefNetworkImpl
 
shallowestContiguousConcreteDeclarer(Class<T>, String, Class<?>...) - Static method in enum Flavor
Beginning with child, considers the ancestry of child up to the first abstract ancestor.
ShenoyShaferAlgorithm - Class in il2.inf.map
 
ShenoyShaferAlgorithm(IndexedJoinTree, Table[]) - Constructor for class ShenoyShaferAlgorithm
 
ShouldBeCached - Static variable in class RCNodeCache
 
shouldReflectY() - Method in class HuginFileVersion
 
shouldRun(String) - Method in class ScriptTest
 
shouldRun(String) - Method in class Test
 
shouldWriteFlat(DecisionNode) - Method in class XmlWriter.GroupedOutcomeWriter
override here
shouldWriteFlat(DecisionNode) - Method in class XmlWriter.GroupedParameterWriter
 
shrink(Map) - Method in class Table
 
shrink(Map) - Method in class TableScaled
 
shrink(Table[], IntMap) - Static method in class Table
 
shrink(IntMap) - Method in class Table
 
shrink(int, int) - Method in class Table
 
shrinkAll(Collection, Map) - Static method in class Table
102502 Modified to accomodate CPTShell
shrinkIndex(IntSet) - Method in class Index
 
shrinkInto(Table, IntMap) - Method in class Table
 
shrinkInto(Table, IntMap, int[]) - Method in class Table
 
shrinkMapping(TableIndex, Map) - Method in class TableIndex
Returns an array where result[i] is the entry in ind2 that is compatible with the ith entry of this index and is compatible with inst.
shuffle(double[]) - Static method in class DblArrays
Will shuffle the values in the double array.
shuffle(int[]) - Static method in class IntArrays
Will shuffle the values in the integer array.
shuffle(Object[]) - Static method in class ObjArrays
Will shuffle the values in the object array.
sign() - Method in class SingleParamSuggestion
 
simple(Class) - Static method in class ProbabilityQueryCoder
 
SimpleCharStream - Class in edu.ucla.belief.io
An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).
SimpleCharStream(Reader, int, int, int) - Constructor for class SimpleCharStream
 
SimpleCharStream(Reader, int, int) - Constructor for class SimpleCharStream
 
SimpleCharStream(Reader) - Constructor for class SimpleCharStream
 
SimpleCharStream(InputStream, String, int, int, int) - Constructor for class SimpleCharStream
 
SimpleCharStream(InputStream, int, int, int) - Constructor for class SimpleCharStream
 
SimpleCharStream(InputStream, String, int, int) - Constructor for class SimpleCharStream
 
SimpleCharStream(InputStream, int, int) - Constructor for class SimpleCharStream
 
SimpleCharStream(InputStream, String) - Constructor for class SimpleCharStream
 
SimpleCharStream(InputStream) - Constructor for class SimpleCharStream
 
simplifiedPotentials - Variable in class UaiPreprocessResult
The simplified potentials.
simplify(IntSet, IntMap) - Method in class BayesianNetwork
 
simplify(IntSet) - Method in class BayesianNetwork
 
simplifyNetwork(BeliefNetwork, double, Map<FiniteVariable, Set<FiniteVariable>>, Map<FiniteVariable, FiniteVariable>) - Static method in class UaiEdgeCutter
 
simulate(int, double, int, Simulator.SimulationListener) - Method in class Simulator
 
simulate() - Method in class Simulator
 
simulate(int, double) - Method in class Simulator
 
simulate(Random) - Method in class Table
simulates an instantiation according to the Table, assuming that it is a valid probability distribution.
simulate(Random, int[]) - Method in class Table
simulates an instantiation according to the Table, assuming that it is a valid probability distribution.
simulationDone(LearningData) - Method in interface Simulator.SimulationListener
 
Simulator - Class in edu.ucla.belief.learn
 
Simulator(BeliefNetwork) - Constructor for class Simulator
 
Simulator.SimulationListener - Interface in edu.ucla.belief.learn
 
singleCPTSolve(FiniteVariable, double, double[], double, double[], Object, double, SensitivityTable) - Method in class SensitivityEngine
 
SingleCPTSuggestion - Class in edu.ucla.belief.sensitivity
 
SingleCPTSuggestion(CPTShell, Interval[], boolean[], double) - Constructor for class SingleCPTSuggestion
 
singleParamSolve(FiniteVariable, double, double[], double, double[], Object, double) - Method in class SensitivityEngine
 
SingleParamSuggestion - Class in edu.ucla.belief.sensitivity
 
SingleParamSuggestion(CPTParameter, double, ProbabilityInterval) - Constructor for class SingleParamSuggestion
 
SingleParamSuggestion(int, CPTParameter[], double[], ProbabilityInterval[]) - Constructor for class SingleParamSuggestion
 
singleton(int) - Static method in class IntSet
 
sink(BeliefNetwork) - Method in class Macros.Recoverable
 
sinks(DirectedGraph) - Static method in class Graphs
 
sit(ScriptExecution.ProcessCustodian, long) - Method in class ScriptExecution
 
size() - Method in class Macros.RecoveryInfo
 
size(FiniteVariable, Map<Object, Object>, Dimension) - Static method in class Macros
 
size(Map<Object, Object>, Object) - Static method in class Macros
 
size() - Method in class BeliefNetworkImpl
 
size() - Method in class EvidenceController
 
size() - Method in interface FiniteVariable
Returns the number of possible values.
size() - Method in class FiniteVariableImpl
Returns the number of possible values.
size(Collection) - Static method in class FiniteVariableImpl
Returns the number of instantiations of the collection of variables.
size - Variable in class ExactMap.SizedOrder
 
size() - Method in class LearningData
 
size() - Method in class SensitivityTable
 
size() - Method in class TableIndex
returns the total number of elements that the index represents.
size() - Method in class EliminationTree
 
size - Variable in class UaiEdgeCutter.MyRecord
 
size() - Method in class AbstractDirectedGraph
 
size() - Method in interface DirectedGraph
Returns the number of vertices in the graph.
size() - Method in interface Graph
Returns the number of vertices in the graph.
size() - Method in class HashGraph
Returns the number of vertices in the graph.
size() - Method in class Heap
Returns the number of elements currently in the heap.
size() - Method in class IdentityArrayMap
 
size() - Method in class IntDirectedGraph
 
size() - Method in class IntGraph
 
size() - Method in class MappedList
Returns the number of elements in this list.
size() - Method in class CSITypeProperty
 
size() - Method in interface EnumProperty
 
size() - Method in class FlagProperty
 
size() - Method in class InOutDegreeProperty
 
size() - Method in class UserEnumProperty
 
size() - Method in class WeakLinkedList
Returns the number of elements in this list.
size - Variable in class EliminationOrders.Record
 
size() - Method in class IntPriorityQueue
 
size() - Method in class PriorityQueue
Returns the number of elements in the queue.
size() - Method in class BayesianNetwork
 
size() - Method in class Domain
 
size(int) - Method in class Domain
 
size(IntSet) - Method in class Domain
 
size() - Method in class DoubleList
 
size() - Method in class DoubleMap
 
size() - Method in class Graph
 
size() - Method in class Heap
Returns the number of elements currently in the heap.
size() - Method in class IntList
 
size() - Method in class IntMap
 
size() - Method in class IntSet
 
size() - Method in class MPE
 
sizeBig() - Method in class Index
 
sizeDefault(BeliefNetwork) - Static method in class Macros
 
sizeDouble() - Method in class Index
 
sizeExponential - Variable in class Stats.Stat
 
sizeInt() - Method in class Index
 
sizeLong() - Method in class Index
 
sizeNetwork - Variable in class Test
 
sizeOfClone(Dimension) - Static method in class Macros
 
sizes() - Method in class Index
 
sizeTable - Variable in class HuginClique
 
skimFile(File) - Method in class Xmlizer
 
SkimmerEstimator - Class in edu.ucla.belief.io.hugin
This class makes a lot of dangerous assumptions in order to achieve fast performance.
SkimmerEstimator(File) - Constructor for class SkimmerEstimator
 
SkimmerEstimator(InputStream) - Constructor for class SkimmerEstimator
 
SkimmerEstimator() - Constructor for class SkimmerEstimator
 
SkimmerEstimator - Class in edu.ucla.belief.io.xmlbif
On smaller files costs about 13% or parse time, on larger files only costs about 4% of parse time.
SkimmerEstimator(File) - Constructor for class SkimmerEstimator
 
SkimmerEstimator(InputStream) - Constructor for class SkimmerEstimator
 
SkimmerEstimator() - Constructor for class SkimmerEstimator
 
skl(double[], double[]) - Method in class EDAlgorithm
 
smaller(Collection, Collection) - Static method in class SetOperation
 
smallestClusterContaining(IntSet) - Method in class JoinTree
 
SMILEReader - Class in edu.ucla.belief.io.dsl
 
SMILEReader() - Constructor for class SMILEReader
 
snapshot() - Method in interface DecisionTree
 
snapshot() - Method in class DecisionTreeImpl
interface DecisionTree
Snapshot - Class in edu.ucla.belief
Takes a snapshot of the current network state, including evidence and its probability, the cpts, the conditionals, and the partial derivatives
Snapshot(BeliefNetwork, InferenceEngine, PartialDerivativeEngine) - Constructor for class Snapshot
 
snapshot(E) - Method in interface Setting.Settings
 
snapshot(E) - Method in class SettingsImpl
 
softevidence(BeliefNetwork) - Method in class Macros.Recoverable
 
softEvidenceConditional(FiniteVariable) - Method in class Macros.Bridge
 
softevidences2edgeindices - Variable in class Macros.Bridge
 
SoftwareEntity - Class in edu.ucla.util.code
 
SoftwareEntity(String, String) - Constructor for class SoftwareEntity
 
sort(Optimizer.Unsortable[], FiniteVariable) - Method in class Optimizer.ParameterOptimizationOn
 
sort() - Method in class DataSetStatistic
 
sort() - Method in class QuickSort
 
sortEdges(int[][]) - Static method in class EDEdgeDeleter
Sort edges, in-place, in topological order.
sortedInds(double[]) - Static method in class ArrayUtils
Returns an array of indices of the the values in the given array sorted according to the values they index.
sortedInds(int[]) - Static method in class ArrayUtils
Returns an array of indices of the the values in the given array sorted according to the values they index.
source(BeliefNetwork) - Method in class Macros.Recoverable
 
sourcefile - Variable in class JDKRun.CompiledClassInfo
 
sources(DirectedGraph) - Static method in class Graphs
 
sourcesToString(String, BeliefNetwork) - Method in class Macros.RecoveryInfo
 
specialToken - Variable in class Token
This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
split - Variable in class Macros.Recoverable
 
splitSingleParamSuggestions() - Method in class SensMPEReport
 
squareEntries() - Method in class Table
 
SSEngine - Class in edu.ucla.belief.inference
 
SSEngine(BeliefNetwork, Dynamator) - Constructor for class SSEngine
 
SSEngine(BeliefNetwork, Dynamator, List) - Constructor for class SSEngine
 
SSEngine(BeliefNetwork, Dynamator, EliminationOrders.JT) - Constructor for class SSEngine
 
SSEngine(BeliefNetwork, Collection, Map, Dynamator) - Constructor for class SSEngine
 
SSEngineGenerator - Class in edu.ucla.belief.inference
 
SSEngineGenerator() - Constructor for class SSEngineGenerator
 
SSWrapper - Class in edu.ucla.belief.inference
 
SSWrapper(BeliefNetwork) - Constructor for class SSWrapper
 
SSWrapper(BeliefNetwork, Collection, Map) - Constructor for class SSWrapper
 
SSWrapper(BeliefNetwork, List) - Constructor for class SSWrapper
 
SSWrapper(BeliefNetwork, EliminationOrders.JT) - Constructor for class SSWrapper
 
SSWrapper(BeliefNetwork, EliminationOrders.JT, QuantitativeDependencyHandler) - Constructor for class SSWrapper
 
STANDARD - Static variable in class AbstractCopier
An instantiable AbstractCopier that makes FiniteVariableImpl copies.
StandardNode - Interface in edu.ucla.belief.io
A class for encapsulating a hugin node description.
StandardNodeImpl - Class in edu.ucla.belief.io
 
StandardNodeImpl(String, List, Map) - Constructor for class StandardNodeImpl
 
StandardNodeImpl(String, List) - Constructor for class StandardNodeImpl
 
StandardNodeImpl.Struct - Class in edu.ucla.belief.io
 
StandardNodeImpl.Struct(int) - Constructor for class StandardNodeImpl.Struct
 
start() - Method in class RunReadNetwork
 
start() - Method in class EMThread
 
start() - Method in class ScriptExecution.Pipe
 
start() - Method in class ScriptExecution.ProcessSitter
 
start() - Method in class Interruptable
Run the expensive task in a new Thread.
start(Object) - Method in class Interruptable
Run the expensive task in a new Thread.
start(long) - Method in class Interruptable
Run the expensive task in a new Thread that waits for the specified number of milliseconds before beginning the task.
start(long, Object) - Method in class Interruptable
Run the expensive task in a new Thread that waits for the specified number of milliseconds before beginning the task.
start() - Method in class RepetitionThread
 
startDocument() - Method in class AbstractSaxHandler
 
startDocument() - Method in class InstantiationXmlizer
 
startDocument() - Method in class StatsHandler
 
startElement(String, String, String, Attributes) - Method in class XmlElementHandler
 
startElement(String, String, String, Attributes) - Method in class AbstractSaxHandler
 
startElement(String, String, String, Attributes) - Method in interface ElementHandler
 
startElement(String, String, String, Attributes) - Method in class InstantiationXmlizer.RootCheckHandler
 
startElement(String, String, String, Attributes) - Method in class InstantiationXmlizer
 
startElement(String, String, String, Attributes) - Method in class InstantiationXmlizer.ValidRootHandler
 
startElement(String, String, String, Attributes) - Method in class SkimmerEstimator
 
startElement(String, String, String, Attributes) - Method in class StatsHandler
 
startGroup() - Method in class RepetitionThread
 
startGroup() - Method in class SystemGCThread
 
startInterruptsGroup() - Method in class RepetitionThread
 
startInterruptsGroup() - Method in class SystemGCThread
 
startPriority() - Method in class RepetitionThread
 
startTime1 - Variable in class UaiMain
 
startTime2 - Variable in class UaiMain
 
startTimer() - Method in class VEVariance
 
statement(NeticaObject) - Method in class NeticaReader
 
StateNotFoundException - Exception in edu.ucla.belief
 
StateNotFoundException(FiniteVariable, Object) - Constructor for exception StateNotFoundException
 
STATIC_LEXER_ERROR - Static variable in error TokenMgrError
An attempt wass made to create a second instance of a static token manager.
staticFlag - Static variable in class SimpleCharStream
 
Stats - Class in edu.ucla.belief.decision
 
Stats() - Constructor for class Stats
 
stats - Variable in class Stats
 
Stats - Class in edu.ucla.belief.dtree
 
Stats() - Constructor for class Stats
 
stats - Variable in class FileInfo
 
Stats.Stat - Class in edu.ucla.belief.decision
 
Stats.Stat(String) - Constructor for class Stats.Stat
 
statsAll() - Method in class RC
 
StatsHandler - Class in edu.ucla.belief.recursiveconditioning
 
StatsHandler() - Constructor for class StatsHandler
 
statsPe() - Method in class RC
 
stepSizes() - Method in class Index
 
stepToString(int) - Static method in class CPTCoder
 
stop() - Method in class Interruptable
 
stopAndWaitRecCondAsThread() - Method in class RC
Will stop any running functions and wait for them to finish.
stopTimer(String) - Method in class VEVariance
 
stopTimerLn(String) - Method in class VEVariance
 
STR_ARG_ACE - Static variable in class UaiMain
 
STR_ARG_BNB - Static variable in class UaiMain
 
STR_ARG_DOT - Static variable in class GraphvizIO
 
STR_ARG_HELP - Static variable in class UaiMain
 
STR_ARG_INPUTFILEPATH - Static variable in class GraphvizIO
 
STR_ARG_MEMORY_LIMIT - Static variable in class RCInfo
 
STR_ARG_NETWORK - Static variable in class UaiMain
 
STR_ARG_NORMALIZE - Static variable in class UaiMain
 
STR_ARG_OUTPUTFILEPATH - Static variable in class GraphvizIO
 
STR_ARG_PATH_INPUT - Static variable in class RCInfo
 
STR_ARG_PATH_OUTPUT - Static variable in class RCInfo
 
STR_ARG_RC - Static variable in class UaiMain
 
STR_ARG_RCLINK - Static variable in class UaiMain
 
STR_ARG_RCLINK2 - Static variable in class UaiMain
 
STR_ARG_TEST - Static variable in class UaiMain
 
STR_ARG_VERBOSE - Static variable in class UaiMain
 
STR_ARG_VERBOSE1 - Static variable in class UaiMain
 
STR_ATTR_CANCOMPUTE_NAME - Static variable in class Xmlizer
 
STR_ATTR_CREATIONMETHOD_NAME - Static variable in class Xmlizer
 
STR_ATTR_DATE - Static variable in class InstantiationXmlizer
 
STR_ATTR_DTREECONTEXT_NAME - Static variable in class Xmlizer
 
STR_ATTR_DTREECUTSET_NAME - Static variable in class Xmlizer
 
STR_ATTR_DTREEHEIGHT_NAME - Static variable in class Xmlizer
 
STR_ATTR_DTREEMAXCLUSTER_NAME - Static variable in class Xmlizer
 
STR_ATTR_EDITABLE - Static variable in class XmlWriter
 
STR_ATTR_EPSILON - Static variable in class XmlWriter
 
STR_ATTR_ESTIMATEDTIME_NAME - Static variable in class Xmlizer
 
STR_ATTR_FACTOR_NAME - Static variable in class Xmlizer
 
STR_ATTR_ID - Static variable in class XmlWriter
 
STR_ATTR_ID - Static variable in class InstantiationXmlizer
 
STR_ATTR_ID_NAME - Static variable in class Xmlizer
 
STR_ATTR_INDEX - Static variable in class XmlWriter
 
STR_ATTR_INSTANCELIST - Static variable in class XmlWriter
 
STR_ATTR_JOINT - Static variable in class XmlWriter
 
STR_ATTR_LEFT_NAME - Static variable in class Xmlizer
 
STR_ATTR_MARGINALVARS_NAME - Static variable in class Xmlizer
 
STR_ATTR_NEGATIVE - Static variable in class InstantiationXmlizer
 
STR_ATTR_NETWORKNAME_NAME - Static variable in class Xmlizer
 
STR_ATTR_OPTIMALMEMORY_NAME - Static variable in class Xmlizer
 
STR_ATTR_PARENTORDER - Static variable in class XmlWriter
 
STR_ATTR_RIGHT_NAME - Static variable in class Xmlizer
 
STR_ATTR_SERIAL - Static variable in class XmlWriter
 
STR_ATTR_TYPE_L - Static variable in class XmlbifParser
 
STR_ATTR_TYPE_U - Static variable in class XmlbifParser
 
STR_ATTR_USERMEMORY_NAME - Static variable in class Xmlizer
 
STR_ATTR_VALUE - Static variable in class XmlWriter
 
STR_ATTR_VALUE - Static variable in class InstantiationXmlizer
 
STR_ATTR_VARIABLE - Static variable in class XmlWriter
 
STR_ATTR_VARSNULLROOT_NAME - Static variable in class Xmlizer
 
STR_ATTR_VERSION_L - Static variable in class XmlbifParser
 
STR_ATTR_VERSION_U - Static variable in class XmlbifParser
 
STR_BALANCE_FACTOR_ALL - Static variable in class MethodHmetis
 
STR_BYTE_UNIT - Static variable in class RCSettings
 
STR_BYTE_UNIT - Static variable in class Settings
 
STR_CACHE_FALSE - Static variable in class DGraph
 
STR_CACHE_TRUE - Static variable in class DGraph
 
STR_CHARACTER_CLONE - Static variable in class Macros
 
STR_CHARACTER_SEP - Static variable in class Macros
 
STR_CHARACTER_SOFT_EVIDENCE - Static variable in class Macros
 
STR_CHMOD - Static variable in class JDKToolScript
 
STR_CHMOD_ARG1 - Static variable in class JDKToolScript
 
STR_CLASSNAME_ESTIMATOR - Static variable in class RunReadBIF
 
STR_CLASSNAME_PARSER - Static variable in class RunReadBIF
 
STR_CLASSNAME_PARSER_ORIG - Static variable in class RunReadBIF
 
STR_CLASSNAME_UAI06PARSER - Static variable in class RunReadBIF
 
STR_CLASSNAME_WRITER - Static variable in class RunWriteBIF
 
STR_COMMENT - Static variable in class XmlbifWriter
 
STR_CONSOLE_MESSAGE_COMP_MEM - Static variable in class AbstractInferenceEngine
 
STR_CONSOLE_MESSAGE_COMP_TIME - Static variable in class AbstractInferenceEngine
 
STR_CONSOLE_MESSAGE_PROP_TIME - Static variable in class AbstractInferenceEngine
 
STR_DEFAULT_RCFILEPATH - Static variable in class Settings
 
STR_DELIMITER - Static variable in class HuginLogReader
 
STR_DELIMITERS - Static variable in class Builder
 
STR_DELIMITERS - Static variable in class CPTImport
 
STR_DELIMITERS - Static variable in class Xmlizer
 
STR_DISPLAY - Static variable in class EdgeDeletionEngineGenerator
 
STR_DISPLAY - Static variable in class RecoveryEngineGenerator
 
STR_DISPLAY_DEBUG - Static variable in class EdgeDeletionEngineGenerator
 
STR_DISPLAY_DEBUG - Static variable in class RecoveryEngineGenerator
 
STR_EDGE - Static variable in class RecursiveDepthFirstIterator
 
STR_ELEMENT_NODE_GENERIC - Static variable in class XmlWriter
 
STR_ELEMENT_NODE_INTERNAL - Static variable in class XmlWriter
 
STR_ELEMENT_NODE_LEAF - Static variable in class XmlWriter
 
STR_ELEMENT_PARAMETER - Static variable in class XmlWriter
 
STR_ELEMENT_ROOT - Static variable in class XmlWriter
 
STR_ELT_RCNODE_NAME - Static variable in class Xmlizer
 
STR_ELT_ROOT_NAME - Static variable in class Xmlizer
 
STR_ELT_VARIABLE_NAME - Static variable in class Xmlizer
 
STR_EM_FILENAME_PREFIX - Static variable in class Learning
 
STR_EMPTY_UNIT - Static variable in class RCSettings
 
STR_ERR_MSG_FROZEN - Static variable in class EvidenceController
 
STR_ERROR_WEIGHTS_LEN - Static variable in class NoisyOrShellHenrion
 
STR_ERROR_WEIGHTS_LEN - Static variable in class NoisyOrShellPearl
 
STR_EXCEPTION_EVIDENCE - Static variable in class RC
 
STR_EXCEPTION_ILLEGAL_JOINTREE - Static variable in class DefaultGenerator
 
STR_FILENAME_CLASSFILELIST - Static variable in class Test
 
STR_FILENAME_JAVAFILELIST - Static variable in class Test
 
STR_FLAG_EM_DATA_FILE - Static variable in class Test
 
STR_FLAG_MINUS - Static variable in class ScriptTest
 
STR_FLAG_MINUS - Static variable in class Test
 
STR_FLAG_NETWORK_FILE - Static variable in class Test
 
STR_FLAG_PLUS - Static variable in class ScriptTest
 
STR_FLAG_PLUS - Static variable in class Test
 
STR_GENERIC_ALLOCATION_ERROR - Static variable in class RCEngineGenerator
 
STR_GENERIC_ALLOCATION_ERROR - Static variable in class RCEngineGenerator
 
STR_HOURS_UNIT - Static variable in class RCSettings
 
STR_HOURS_UNIT - Static variable in class Computation
 
STR_HOURS_UNIT - Static variable in class Settings
 
STR_ID_ALPHABET - Static variable in class ParameterImpl
 
STR_IO_SEPARATE_FIELDS - Static variable in class Macros
 
STR_IO_SEPARATE_OBJECTS - Static variable in class Macros
 
STR_KEY_PREFIX - Static variable in class DSLConstants
 
STR_KILOBYTE_UNIT - Static variable in class RCSettings
 
STR_KILOBYTE_UNIT - Static variable in class Settings
 
STR_LABEL_SOFT_EVIDENCE - Static variable in class Macros
 
STR_MAP_TOKEN - Static variable in class HuginReader
 
STR_MEGABYTE_UNIT - Static variable in class RCSettings
 
STR_MEGABYTE_UNIT - Static variable in class Settings
 
STR_METHOD_FOUNDATION - Static variable in class CPTCoder
 
STR_METHOD_NAME - Static variable in class CPTCoder
 
STR_METHOD_NAME - Static variable in class EMCoder
 
STR_METHOD_NAME - Static variable in class MAPCoder
 
STR_METHOD_NAME - Static variable in class MPECoder
 
STR_METHOD_NAME - Static variable in class ProbabilityQueryCoder
 
STR_METHOD_NAME - Static variable in class SensitivityCoder
 
STR_METHOD_READNETWORK_NAME - Static variable in class ProbabilityQueryCoder
 
STR_MINUTE_UNIT - Static variable in class RCSettings
 
STR_MINUTE_UNIT - Static variable in class Computation
 
STR_MINUTE_UNIT - Static variable in class Settings
 
STR_MSG_OVERFLOW - Static variable in class RCSettings
 
STR_NAME_CLASS_ALGORITHM - Static variable in class Dynamator
 
STR_NAME_CLASS_TIGER - Static variable in class Dynamator
 
STR_NAME_METHOD - Static variable in class ModelCoder
 
STR_NAME_METHOD() - Static method in enum Flavor
name factory methods
STR_NAME_METHOD_FORCLASS - Static variable in class Dynamator
 
STR_NAME_METHOD_NORMALIZED() - Static method in enum Flavor
 
STR_NAME_METHOD_TOIL2 - Static variable in class Dynamator
 
STR_NAME_OUTPUT_CLASS - Static variable in class CPTCoder
 
STR_NAME_OUTPUT_CLASS - Static variable in class EMCoder
 
STR_NAME_OUTPUT_CLASS - Static variable in class MAPCoder
 
STR_NAME_OUTPUT_CLASS - Static variable in class ModelCoder
 
STR_NAME_OUTPUT_CLASS - Static variable in class MPECoder
 
STR_NAME_OUTPUT_CLASS - Static variable in class ProbabilityQueryCoder
 
STR_NAME_OUTPUT_CLASS - Static variable in class SensitivityCoder
 
STR_NAME_PREFIX - Static variable in class Interruptable
 
STR_NATIVE_LIBRARY_NAME - Static variable in class SMILEReader
 
STR_OOME - Static variable in class Dynamator
 
STR_OUTOFMEMORY_MSG - Static variable in class RC
 
STR_PAREN_LEFT - Static variable in class HuginLogReader
 
STR_PAREN_RIGHT - Static variable in class HuginLogReader
 
STR_PATH_OUTPUT_DEFAULT - Static variable in class RCInfo
 
STR_POSITION_INFIX - Static variable in class XmlbifWriter
 
STR_POSITION_POSTFIX - Static variable in class XmlbifWriter
 
STR_POSITION_PREFIX - Static variable in class XmlbifWriter
 
STR_PREFIX_CLONE - Static variable in class Macros
 
STR_PREFIX_ID_ROOT - Static variable in class Xmlizer
 
STR_PREFIX_INTERNAL - Static variable in class DGraph
 
STR_PREFIX_LEAF - Static variable in class DGraph
 
STR_PREFIX_ROOT - Static variable in class DGraph
 
STR_PREFIX_SOFT_EVIDENCE - Static variable in class Macros
 
STR_REGEX_AFTER_LAST_FILE_SEPARATOR_NO_PERIODS - Static variable in class ParanoidFileFinder
 
STR_REGEX_ANY_NONSEPS - Static variable in class ParanoidFileFinder
 
STR_REGEX_AUXILIARY_VAR - Static variable in class Macros
 
STR_REGEX_CLONE - Static variable in class Macros
 
STR_REGEX_ENDQUOTE - Static variable in class ParanoidFileFinder
 
STR_REGEX_INTEGER_ID - Static variable in class Macros
 
STR_REGEX_JDK - Static variable in class ParanoidFileFinder
 
STR_REGEX_NONWORD_NONPERIOD_NONSEP - Static variable in class ParanoidFileFinder
 
STR_REGEX_NONWORD_NONSEP - Static variable in class ParanoidFileFinder
 
STR_REGEX_POST_BEST - Static variable in class ParanoidFileFinder
 
STR_REGEX_POST_EXECUTABLE - Static variable in class ParanoidFileFinder
 
STR_REGEX_POST_SEARCH_SECURITY - Static variable in class ParanoidFileFinder
 
STR_REGEX_PRE_BEST - Static variable in class ParanoidFileFinder
 
STR_REGEX_PRE_EXECUTABLE - Static variable in class ParanoidFileFinder
 
STR_REGEX_PRE_SEARCH_SECURITY - Static variable in class ParanoidFileFinder
 
STR_REGEX_QUOTE - Static variable in class ParanoidFileFinder
 
STR_REGEX_SOFT_EVIDENCE - Static variable in class Macros
 
STR_SAMIAM_ACRONYM - Static variable in class Definitions
 
STR_SECOND_UNIT - Static variable in class RCSettings
 
STR_SECOND_UNIT - Static variable in class Computation
 
STR_SECOND_UNIT - Static variable in class Settings
 
STR_SOFT_EVIDENCE_STATE0 - Static variable in class Macros
 
STR_SOFT_EVIDENCE_STATE1 - Static variable in class Macros
 
STR_STACKOVERFLOW_MSG - Static variable in class RC
 
STR_TAG_ANONYMOUS_VALUES - Static variable in class XmlbifParser
 
STR_TAG_DEFINITION_0_3 - Static variable in class XmlbifParser
 
STR_TAG_FOR - Static variable in class XmlbifParser
 
STR_TAG_GIVEN - Static variable in class XmlbifParser
 
STR_TAG_INST - Static variable in class InstantiationXmlizer
 
STR_TAG_NAME - Static variable in class XmlbifParser
 
STR_TAG_NETWORK - Static variable in class XmlbifParser
 
STR_TAG_OBSERVATION - Static variable in class XmlbifParser
 
STR_TAG_OUTCOME - Static variable in class XmlbifParser
 
STR_TAG_PROBABILITY_0_3A - Static variable in class XmlbifParser
 
STR_TAG_PROPERTY - Static variable in class XmlbifParser
 
STR_TAG_ROOT - Static variable in class InstantiationXmlizer
 
STR_TAG_ROOT_0_3 - Static variable in class XmlbifParser
 
STR_TAG_ROOT_0_3A - Static variable in class XmlbifParser
 
STR_TAG_TABLE - Static variable in class XmlbifParser
 
STR_TAG_VARIABLE - Static variable in class XmlbifParser
 
STR_TYPE_CPT - Static variable in class DGraph
 
STR_TYPE_EVIDENCE_INDICATOR - Static variable in class DGraph
 
STR_UNINITIALIZED - Static variable in class Dynamator
 
STR_VALUE_TRUE - Static variable in class InstantiationXmlizer
 
STR_VERBOSE_TRACE_MESSAGE - Static variable in class Definitions
 
STR_VERSION_0_3 - Static variable in class XmlbifParser
 
STR_VERSION_0_3A - Static variable in class XmlbifParser
 
STR_WARNING_NOISY_OR - Static variable in class ModelCoder
 
STR_XBIF - Static variable in class UaiEdgeCutter
 
STR_XBIF - Static variable in class UaiMain
 
STR_XML_VERSION - Static variable in class XmlbifWriter
 
STREAM_DEBUG - Static variable in class Definitions
 
STREAM_DEBUG - Static variable in class EOGenerator
 
STREAM_DEBUG - Static variable in class AbstractDirectedGraph
 
STREAM_DEBUG - Static variable in class DepthFirstIterator
 
STREAM_DEBUG - Static variable in class HashDirectedGraph
 
STREAM_DEBUG - Static variable in class RecursiveDepthFirstIterator
 
STREAM_DEBUG - Static variable in class Interruptable
 
STREAM_TEST - Static variable in class Definitions
 
STREAM_VERBOSE - Static variable in class ApproxEngine
 
STREAM_VERBOSE - Static variable in class Definitions
 
STREAM_VERBOSE - Static variable in class SensitivityEngine
 
STREAM_VERBOSE - Static variable in class Interruptable
 
strengths - Variable in class PotentialInfo
 
strengths() - Method in class NoisyOrShellPearl
 
strengthsClone() - Method in class NoisyOrShellPearl
 
STRING - Static variable in interface HuginReaderConstants
 
STRING - Static variable in interface NeticaReaderConstants
 
string - Variable in class LearningData.Struct
 
Stringifier - Interface in edu.ucla.util
 
Stringifier.Selector - Interface in edu.ucla.util
 
stroke - Variable in enum EdgeDeletionInferenceEngine.Command
 
stroke - Variable in enum Macros.Category
 
SubDomain - Interface in il2.model
 
sublevel - Variable in class Optimizer.EquivalenceKey
 
subList(int, int) - Method in class MappedList
Not supported.
subMap(Map, Collection) - Static method in class Maps
 
subMap(IntSet) - Method in class IntMap
 
subset(int[]) - Method in class IntSet
 
subsettings(Dynamator, PropertySuperintendent) - Static method in class Macros
 
SUBTRACT - Static variable in class SetOperation
 
subtract(double[], double[]) - Static method in class DblArrays
 
subtract(LinearFunction) - Method in class LinearFunction
 
suggestEpsilon(Table) - Static method in class Optimizer
 
sum() - Method in class DecisionLeaf
 
sum(Collection) - Method in class DecisionLeaf
 
sum(Collection) - Static method in class ParameterImpl
 
sum(double[], int, int) - Static method in class Table
 
sum(double[], double, int, int) - Static method in class TableScaled
 
sum() - Method in class Table
 
sum(double[]) - Static method in class ArrayUtils
Returns the sum of the values in the given array.
sum - Variable in class IntStats
 
SUM_SIZE_COST - Static variable in class Trees
A cost function which is the sum of the sizes(# of instantiations) of the two cliques.
sumOut(Index, double[], int, double[]) - Static method in class Table
 
sumProduct(Collection) - Static method in class BasicInference
 
sumReduce(Collection, double) - Static method in class BasicInference
 
suspendKB() - Method in class RC
Warning: This function should not really be public and should not be called from outside of the package unless you are sure it will not lead to computation errors!
swap(int, int) - Method in class MappedList
Swaps the elements at i and j
swapWithLastAndRemove(int) - Method in class IntList
 
SwitchTo(int) - Method in class HuginLogReaderTokenManager
 
SwitchTo(int) - Method in class HuginReaderTokenManager
 
SwitchTo(int) - Method in class NeticaReaderTokenManager
 
synchEvidWithBN() - Method in class RC2
 
SynchronizedInferenceEngine - Class in edu.ucla.belief.inference
 
SynchronizedInferenceEngine.SynchronizedPartialDerivativeEngine - Class in edu.ucla.belief.inference
 
synchronizeMemoryProportion() - Method in class RCSettings
 
SystemGCThread - Class in edu.ucla.util
 
SystemGCThread() - Constructor for class SystemGCThread
 
SystemGCThread(long, int) - Constructor for class SystemGCThread
 
SystemSoftwareSource - Interface in edu.ucla.util.code
 

T

table(FiniteVariable, Macros.Bridge) - Method in enum Macros.Category
 
table - Variable in class XmlbifParser.Definition
 
Table - Class in edu.ucla.belief
 
Table(Table) - Constructor for class Table
Creates a copy of the table.
Table(TableIndex) - Constructor for class Table
Creates a table with the supplied index.
Table(TableIndex, double[]) - Constructor for class Table
Creates a new Table.
Table(TableIndex, double[], boolean) - Constructor for class Table
 
Table(List, double[]) - Constructor for class Table
Creates a new table that has a TableIndex generated from the variables supplied.
Table(List) - Constructor for class Table
Creates a new table that has a TableIndex generated from the variables supplied.
Table(FiniteVariable[]) - Constructor for class Table
Creates a new table that has a TableIndex generated from the variables supplied.
Table(Object[], double[]) - Constructor for class Table
Creates a new table that has a TableIndex generated from the variables supplied.
Table - Class in il2.model
 
Table(Domain, IntSet) - Constructor for class Table
 
Table(Index, double[]) - Constructor for class Table
 
Table(Domain, IntSet, double[]) - Constructor for class Table
 
tableConditional(int) - Method in class BeliefPropagation
 
tableConditional(int) - Method in class MaxProduct
 
tableConditional(int) - Method in interface JointEngine
 
tableConditional(int) - Method in class JoinTreeAlgorithm
 
tableConditional(int) - Method in class RCEngine
 
TableIndex - Class in edu.ucla.belief
A class for mapping from variable instantiations to a linear index.
TableIndex(TableIndex) - Constructor for class TableIndex
 
TableIndex(Collection) - Constructor for class TableIndex
creates an index over the variables supplied.
TableIndex(Object[]) - Constructor for class TableIndex
creates an index over the variables.
TableIndex.Iterator - Class in edu.ucla.belief
A class for stepping through the instantiations of an index.
TableIndex.Iterator() - Constructor for class TableIndex.Iterator
creates an iterator.
tableIndexOfEdgeHead(int) - Method in class EDNetwork
 
tableIndexOfEdgeTail(int) - Method in class EDNetwork
 
tableJoint(int) - Method in class BeliefPropagation
 
tableJoint(int) - Method in class MaxProduct
 
tableJoint(int) - Method in interface JointEngine
 
tableJoint(int) - Method in class JoinTreeAlgorithm
 
tableJoint(int) - Method in class RCEngine
 
tableOfPair(Pair) - Method in class MessagePassingScheduler
 
tablePartial(FiniteVariable) - Method in class PartialDerivativeWrapper
 
tablePartial(int) - Method in class AbstractSSAlgorithm
 
tablePartial(int) - Method in class MPEAlgorithm
 
tablePartial(int) - Method in class NormalizedMaxSSAlgorithm
 
tablePartial(int) - Method in class UnindexedSSAlgorithm
 
tablePartial(int) - Method in class UnindexedZCAlgorithm
 
tablePartial(int) - Method in interface PartialDerivativeEngine
 
tablePartial(int) - Method in class RCEngine
 
tables() - Method in interface BeliefNetwork
 
tables() - Method in class BeliefNetworkImpl
 
TableScaled - Class in edu.ucla.belief
 
TableScaled(Table) - Constructor for class TableScaled
Creates a copy of the table.
TableScaled(Table, double) - Constructor for class TableScaled
Creates a copy of the table.
TableScaled(TableIndex, double) - Constructor for class TableScaled
Creates a table with the supplied index.
TableScaled(TableIndex, double[], double) - Constructor for class TableScaled
Creates a new Table.
TableScaled(List, double) - Constructor for class TableScaled
Creates a new table that has a TableIndex generated from the variables supplied.
TableScaled(List, double[], double) - Constructor for class TableScaled
Creates a new table that has a TableIndex generated from the variables supplied.
TableScaled(FiniteVariable[], double) - Constructor for class TableScaled
Creates a new table that has a TableIndex generated from the variables supplied.
TableScaled(Object[], double[], double) - Constructor for class TableScaled
Creates a new table that has a TableIndex generated from the variables supplied.
TableShell - Class in edu.ucla.belief
 
TableShell(Table) - Constructor for class TableShell
 
tableString(String) - Method in class Table
 
tableString() - Method in class Table
 
tableSuggestions(TableShell, SensitivityTable) - Static method in class SingleParamSuggestion
 
TABOO - Static variable in class SearchMethod
 
TARGET - Static variable in class DiagnosisType
 
TARGET - Static variable in class SMILEReader
 
TARGET_ST - Variable in class VEVariance
 
TARGET_STATE - Variable in class VEVariance
 
team(PropertySuperintendent) - Method in class ApproxEngineGenerator
 
test(InferenceEngine, InferenceEngine, EvidenceController, double, int) - Static method in class AbstractInferenceEngine
 
Test - Class in edu.ucla.util.code
Tests each of the CodeGenius sub classes by writing one or more Java files intended to be compiled and run.
Test(Map) - Constructor for class Test
 
TestClass - Class in edu.ucla.belief.rc2.tools
 
TestClass(TestClass.CmdLn) - Constructor for class TestClass
 
testCompile(BeliefNetwork, double, PrintStream, int) - Static method in class Macros
 
testCPTCoder() - Method in class Test
 
testEMCoder() - Method in class Test
 
testMAPCoder() - Method in class Test
 
testMode - Static variable in class UaiMain
 
testModelCoder() - Method in class Test
 
testMPECoder() - Method in class Test
 
TestMpeEngine - Class in edu.ucla.belief.uai2006
An interface for an algorithm that computes MAP for the 2006 UAI evaluation.
TestMpeEngine() - Constructor for class TestMpeEngine
 
TestPeEngine - Class in edu.ucla.belief.uai2006
An interface for an algorithm that computes MAP for the 2006 UAI evaluation.
TestPeEngine() - Constructor for class TestPeEngine
 
testProbabilityQueryCoder() - Method in class Test
 
testRoot() - Method in class ScriptTest
 
testRoot(File) - Method in class Test
 
testSensitivityCoder() - Method in class Test
 
theCharactersNoop - Variable in class AbstractSaxHandler
 
theCollator - Static variable in class VariableImpl
 
theComputation - Static variable in class RCComparator
 
thereExists(EnumProperty, EnumValue) - Method in interface BeliefNetwork
 
thereExists(EnumProperty, EnumValue) - Method in class BeliefNetworkImpl
 
thereExists(Collection, DSLNodeType) - Static method in class FiniteVariableImpl
moved from DSLNodeType 20081110
thereExistsModifiedUserEnumProperty() - Method in interface BeliefNetwork
 
thereExistsModifiedUserEnumProperty() - Method in class BeliefNetworkImpl
 
theRootCheckHandler - Variable in class AbstractSaxHandler
 
theRootCheckHandler - Variable in class InstantiationXmlizer
 
theseVarsAppearInCNF() - Method in class MultiValuedCNF
Will return an array indexed by the vars list (from createFromBN), with true if it appears in any CNF clause and false if it doesn't appear anywhere.
thetaLocations() - Method in class BeliefCompilation
 
theValidRootHandler - Variable in class XmlDocumentHandler
 
theValidRootHandler - Variable in class InstantiationXmlizer
 
theVariableComparator - Static variable in class VariableInstance
 
thisCacheOverFlowed - Variable in class RCNodeCache
 
timeMillis() - Method in class PropagationInferenceEngineImpl
 
timeMillis() - Method in class BeliefPropagation
 
timeMillis() - Method in class EDAlgorithm
 
TimePeVsIl2 - Class in edu.ucla.belief.rc2.tools
This class should be removed TODO!
TimePeVsIl2() - Constructor for class TimePeVsIl2
 
timestamp() - Static method in class EdgeDeletionInferenceEngine.DateFormatFilename
 
timestamp(Date) - Method in class EdgeDeletionInferenceEngine.DateFormatFilename
 
timestamp(Date, Appendable) - Method in class EdgeDeletionInferenceEngine.DateFormatFilename
 
tip - Variable in enum EdgeDeletionInferenceEngine.CPTPolicy
 
tmpVars_last() - Method in class CachingDFBnB
 
toArray(Object[]) - Method in class BeliefNetworkImpl
 
toArray() - Method in class BeliefNetworkImpl
 
toArray(Object[]) - Method in class AbstractDirectedGraph
 
toArray() - Method in class AbstractDirectedGraph
 
toArray(Object[]) - Method in class HashGraph
 
toArray() - Method in class HashGraph
 
toArray() - Method in class MappedList
Returns an array containing all of the elements in this list proper sequence.
toArray(Object[]) - Method in class MappedList
Returns an array containing all of the elements in this list in proper sequence; the runtime type of the returned array is that of the specified array.
toArray() - Method in class WeakLinkedList
Returns an array containing all of the elements in this list in the correct order.
toArray(Object[]) - Method in class WeakLinkedList
Returns an array containing all of the elements in this list in the correct order; the runtime type of the returned array is that of the specified array.
toArray() - Method in class IntList
 
toArray() - Method in class IntSet
 
toBigDecimal(double) - Static method in class UaiMapSolution
Converts a double to a big decimal.
toBoolean(EnumValue) - Method in class AbstractEnumProperty
 
toBoolean(EnumValue) - Method in class CSITypeProperty
 
toBoolean(EnumValue) - Method in interface EnumProperty
 
toBoolean(EnumValue) - Method in class FlagProperty
 
toBoolean(EnumValue) - Method in class InOutDegreeProperty
 
toBoolean(EnumValue) - Method in class UserEnumProperty
 
toCode(Object) - Static method in class MAPCoder
 
TODO_REMOVE_DO_EXTRA_LOOKAHEAD - Static variable in class RC
 
TODO_REMOVE_DO_INDEX_CACHING_DURING_CREATION - Static variable in class RC
This variable needs to be set during RC creation and stay the same during computations!
TODO_REMOVE_DO_LEAF_CACHING_DURING_CREATION - Static variable in class RC
This variable is only used during RC creation, not dynamically!
TODO_REMOVE_DO_LOOKAHEAD_LOWERBOUND - Static variable in class RC
 
TODO_REMOVE_DO_PROP_UP - Static variable in class RC
 
TODO_REMOVE_REVERSE_ORDER - Static variable in class RC
 
toDoubleArray(List) - Static method in class ListConverter
 
toDoubles(int[]) - Static method in class ArrayUtils
Returns an array of doubles containing the same values as the given array of ints.
toFiniteVariable() - Method in class XmlbifParser.Variable
 
toIL2Engine(Dynamator, BeliefNetwork, Converter) - Static method in class CrouchingTiger
 
toIL2Settings(BeliefNetwork, Map<CrouchingTiger.DynamatorImpl, Dynamator>) - Method in enum CrouchingTiger.DynamatorImpl
 
toIL2Settings(Object) - Static method in class CrouchingTiger
 
toIL2Settings(EliminationHeuristic) - Static method in class CrouchingTiger
 
toIL2Settings(JoinTreeSettings) - Static method in class CrouchingTiger
 
toIL2Settings(RCSettings) - Static method in class CrouchingTiger
 
toIL2Settings(PropertySuperintendent) - Method in class Dynamator
 
toInt() - Method in class CachingDFBnB.ChildExpansion
 
toInt() - Method in class CachingDFBnB.HeurFunct
 
toInt() - Method in class CachingDFBnB.OrderingAlgo
 
toIntArray(List) - Static method in class ListConverter
 
toIntList() - Method in class IntSet
 
toInts(double[]) - Static method in class ArrayUtils
Returns an array of ints containing the same values as the given array of doubles after the double values are rounded.
toJavaCode(Object) - Static method in class ApproxEngineGenerator
 
toJavaCodeIL1(BeliefNetwork, String, boolean, CodeOptionValue, PrintStream) - Method in class ModelCoder
 
toJavaCodeIL2(BayesianNetwork, String, boolean, CodeOptionValue, PrintStream) - Method in class ModelCoder
 
token - Variable in class HuginLogReader
 
token - Variable in class HuginReader
 
token - Variable in class NeticaReader
 
Token - Class in edu.ucla.belief.io
Describes the input token stream.
Token() - Constructor for class Token
 
token_source - Variable in class HuginLogReader
 
token_source - Variable in class HuginReader
 
token_source - Variable in class NeticaReader
 
tokenImage - Static variable in interface HuginLogReaderConstants
 
tokenImage - Static variable in interface HuginReaderConstants
 
tokenImage - Static variable in interface NeticaReaderConstants
 
tokenImage - Variable in exception ParseException
This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.
TokenMgrError - Error in edu.ucla.belief.io
 
TokenMgrError() - Constructor for error TokenMgrError
 
TokenMgrError(String, int) - Constructor for error TokenMgrError
 
TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error TokenMgrError
 
toList(int[]) - Static method in class ListConverter
 
toList(double[]) - Static method in class ListConverter
 
toMap(List) - Static method in class Maps
 
toOriginal(IntMap) - Method in class Factorizer
 
TOPDOWNBOTTUMUP - Static variable in class MessagePassingScheduler
 
topologicalOrder() - Method in class BeliefNetworkImpl
 
topologicalOrder() - Method in class AbstractDirectedGraph
 
topologicalOrder() - Method in interface DirectedGraph
 
toRealPr(double) - Method in class RC
 
toRealPr(double[]) - Method in class RC
 
toRealPr(double) - Method in class TableScaled
 
toRealPr(double[]) - Method in class TableScaled
 
toRealPr(double, double) - Static method in class TableScaled
 
toRealPr(double[], double) - Static method in class TableScaled
 
toScaled(double) - Method in class TableScaled
 
toScaled(double[]) - Method in class TableScaled
 
toScaled(double, double) - Static method in class TableScaled
 
toScaled(double[], double) - Static method in class TableScaled
 
toString() - Method in enum EdgeDeletionInferenceEngine.Attribute
 
toString() - Method in enum EdgeDeletionInferenceEngine.CPTPolicy
 
toString() - Method in class Macros.Recoverable
 
toString() - Method in class Macros.Recoverables
 
toString() - Method in class Macros.RecoveryInfo
 
toString() - Method in class BeliefNetworkImpl
 
toString() - Method in class CPTParameter
 
toString(VariableStringifier) - Method in class CPTParameter
 
toString() - Method in enum CrouchingTiger.DynamatorImpl
 
toString() - Method in class DecisionEvent
 
toString() - Method in class DecisionEvent.Type
 
toString() - Method in class DecisionNodeAbstract
 
toString() - Method in class Optimizer.ParameterOptimizationLevel
 
toString() - Method in class ParameterImpl
 
toString() - Method in class Stats
 
toString() - Method in class CreationMethod
 
toString() - Method in class Dtree
 
toString() - Method in class DtreeNodeInternal
 
toString() - Method in class DtreeNodeLeaf
 
toString() - Method in class Stats
 
toString() - Method in class EvidenceChangeEvent
 
toString() - Method in class FiniteVariableImpl
 
toString() - Method in class SynchronizedInferenceEngine
 
toString() - Method in class CPTImportColumnInfo
 
toString() - Method in class DiagnosisType
Call this method to get the standardized string representation of a DiagnosisType.
toString() - Method in class DSLNodeImpl
 
toString() - Method in class DSLNodeType
Call this method to get the standardized string representation of a DSLNodeType.
toString() - Method in class DSLSubmodel
 
toString() - Method in class GenieNetImpl
 
toString() - Method in class FileType
 
toString() - Method in class Loci.Footer.BinaryILink
 
toString() - Method in class Loci.Footer.GH
 
toString() - Method in class Loci.Footer.Linkmap
 
toString() - Method in class Loci.Footer.Mlink
 
toString() - Method in class Loci.Footer
 
toString() - Method in class Loci.Header
 
toString() - Method in class Loci.Locus
 
toString() - Method in class Loci.LocusData
 
toString() - Method in class Loci.LocusDataAffectionStatus
 
toString() - Method in class Loci.LocusDataComplexAffection1
 
toString() - Method in class Loci.LocusDataComplexAffection2
 
toString() - Method in class Loci.LocusDataNumberedAlleles
 
toString() - Method in class Loci
 
toString() - Method in class NuclearFamily
 
toString() - Method in class Pedigree
 
toString() - Method in class Person
 
toString() - Method in class HuginFileVersion
Call this method to get the standardized string representation of a HuginFileVersion.
toString() - Method in class HuginNetImpl
 
toString() - Method in class HuginNodeImpl
 
toString() - Method in class HuginPotential
 
toString() - Method in class Token
Returns the image.
toString() - Method in class XmlbifParser.Variable
 
toString() - Method in class LearningData.Struct
 
toString() - Method in class RC2CachingScheme_Collection
 
toString() - Method in class RC2CachingScheme_DFBnB
 
toString() - Method in class RC2CachingScheme_Full
 
toString() - Method in class RC2CachingScheme_Greedy
 
toString() - Method in class RC2CachingScheme_None
 
toString() - Method in interface RC2.CachingScheme
 
toString() - Method in class RC2.ComputationStats
 
toString(String) - Method in class RC2.ComputationStats
 
toString() - Method in class RC2.StoredComputationStats
 
toString() - Method in class RC2Node
 
toString() - Method in class RC2NodeInternal
 
toString() - Method in class RC2NodeLeaf
 
toString() - Method in class RC2NodeLeafEvidInd
 
toString() - Method in class RC2Utils.MiscStats
 
toString() - Method in class RC_Link.RC_Results
 
toString() - Method in class RCGenerator.EO
 
toString() - Method in class CachingDFBnB.CacheFactorInstance
 
toString() - Method in class CachingDFBnB.ChildExpansion
 
toString() - Method in class CachingDFBnB.HeurFunct
 
toString() - Method in class CachingDFBnB.HeurResult
 
toString() - Method in class CachingDFBnB.OrderingAlgo
 
toString() - Method in class CachingDFBnB
 
toString() - Method in class CachingFull
 
toString() - Method in class CachingGreedy
 
toString() - Method in class CachingNone
 
toString() - Method in class CachingNonOptimalSize
 
toString() - Method in class CachingScheme
 
toString() - Method in class CachingUniform
 
toString() - Method in class FileInfo
 
toString() - Method in class RC.RCCounters
 
toString(boolean) - Method in class RC.RCCounters
 
toString() - Method in class RCComparator
 
toString() - Method in class RCNode
 
toString(List) - Static method in class Xmlizer
 
toString() - Method in class ExcludePolicy
 
toString() - Method in class SensitivityConstraint
 
toString() - Method in class SensitivityEquation
 
toString() - Method in class SensitivityTable
Copied and slightly modified from Table.java
toString() - Method in class SingleParamSuggestion
 
toString(VariableStringifier, NumberFormat) - Method in class SingleParamSuggestion
 
toString() - Method in class Table
 
toString() - Method in class VariableInstance
 
toString() - Method in class Edge
 
toString(DirectedGraph) - Static method in class Graphs
 
toString() - Method in class HashDirectedGraph
 
toString() - Method in class Heap.HeapElement
 
toString() - Method in class MappedList
 
toString() - Method in class SetOperation
 
toString() - Method in class AbstractEnumProperty
 
toString() - Method in class CodeOptionValue
 
toString() - Method in class JDKToolScript
 
toString() - Method in interface EnumValue
 
toString() - Method in class FlagProperty.FlagValue
 
toString() - Method in class Interval
 
toString(NumberFormat) - Method in class Interval
 
toString() - Method in class LinearFunction
 
toString() - Method in class NamedObject
 
toString() - Method in class UserEnumValue
 
toString() - Method in enum EDAlgorithm.RankingHeuristic
 
toString() - Method in class MapInitializer.MapResult
 
toString() - Method in class MapSearch.MapResult
 
toString() - Method in class IntPriorityQueue
 
toString() - Method in class Table
 
toString(int[]) - Static method in class ArrayUtils
Returns a string representation of the given array.
toString(double[]) - Static method in class ArrayUtils
Returns a string representation of the given array.
toString() - Method in class DoubleList
 
toString() - Method in class DoubleMap
 
toString() - Method in class Instantiation
 
toString() - Method in class IntList
 
toString() - Method in class IntMap
 
toString() - Method in class IntSet
 
toString() - Method in class MPE
 
toString_all() - Method in class RC2.ComputationStats
 
toString_pe() - Method in class RC2.ComputationStats
 
toStringFull() - Method in class Stats
 
toStringGrouped(BigInteger) - Static method in class JoinTreeStats
 
toStringGrouped(BigInteger, char, int, int) - Static method in class JoinTreeStats
 
toStrings(IntMap) - Method in class Domain
 
toStringShort() - Method in class RC.RCCounters
 
toTable(BeliefNetwork) - Method in class XmlbifParser.Definition
 
total - Variable in class Stats.Stat
 
total(Collection) - Method in class Stats
 
totalCalls() - Method in class RC.RCCounters
 
totalCallsPlusLkAhd() - Method in class RC.RCCounters
 
totalStateSpace() - Method in class RC2Index
 
totalStateSpaceLargerThanInt() - Method in class RC2Index
 
touch() - Method in class NodeLinearTask
The computation code should call this every time it processes a node, thus updating the overall progress.
traditionalJoinTree(BeliefNetwork, int, Random) - Static method in class Trees
 
traditionalJoinTree(BeliefNetwork, List) - Static method in class Trees
Generates a traditional JoinTree using the method described in [1].
traditionalJoinTree(Graph, List, CostFunction) - Static method in class Trees
Warning: It is safe to use this method only in the absence of a BeliefNetwork.
traditionalJoinTree(Collection) - Static method in class EliminationOrders
This method is safe to use only in the absence of a BayesianNetwork object.
traditionalJoinTree(Collection, IntList) - Static method in class EliminationOrders
This method is safe to use only in the absence of a BayesianNetwork object.
traditionalJoinTree(Collection, IntList, Converter, BayesianNetwork) - Static method in class EliminationOrders
This method produces a jointree using max-spanning tree on a clique graph.
traditionalJoinTree(BayesianNetwork, Converter, IntList) - Static method in class EliminationOrders
 
translate(Point, int, int, boolean) - Static method in class Macros
 
translateToIdentifier(String) - Static method in class XmlbifParser
 
tree - Variable in class DecisionEvent
 
tree() - Method in class AbstractEliminationTreeGenerator
 
tree() - Method in class JoinTree
 
Tree - Interface in edu.ucla.util.code
 
tree - Variable in class EliminationOrders.JT
 
tree() - Method in class JoinTree
 
treeLeaves() - Method in class Graph
 
Trees - Class in edu.ucla.belief.tree
A collection of static routines for creation and conversion of the various structured tree representations.
TreeSchedule - Class in il2.inf.bp.schedules
 
TreeSchedule(Table[], int[][]) - Constructor for class TreeSchedule
 
TRIAGULATE_LIT1 - Static variable in interface HuginLogReaderConstants
 
TRIAGULATE_LIT2 - Static variable in interface HuginLogReaderConstants
 
TRIAGULATE_LIT3 - Static variable in interface HuginLogReaderConstants
 
TRIAGULATE_LIT4 - Static variable in interface HuginLogReaderConstants
 
TRIANGULATE_LIT5 - Static variable in interface HuginLogReaderConstants
 
TRIANGULATE_LIT6 - Static variable in interface HuginLogReaderConstants
 
TRIANGULATE_LIT7 - Static variable in interface HuginLogReaderConstants
 
TRIANGULATE_LIT8 - Static variable in interface HuginLogReaderConstants
 
triangulateBlock() - Method in class HuginLogReader
 
trivialDecomposition(ProgressMonitorable) - Static method in class CompoundTask
 
TRUE - Variable in class FlagProperty
 
TRUTHTABLE - Static variable in class DSLNodeType
 
tsScore() - Method in class EOGenerator.EO
 
type - Variable in class DecisionEvent
 
type - Variable in class XmlbifParser.Variable
 
type(int) - Method in class EliminationTree
 

U

u2id - Variable in class Macros.Bridge
 
UAI06_ANON - Static variable in class UAI06Parser
 
UAI06_FOR - Static variable in class UAI06Parser
 
UAI06_GIVE - Static variable in class UAI06Parser
 
UAI06_NAME - Static variable in class UAI06Parser
 
UAI06_OBSE - Static variable in class UAI06Parser
 
UAI06_OUTC - Static variable in class UAI06Parser
 
UAI06_PROB - Static variable in class UAI06Parser
 
UAI06_ROOT - Static variable in class UAI06Parser
 
UAI06_TABL - Static variable in class UAI06Parser
 
UAI06_TYPE - Static variable in class UAI06Parser
 
UAI06_VAR - Static variable in class UAI06Parser
 
UAI06Parser - Class in edu.ucla.belief.io.xmlbif
This class is intentionally stripped down, with the hope of achieving the fastest possible performance on the UAI '06 input files.
UAI06Parser() - Constructor for class UAI06Parser
 
UaiEdgeCutter - Class in edu.ucla.belief.uai2006
 
UaiEdgeCutter() - Constructor for class UaiEdgeCutter
 
UaiEdgeCutter.BpInstanceComparator - Class in edu.ucla.belief.uai2006
 
UaiEdgeCutter.BpInstanceComparator(FiniteVariable, Table) - Constructor for class UaiEdgeCutter.BpInstanceComparator
 
UaiEdgeCutter.BpVarComparator - Class in edu.ucla.belief.uai2006
 
UaiEdgeCutter.BpVarComparator(PropagationInferenceEngineImpl) - Constructor for class UaiEdgeCutter.BpVarComparator
 
UaiEdgeCutter.MyIndex - Class in edu.ucla.belief.uai2006
 
UaiEdgeCutter.MyIndex(Domain, IntSet, Collection) - Constructor for class UaiEdgeCutter.MyIndex
 
UaiEdgeCutter.MyRecord - Class in edu.ucla.belief.uai2006
 
UaiEdgeCutter.MyRecord(IntList, double, IntSet[], Bucketer) - Constructor for class UaiEdgeCutter.MyRecord
 
UaiMain - Class in edu.ucla.belief.uai2006
UAI-06 Evaluation : Main Program todo: load evidence todo: load MAP variables
UaiMain(String[]) - Constructor for class UaiMain
 
UaiMain(String) - Constructor for class UaiMain
 
UaiMapEngine - Interface in edu.ucla.belief.uai2006
An interface for an algorithm that computes MAP for the 2006 UAI evaluation.
UaiMapSolution - Class in edu.ucla.belief.uai2006
A solution for a problem.
UaiMapSolution() - Constructor for class UaiMapSolution
The constructor, which sets instantiation, probability, and info to null and log_probability to Double.NaN.
UaiMpeEngine - Interface in edu.ucla.belief.uai2006
An interface for an algorithm that computes MPE for the 2006 UAI evaluation.
UaiMpeMain - Class in edu.ucla.belief.uai2006
UAI-06 Evaluation : MAP Main Program
UaiMpeMain(String[]) - Constructor for class UaiMpeMain
 
UaiMpeMain(String) - Constructor for class UaiMpeMain
 
UaiPeEngine - Interface in edu.ucla.belief.uai2006
An interface for an algorithm that computes P(e) for the 2006 UAI evaluation.
UaiPeMain - Class in edu.ucla.belief.uai2006
UAI-06 Evaluation : MAP Main Program
UaiPeMain(String[]) - Constructor for class UaiPeMain
 
UaiPeMain(String) - Constructor for class UaiPeMain
 
UaiPreprocessResult - Class in edu.ucla.belief.uai2006
The result of preprocessing a network.
UaiPreprocessResult() - Constructor for class UaiPreprocessResult
 
UaiUnderflowException - Exception in edu.ucla.belief.uai2006
An exception thrown by Mark's RC, cought by UaiPeMain to run David's RC.
UaiUnderflowException() - Constructor for exception UaiUnderflowException
 
UaiUtilsIf - Interface in edu.ucla.belief.uai2006
Utilities to make avaiable to the uai main program.
ultimately() - Method in class RepetitionThread
 
ultimately() - Method in class SystemGCThread
 
UNBALANCED - Static variable in class MethodHuginLog
 
UNDEF - Static variable in interface NeticaReaderConstants
 
UNDEFINED - Static variable in class InOutDegreeProperty
 
UNDEFINED_NODE_TYPE - Static variable in class SMILEReader
 
underlyingCompilation() - Method in class JoinTreeInferenceEngineImpl
 
underlyingCompilation() - Method in class RCInferenceEngine
 
undirect(DirectedGraph) - Static method in class Graphs
 
undo() - Method in class SingleParamSuggestion
 
undo_decide() - Method in class KB_SAT
 
UnindexedHuginAlgorithm - Class in il2.inf.jointree
 
UnindexedSSAlgorithm - Class in il2.inf.jointree
 
UnindexedZCAlgorithm - Class in il2.inf.jointree
 
UnindexedZCAlgorithm(EliminationOrders.JT, Table[]) - Constructor for class UnindexedZCAlgorithm
 
UNION - Static variable in class SetOperation
 
union(int, int) - Method in class UnionFind
Merges the sets that the parameters belong to.
union(IntSet) - Method in class IntSet
 
UNION_SIZE_COST - Static variable in class Trees
A cost function which is the size of the union of the variables in the cluster.
UnionFind - Class in edu.ucla.structure
Implements a union find set.
UnionFind(int) - Constructor for class UnionFind
Creates a union find set of the specified size.
unique - Variable in class Macros.Recoverable
 
unit - Variable in class BeliefNetwork.Auditor.Deed
 
unitTests(boolean) - Static method in class Macros
 
unitTests(PrintStream, boolean, int, HuginNet, FiniteVariable, FiniteVariable, FiniteVariable, FiniteVariable, FiniteVariable, FiniteVariable) - Static method in class Macros
 
UNKNOWN - Variable in class CSITypeProperty
 
unobserve(FiniteVariable) - Method in class EvidenceController
Sets the state of the variable to unobserved.
unobserve(FiniteVariable) - Method in class RC2
 
unobserve(int) - Method in class RC2NodeLeaf
 
unobserve(int) - Method in class RC2NodeLeafEvidInd
 
unobserve(FiniteVariable) - Method in class RC
 
unobserveAll() - Method in class RC2NodeLeaf
 
unobserveAll() - Method in class RC2NodeLeafEvidInd
 
unobserveNotifyOnlyPriorityListeners(FiniteVariable) - Method in class EvidenceController
 
unpopulate() - Method in class Dtree
 
unsatisfiable() - Method in class MultiValuedCNF
 
UNSPECIFIED - Static variable in class HuginFileVersion
 
UPair - Class in il2.util
A sorted pair of ints.
UPair(Pair) - Constructor for class UPair
Initializes the upair from another upair.
UPair(Integer, Integer) - Constructor for class UPair
Initializes the upair; sorts the ints before storing them.
UPair(int, int) - Constructor for class UPair
Initializes the upair; sorts the ints before storing them.
update(Dtree) - Method in class Stats
 
update(int[][], int[], int, boolean[], boolean[][]) - Static method in class Util
Removes edges in one direction from each one-hop neighbor to the given node.
updateCosts(int[][], int[], int, boolean[], boolean[][], IntPriorityQueue) - Method in class MinfillEoe
 
updateElapsedTimeDisplay(double) - Method in class Computation
 
updateElapsedTimeDisplay(double) - Method in class Settings
 
updateEstimatedMillisDisplay(double) - Method in class RCSettings
 
updateEstimatedMinutesDisplay() - Method in class RCSettings
 
updateEstimatedMinutesDisplay(int, int, int) - Method in class RCSettings
 
updateEstimatedMinutesDisplay() - Method in class Computation
 
updateEstimatedTimeDisplay(double) - Method in class RCSettings
 
updateOptimalMemoryDisplay() - Method in class RCSettings
 
updateOptimalMemoryDisplay(Computation) - Method in class Settings
 
updatePriorities(Map) - Method in class MappedHeap
 
updatePriority(Object, Object) - Method in class MappedHeap
 
updateSMILE(File, FileType, File, FileType, GenieNet) - Method in class SMILEReader
 
updateSMILE(File, FileType, File, FileType, GenieNet, Collection) - Method in class SMILEReader
 
updateUserMemoryDisplay() - Method in class RCSettings
 
updateUserMemoryDisplay(double) - Method in class RCSettings
 
updateUserMemoryDisplay(Computation) - Method in class Settings
 
updateUserMemoryDisplay(Computation, double) - Method in class Settings
 
USE_CachingGreedy_As_Seed - Variable in class CachingDFBnB
 
USE_CachingNonOptimalSize_As_Seed - Variable in class CachingDFBnB
 
USE_INCORRECT_worthless_test - Static variable in class CachingDFBnB
 
useKB - Variable in class RC.RCCreationParams
 
useKB() - Method in class RC
 
useKBflag() - Method in class RC
 
useKBinst - Variable in class RC2.RCCreationParams
 
userDefinedInt - Variable in class RCNode
Used by DFBnB during allocate memory and by DecompositionStructureUtils during RC object creation.
UserEnumProperty - Class in edu.ucla.util
 
UserEnumProperty() - Constructor for class UserEnumProperty
 
UserEnumProperty(UserEnumProperty) - Constructor for class UserEnumProperty
 
UserEnumValue - Class in edu.ucla.util
 
UserEnumValue(Object, EnumProperty) - Constructor for class UserEnumValue
 
UserEnumValue(EnumValue) - Constructor for class UserEnumValue
 
userMemory - Variable in class FileInfo
 
userobject - Variable in class BeliefNetworkImpl
 
userobject - Variable in class DSLSubmodel
 
userobject - Variable in class VariableImpl
 
UserObject - Interface in edu.ucla.util
 
userobject2 - Variable in class BeliefNetworkImpl
 
usingEClauses() - Method in class MultiValuedCNF
 
Util - Class in il2.inf.structure.minfill2
Static utility routines.
Util() - Constructor for class Util
 
UtilGeneReader - Class in edu.ucla.belief.io.geneticlinkage
 
UTILITY - Static variable in interface HuginReaderConstants
 

V

v1() - Method in class Edge
 
v2() - Method in class Edge
 
V57 - Static variable in class HuginFileVersion
 
V61 - Static variable in class HuginFileVersion
 
VALID_NET - Static variable in class Pedigree
 
validateAllocation(BeliefNetwork) - Method in class RCSettings
 
validateDtree(BeliefNetwork) - Method in class Settings
 
validateExtension(File) - Method in class InflibFileFilter
 
validateHeapProperty() - Method in class PriorityQueue
Throws an exception if the heap property is not satisfied.
validatePropertyNameAndID(Object, Object) - Static method in class VariableImpl
 
validateRC(BeliefNetwork) - Method in class RCSettings
 
validateRC(BeliefNetwork) - Method in class Settings
 
VALSTRING - Static variable in interface HuginReaderConstants
 
value - Variable in class Optimizer.Unsortable
 
VALUE - Static variable in interface ArithmeticExpression
 
value - Variable in class CPTInfo.Parameter
 
value(boolean) - Method in class HuginReader
 
value() - Method in class NeticaReader
 
value - Variable in exception StateNotFoundException
 
value(int[]) - Method in class Table
Returns the value of the table entry referenced by ind.
value(Object[]) - Method in class Table
 
VALUE - Static variable in class EliminationTree
 
value(Algorithm.Setting, Map<Algorithm.Setting, ?>) - Static method in enum Algorithm.Setting
 
value() - Method in class RC
 
value(int) - Method in class IntMap
 
VALUE_PERMISSIVE - Static variable in interface PropertySuperintendent
 
VALUE_STRICT - Static variable in interface PropertySuperintendent
 
VALUE_TRUE - Static variable in interface PropertySuperintendent
 
valueChanged(int) - Method in class MiniTree
 
valueCPT - Static variable in class DSLConstants
 
valueElimination() - Method in class Table
For any variable=state, if all possible combinations of other variables have prob=0, then this state can be removed.
valueElimination() - Method in class TableShell
 
valueFALSE - Static variable in class DSLConstants
 
valueFor(Variable, BeliefNetwork) - Static method in class CSITypeProperty
 
valueFor(Variable, EvidenceController) - Static method in class EvidenceAssertedProperty
 
valueFor(Variable, BeliefNetwork) - Static method in class InOutDegreeProperty
 
valueList() - Method in class HuginReader
 
valueNOISY_OR - Static variable in class DSLConstants
 
valueOf(String) - Static method in enum EdgeDeletionBeliefPropagationSetting
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum EdgeDeletionInferenceEngine.Attribute
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum EdgeDeletionInferenceEngine.Command
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum EdgeDeletionInferenceEngine.CPTPolicy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum Macros.Category
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum Macros.Doubler
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum RecoverySetting
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum CrouchingTiger.DynamatorImpl
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum XmlbifParser.VariableType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum XmlbifWriter.Element
Returns the enum constant of this type with the specified name.
valueOf(boolean) - Method in class CSITypeProperty
 
valueOf(boolean) - Method in interface EnumProperty
 
valueOf(boolean) - Method in class FlagProperty
 
valueOf(boolean) - Method in class InOutDegreeProperty
 
valueOf(String) - Static method in enum PropertyKey
Returns the enum constant of this type with the specified name.
valueOf(boolean) - Method in class UserEnumProperty
 
valueOf(String) - Static method in enum Algorithm.EliminationOrderHeuristic
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum Algorithm.Key
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum Algorithm.Order2JoinTree
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum Algorithm.Query
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum Algorithm.Result
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum Algorithm.Setting
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum Algorithm
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum EDAlgorithm.RankingHeuristic
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum Flavor
Returns the enum constant of this type with the specified name.
values() - Static method in enum EdgeDeletionBeliefPropagationSetting
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum EdgeDeletionInferenceEngine.Attribute
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum EdgeDeletionInferenceEngine.Command
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum EdgeDeletionInferenceEngine.CPTPolicy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum Macros.Category
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum Macros.Doubler
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum RecoverySetting
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum CrouchingTiger.DynamatorImpl
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class HuginPotential
 
values() - Static method in enum XmlbifParser.VariableType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum XmlbifWriter.Element
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class LearningData
 
values() - Static method in class ExcludePolicy
 
values() - Method in class IdentityArrayMap
 
values() - Static method in enum PropertyKey
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum Algorithm.EliminationOrderHeuristic
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum Algorithm.Key
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum Algorithm.Order2JoinTree
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum Algorithm.Query
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum Algorithm.Result
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum Algorithm.Setting
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum Algorithm
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum EDAlgorithm.RankingHeuristic
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum Flavor
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class Table
 
values() - Method in class DoubleMap
 
values() - Method in class IntMap
 
valuesAsArray() - Static method in class DiagnosisType
 
valuesAsArray() - Static method in class DSLNodeType
 
valuesAsArray() - Static method in class HuginFileVersion
 
valuesAsArray() - Method in class CSITypeProperty
 
valuesAsArray() - Method in interface EnumProperty
 
valuesAsArray() - Method in class FlagProperty
 
valuesAsArray() - Method in class InOutDegreeProperty
 
valuesAsArray() - Method in class UserEnumProperty
 
valuesToString() - Method in class LearningData
 
valuesToString(Map) - Method in class LearningDataOld
 
valueTRUE - Static variable in class DSLConstants
 
valueTRUTHTABLE - Static variable in class DSLConstants
 
valueUpdated(int) - Method in class IndexedHeap
 
var - Variable in exception StateNotFoundException
 
varConditional(FiniteVariable) - Method in class Macros.Bridge
 
varConditional(int) - Method in class BeliefPropagation
 
varConditional(int) - Method in class MaxProduct
 
varConditional(int) - Method in class EDAlgorithm
 
varConditional(int) - Method in interface JointEngine
 
varConditional(int) - Method in class JoinTreeAlgorithm
 
varConditional(int) - Method in class RCEngine
 
variable(int) - Method in class TableIndex
returns the variable index of the specified dimesion.
Variable - Interface in edu.ucla.belief
Define variables.
VARIABLE_ID - Static variable in class AbstractStringifier
 
VARIABLE_LABEL - Static variable in class AbstractStringifier
 
VariableComparator - Class in edu.ucla.belief
 
VariableImpl - Class in edu.ucla.belief
 
VariableImpl(String) - Constructor for class VariableImpl
 
VariableImpl(Variable) - Constructor for class VariableImpl
 
variableIndex(FiniteVariable) - Method in class TableIndex
Returns the position of the variable in the array.
VariableInstance - Class in edu.ucla.belief
 
VariableInstance(FiniteVariable, Object) - Constructor for class VariableInstance
 
VariableInstance(FiniteVariable, int) - Constructor for class VariableInstance
 
variables() - Method in class EdgeDeletionInferenceEngine
 
variables - Variable in class Macros.Bridge
 
variables() - Method in class Macros.Bridge
 
variables(Object) - Static method in class Macros
suppress unchecked caste warning
variables() - Method in class PropagationInferenceEngineImpl
 
variables() - Method in class RecoveryInferenceEngine
 
variables() - Method in interface CPTShell
 
variables() - Method in class DecisionShell
 
variables() - Method in class BeliefCompilation
 
variables() - Method in class JoinTreeInferenceEngineImpl
Returns the set of all of the variables.
variables() - Method in class RandomInferenceEngine
 
variables() - Method in class SynchronizedInferenceEngine
 
variables() - Method in class WrapperInferenceEngine
Returns the set of all of the variables.
variables() - Method in interface InferenceEngine
Returns the set of all of the variables.
variables() - Method in class LearningData
Returns the set of variables.
variables() - Method in class LearningDataOld
Returns the set of variables.
variables() - Method in class NoisyOrShellHenrion
 
variables() - Method in class NoisyOrShellPearl
 
variables() - Method in interface Potential
 
variables() - Method in class RCInferenceEngine
Returns the set of all of the variables.
variables() - Method in class Table
Returns the variables that this Table contains.
variables() - Method in class TableIndex
 
variables() - Method in class TableShell
 
variables2ids - Variable in class Macros.Bridge
 
variablesOk(IntSet, int) - Method in class VEVariance
 
VariableStringifier - Interface in edu.ucla.util
 
variableToString(Variable) - Method in class AbstractStringifier
 
variableToString(Variable) - Method in interface VariableStringifier
 
varianceTables(HashSet<Table>, int) - Method in class VEVariance
 
varJoint(FiniteVariable) - Method in class JointWrapper
 
varJoint(int) - Method in class BeliefPropagation
 
varJoint(int) - Method in class MaxProduct
 
varJoint(int) - Method in interface JointEngine
 
varJoint(int) - Method in class JoinTreeAlgorithm
 
varJoint(int) - Method in class RCEngine
 
varMPETable(Domain, int) - Static method in class MPETable
 
varOfPair(Pair) - Method in class MessagePassingScheduler
 
varPartial(FiniteVariable) - Method in class PartialDerivativeWrapper
 
varPartial(int) - Method in class AbstractSSAlgorithm
 
varPartial(int) - Method in class AbstractZCAlgorithm
 
varPartial(int) - Method in class NormalizedMaxSSAlgorithm
 
varPartial(int) - Method in class UnindexedSSAlgorithm
 
varPartial(int) - Method in interface PartialDerivativeEngine
 
varPartial(int) - Method in class RCEngine
 
vars() - Method in class RC2
 
vars - Variable in class RC2Index
 
vars - Variable in class RC2Node
 
vars - Variable in class RC
 
vars() - Method in class RCNode
 
vars(Collection) - Method in class RCNode
 
vars() - Method in class RCNodeInternalBinaryCache
 
vars(Collection) - Method in class RCNodeInternalBinaryCache
 
vars() - Method in class RCNodeLeaf
 
vars(Collection) - Method in class RCNodeLeaf
 
vars() - Method in class Index
 
vars() - Method in interface SubDomain
 
varStatus(int) - Method in class KB_SAT
 
varString() - Method in class Index
 
varTable(Domain, int) - Static method in class Table
 
varToRoot() - Method in class RC
 
varToRoot() - Method in class RCDgraph
 
varToRootIndx - Variable in class RC2CreatorDtToDg.ReducedRootSet
 
ve(HashSet<Table>, IntList) - Method in class VEVariance
 
ve_d(BayesianNetwork, IntMap, int) - Method in class VEVariance
 
ve_var(BayesianNetwork, IntMap, IntSet, int) - Method in class VEVariance
 
verb - Variable in class BeliefNetwork.Auditor.Intention
 
verbose - Static variable in class UaiEdgeCutter
 
verbose - Static variable in class UaiMain
 
verbose() - Method in class Interruptable
Override this to return true to print debug messages.
verboseEngine - Static variable in class UaiMain
 
verboseEnginePrintln(String) - Static method in class UaiMain
 
verbosePrint(String) - Static method in class UaiEdgeCutter
 
verbosePrint(String) - Static method in class UaiMain
Helper methods
verbosePrintln(String) - Static method in class UaiEdgeCutter
 
verbosePrintln(String) - Static method in class UaiMain
 
versionSupported(String) - Method in class UAI06Parser
 
versionSupported(String) - Method in class XmlbifParser
 
verter - Variable in class Macros.Bridge
 
vertices() - Method in class BeliefNetworkImpl
 
vertices() - Method in class AbstractDirectedGraph
 
vertices() - Method in interface DirectedGraph
Constructs an Iterator over all vertices.
vertices() - Method in interface Graph
Return the set of verticies.
vertices() - Method in class HashGraph
Construct an Iterator over all vertices.
vertices() - Method in class Graph
 
vetoInterruption(Interruptable) - Method in interface Interruptable.Veto
Decide whether or not to veto the interruption.
VEVariance - Class in il2.inf.experimental
 
VEVariance(BayesianNetwork, IntMap) - Constructor for class VEVariance
 
VEVariance(BayesianNetwork, IntMap, PrintWriter) - Constructor for class VEVariance
 

W

warning(EvidenceChangeEvent) - Method in class EdgeDeletionInferenceEngine
interface EvidenceChangeListener
warning(EvidenceChangeEvent) - Method in class Macros.Bridge
interface EvidenceChangeListener
warning(EvidenceChangeEvent) - Method in class PropagationInferenceEngineImpl
interface EvidenceChangeListener
warning(EvidenceChangeEvent) - Method in class RecoveryInferenceEngine
interface EvidenceChangeListener
warning(EvidenceChangeEvent) - Method in interface EvidenceChangeListener
warning() means: a real evidence change is about to happen - get ready!
warning(EvidenceChangeEvent) - Method in class JoinTreeInferenceEngineImpl
For interface EvidenceChangeListener
warning(EvidenceChangeEvent) - Method in class RandomInferenceEngine
 
warning(EvidenceChangeEvent) - Method in class SynchronizedInferenceEngine
 
warning(EvidenceChangeEvent) - Method in class WrapperInferenceEngine
For interface EvidenceChangeListener
warning(EvidenceChangeEvent) - Method in class RCInferenceEngine
For interface EvidenceChangeListener
WeakLinkedList - Class in edu.ucla.util
Linked list implementation, based on Sun's java.util.LinkedList, that refers to its contents only weakly.
WeakLinkedList() - Constructor for class WeakLinkedList
Constructs an empty list.
WeakLinkedList(Collection) - Constructor for class WeakLinkedList
Constructs a list containing the elements of the specified collection, in the order they are returned by the collection's iterator.
weakMAP(Collection, IntSet, int) - Static method in class BasicInference
 
weakMAP(Collection, IntSet, IntList) - Static method in class BasicInference
 
weight - Variable in class StandardNodeImpl.Struct
 
weight - Variable in class LearningData.Struct
 
weight() - Method in class WeightedTask
 
WeightedTask - Class in edu.ucla.util
Wrap a monitorable task such that the reported progress is multiplied by a weight factor.
WeightedTask(ProgressMonitorable, float) - Constructor for class WeightedTask
 
weightedwidth(DirectedGraph, List) - Static method in class Graphs
Returns the weighted width of the graph using the elimination order specified (as specified in Darwiche & Hopkins 2001).
weightedwidth(Graph, List) - Static method in class Graphs
Returns the weighted width of the graph using the elimination order specified (as specified in Darwiche & Hopkins 2001).
weightsAsList() - Method in interface NoisyOrShell
 
weightsAsList() - Method in class NoisyOrShellHenrion
 
weightsAsList() - Method in class NoisyOrShellPearl
 
weightsClone() - Method in interface NoisyOrShell
 
weightsClone() - Method in class NoisyOrShellHenrion
 
weightsClone() - Method in class NoisyOrShellPearl
 
width() - Method in class EOGenerator.EO
 
width() - Method in class RCGenerator.EO
 
width(DirectedGraph, List) - Static method in class Graphs
Returns the width of the graph using the elimination order specified.
width(Graph, List) - Static method in class Graphs
Returns the width of the graph using the elimination order specified.
width(DirectedGraph, List, DoubleFunction) - Static method in class Graphs
 
width(Graph, List, DoubleFunction) - Static method in class Graphs
 
withoutIndex(int) - Method in class IntList
 
withoutIndex(int) - Method in class IntSet
 
worthlessCaches() - Method in class CachingDFBnB.SearchGraph
 
WrapperInferenceEngine - Class in edu.ucla.belief.inference
 
write(String) - Method in class XmlWriter.PrintStreamWriter
 
write(String) - Method in class XmlWriter.PrintWriterWriter
 
write(String) - Method in interface XmlWriter.UniWriter
 
write(DecisionTree, PrintStream) - Static method in class XmlWriter
 
write(DecisionTree, PrintWriter) - Static method in class XmlWriter
 
write(File) - Method in class Dtree
 
write(Writer) - Method in class Dtree
 
write(Writer, CharArrayWriter) - Method in class Dtree
 
write(PrintWriter) - Method in class RCInfo
 
write(BeliefNetwork, PrintStream) - Method in interface RunWriteBIF.BeliefNetworkWriter
 
write(String, PrintStream) - Method in enum XmlbifWriter.Element
 
write(BeliefNetwork, PrintStream) - Method in class XmlbifWriter
 
write(PrintStream) - Method in class KnowledgeBase
 
write(PrintStream) - Method in class KnowledgeBaseImpl
 
write(ScriptGenius, SystemSoftwareSource, PrintStream) - Method in class JDKToolScript
 
write(ScriptGenius, SystemSoftwareSource, File) - Method in class JDKToolScript
 
write(ScriptGenius, SystemSoftwareSource, PrintStream) - Method in interface Script
 
write(ScriptGenius, SystemSoftwareSource, File) - Method in interface Script
 
write(PrintWriter, Set, Converter) - Method in class DGraph
 
writeApproximationQuery(boolean, PrintStream) - Method in class MAPCoder
 
writeArgValidation(Script, PrintStream) - Method in class AbstractScriptGenius
 
writeArgValidation(Script, PrintStream) - Method in class BatchScriptGenius
 
writeArgValidation(Script, PrintStream) - Method in class BourneScriptGenius
 
writeArgValidation(Script, PrintStream) - Method in class CShellScriptGenius
 
writeArgValidation(Script, PrintStream) - Method in class PerlScriptGenius
 
writeArgValidation(Script, PrintStream) - Method in interface ScriptGenius
 
writeCode(PrintStream) - Method in interface CodeGenius
 
writeCode(PrintStream) - Method in class CPTCoder
 
writeCode(PrintStream) - Method in class EMCoder
 
writeCode(PrintStream) - Method in class MAPCoder
 
writeCode(PrintStream) - Method in class ModelCoder
 
writeCode(PrintStream) - Method in class MPECoder
 
writeCode(PrintStream) - Method in class ProbabilityQueryCoder
 
writeCode(PrintStream) - Method in class SensitivityCoder
 
writeCode(CodeGenius, String) - Method in class Test
 
writeCommandPost(PrintStream, String) - Method in class AbstractScriptGenius
 
writeCommandPost(PrintStream, String) - Method in class BatchScriptGenius
 
writeCommandPost(PrintStream, String) - Method in interface ScriptGenius
 
writeCommandPrep(PrintStream, String) - Method in class AbstractScriptGenius
 
writeCommandPrep(PrintStream, String) - Method in class BatchScriptGenius
 
writeCommandPrep(PrintStream, String) - Method in class BourneScriptGenius
 
writeCommandPrep(PrintStream, String) - Method in class CShellScriptGenius
 
writeCommandPrep(PrintStream, String) - Method in class PerlScriptGenius
 
writeCommandPrep(PrintStream, String) - Method in interface ScriptGenius
 
writeConstraint(boolean, PrintStream) - Method in class SensitivityCoder
 
writeData(File) - Method in class LearningData
Writes data to a Hugin-style plain text "case" file.
writeData(File) - Method in class LearningDataOld
Writes data to a Hugin-style plain text "case" file.
writeDefinition(Table, PrintStream) - Method in class XmlbifWriter
 
writeDemo(boolean, PrintStream) - Method in class CPTCoder
 
writeDot(DirectedGraph, String, PrintStream) - Method in class GraphvizIO
 
writeDot(DirectedGraph, String, Stringifier, GraphvizIO.ExtraDotInfoSupplier, PrintStream) - Method in class GraphvizIO
 
writeDtreeToVCGFile(File, RC2) - Static method in class RC2Utils
 
writeDynamatorCreation(Dynamator, InferenceEngine, BeliefNetwork, boolean, PrintStream) - Static method in class ProbabilityQueryCoder
 
writeEdges(PrintWriter) - Method in class S4DoubleExpression.CircuitWriter
 
writeEdges(PrintWriter, int, int) - Method in class S4DoubleExpression.CircuitWriter
 
writeEM(boolean, PrintStream) - Method in class EMCoder
 
writeEvidence(Map, boolean, PrintStream) - Static method in class MAPCoder
 
writeEvidenceCases(String, Domain, IntMap[]) - Static method in class IO
 
writeEvidToFile(PrintStream) - Method in class Pedigree.GeneticNetwork
Currently only supports writing positive evidence.
writeEvidToFile_All(PrintStream) - Method in class Pedigree.GeneticNetwork
 
writeExactQuery(boolean, PrintStream) - Method in class MAPCoder
 
writeFile(Writer) - Method in class EOGenerator.RC
 
writeFile(Writer) - Method in class RCGenerator.RC
 
writeFileList(List, File) - Method in class Test
 
writeFileLists() - Method in class Test
 
writeFoundationNetwork(boolean, PrintStream) - Method in class CPTCoder
 
writeHead(PrintStream) - Method in class XmlbifWriter
 
writeHeader(PrintStream) - Method in class AbstractScriptGenius
 
writeHeader(PrintStream) - Method in class BatchScriptGenius
 
writeHeader(PrintStream) - Method in class BourneScriptGenius
 
writeHeader(PrintStream) - Method in class CShellScriptGenius
 
writeHeader(PrintStream) - Method in class PerlScriptGenius
 
writeHeader(PrintStream) - Method in interface ScriptGenius
 
writeInferenceEngineCreation(boolean, PrintStream) - Method in class ProbabilityQueryCoder
 
writeInferenceEngineCreation(Dynamator, InferenceEngine, BeliefNetwork, boolean, PrintStream) - Static method in class ProbabilityQueryCoder
 
writeInferenceImports(boolean, PrintStream) - Method in class EMCoder
 
writeInferenceImports(Dynamator, boolean, PrintStream) - Static method in class ProbabilityQueryCoder
 
writeJavaCodeSettingsManipulation(BeliefNetwork, boolean, PrintStream) - Method in class ApproxEngineGenerator
 
writeJavaCodeSettingsManipulation(BeliefNetwork, boolean, PrintStream) - Method in class PropagationEngineGenerator
 
writeJavaCodeSettingsManipulation(BeliefNetwork, boolean, PrintStream) - Method in class Dynamator
 
writeJavaCodeSettingsManipulation(BeliefNetwork, boolean, PrintStream) - Method in class DefaultGenerator
 
writeJavaCodeSettingsManipulation(BeliefNetwork, boolean, PrintStream) - Method in class RCEngineGenerator
 
writeJavaCodeSettingsManipulation(BeliefNetwork, boolean, PrintStream) - Method in class RCEngineGenerator
 
writeMapEngineQuery(boolean, PrintStream) - Method in class MPECoder
 
writeNetwork(BeliefNetwork, File) - Static method in class NetworkIO
 
writeNetwork(BeliefNetwork, PrintWriter) - Static method in class NetworkIO
Writes out a network in the Hugin file format.
writeNetwork(BeliefNetwork, String) - Static method in class UaiEdgeCutter
 
writeOutcome(Object, Collection, int) - Method in class XmlWriter.GroupedDecisionWriter
 
writeOutcome(Object, Collection, int) - Method in class XmlWriter.GroupedOutcomeWriter
 
writeOutcome(Object, Collection, int) - Method in class XmlWriter.GroupedParameterWriter
 
writeOutcomes(DecisionNode, int) - Method in class XmlWriter.GroupedOutcomeWriter
 
writeOutcomesFlat(DecisionNode, int) - Method in class XmlWriter.GroupedOutcomeWriter
override here
writeOutcomesFlat(DecisionNode, int) - Method in class XmlWriter.GroupedParameterWriter
 
writeOutcomesGrouped(DecisionNode, int) - Method in class XmlWriter.GroupedOutcomeWriter
 
writePost(boolean, CodeOptionValue, PrintStream) - Method in class CPTCoder
 
writePost(boolean, CodeOptionValue, PrintStream) - Method in class EMCoder
 
writePost(boolean, CodeOptionValue, PrintStream) - Method in class MAPCoder
 
writePost(CodeOptionValue, PrintStream) - Method in class ModelCoder
 
writePost(boolean, CodeOptionValue, PrintStream) - Method in class MPECoder
 
writePost(boolean, CodeOptionValue, PrintStream) - Method in class ProbabilityQueryCoder
 
writePost(boolean, CodeOptionValue, PrintStream) - Method in class SensitivityCoder
 
writePre(boolean, CodeOptionValue, PrintStream) - Method in class CPTCoder
 
writePre(boolean, CodeOptionValue, PrintStream) - Method in class EMCoder
 
writePre(boolean, CodeOptionValue, PrintStream) - Method in class MAPCoder
 
writePre(String, boolean, CodeOptionValue, CodeOptionValue, PrintStream) - Method in class ModelCoder
 
writePre(boolean, CodeOptionValue, PrintStream) - Method in class MPECoder
 
writePre(boolean, CodeOptionValue, PrintStream) - Method in class ProbabilityQueryCoder
 
writePre(boolean, CodeOptionValue, PrintStream) - Method in class SensitivityCoder
 
writeQuery(boolean, PrintStream) - Method in class EMCoder
 
writeQuery(boolean, PrintStream) - Method in class MAPCoder
 
writeQuery(boolean, PrintStream) - Method in class MPECoder
 
writeQuery(boolean, PrintStream) - Method in class ProbabilityQueryCoder
 
writeQuery(boolean, PrintStream) - Method in class SensitivityCoder
 
writeRC(RC2, PrintWriter) - Static method in class RC2WriteToFile
 
writeRCToFile(PrintWriter, RC) - Static method in class RCUtilitiesIO
 
writeReadNetworkFile(String, boolean, PrintStream) - Static method in class ProbabilityQueryCoder
 
writeSensitivityRequest(boolean, PrintStream) - Method in class SensitivityCoder
 
writeSetEvidence(boolean, PrintStream) - Static method in class ProbabilityQueryCoder
 
writeSetEvidence(String, boolean, PrintStream) - Static method in class ProbabilityQueryCoder
 
writeSettingsManipulation(Dynamator, BeliefNetwork, boolean, PrintStream) - Static method in class ProbabilityQueryCoder
 
writeTail(PrintStream) - Method in class XmlbifWriter
 
writeTail(Script, PrintStream) - Method in class AbstractScriptGenius
 
writeTail(Script, PrintStream) - Method in class BatchScriptGenius
 
writeTail(Script, PrintStream) - Method in interface ScriptGenius
 
writeToDOTFile(Writer) - Method in class Dtree
Writes this Dtree to a DOT file.
writeToParenFile(Writer) - Method in class DtreeNodeInternal
 
writeToParenFile(Writer) - Method in class DtreeNodeLeaf
 
writeToVCGFile(File) - Method in class BeliefNetworkImpl
 
writeToVCGFile(Writer) - Method in class Dtree
Writes this Dtree to a VCG file.
writeToVCGFileBasic(String, RC) - Static method in class RCUtilitiesIO
 
writeToVCGFileBasic(Writer, RC) - Static method in class RCUtilitiesIO
 
writeToVCGFileDetailed(String, RC) - Static method in class RCUtilitiesIO
 
writeToVCGFileDetailed(Writer, RC) - Static method in class RCUtilitiesIO
 
writeVariable(StandardNode, Object, PrintStream) - Method in class XmlbifWriter
 
writeXML(Document, File) - Static method in class Xmlizer
 

X

x2id - Variable in class Macros.Bridge
 
XDSL - Static variable in class FileType
 
xmlAvailable() - Static method in class NetworkIO
 
XMLBIF_INFLIB - Static variable in class FileType
 
XMLBIF_SMILE - Static variable in class FileType
 
XmlbifParser - Class in edu.ucla.belief.io.xmlbif
xml bif format described
xml schema validation primer
perl script to convert DTD to schema
updated 20060531 for version 0.3a proposed by Jeff Bilmes 20060529
XmlbifParser() - Constructor for class XmlbifParser
 
XmlbifParser.BifNode - Class in edu.ucla.belief.io.xmlbif
 
XmlbifParser.BifNode(XmlbifParser.Variable) - Constructor for class XmlbifParser.BifNode
 
XmlbifParser.Definition - Class in edu.ucla.belief.io.xmlbif
 
XmlbifParser.Definition() - Constructor for class XmlbifParser.Definition
 
XmlbifParser.Variable - Class in edu.ucla.belief.io.xmlbif
 
XmlbifParser.Variable() - Constructor for class XmlbifParser.Variable
 
XmlbifParser.VariableType - Enum in edu.ucla.belief.io.xmlbif
 
XmlbifWriter - Class in edu.ucla.belief.io.xmlbif
xml bif format described
xml schema validation primer
perl script to convert DTD to schema
XmlbifWriter() - Constructor for class XmlbifWriter
 
XmlbifWriter.Element - Enum in edu.ucla.belief.io.xmlbif
 
XmlDocumentHandler - Class in edu.ucla.belief.decision
 
XmlDocumentHandler(BeliefNetwork) - Constructor for class XmlDocumentHandler
 
XmlElementHandler - Class in edu.ucla.belief.decision
 
XmlElementHandler(XmlDocumentHandler) - Constructor for class XmlElementHandler
 
xmlize(Dtree, RC) - Method in class Xmlizer
 
xmlize(Dtree, Stats, RC) - Method in class Xmlizer
 
xmlize(Dtree, Stats, RC, Computation, String) - Method in class Xmlizer
 
Xmlizer - Class in edu.ucla.belief.recursiveconditioning
 
Xmlizer() - Constructor for class Xmlizer
 
XmlWriter - Class in edu.ucla.belief.decision
 
XmlWriter.GroupedDecisionWriter - Class in edu.ucla.belief.decision
 
XmlWriter.GroupedDecisionWriter() - Constructor for class XmlWriter.GroupedDecisionWriter
 
XmlWriter.GroupedOutcomeWriter - Class in edu.ucla.belief.decision
 
XmlWriter.GroupedOutcomeWriter() - Constructor for class XmlWriter.GroupedOutcomeWriter
 
XmlWriter.GroupedParameterWriter - Class in edu.ucla.belief.decision
 
XmlWriter.GroupedParameterWriter() - Constructor for class XmlWriter.GroupedParameterWriter
 
XmlWriter.PrintStreamWriter - Class in edu.ucla.belief.decision
 
XmlWriter.PrintStreamWriter(PrintStream) - Constructor for class XmlWriter.PrintStreamWriter
 
XmlWriter.PrintWriterWriter - Class in edu.ucla.belief.decision
 
XmlWriter.PrintWriterWriter(PrintWriter) - Constructor for class XmlWriter.PrintWriterWriter
 
XmlWriter.UniWriter - Interface in edu.ucla.belief.decision
 
xorCpt - Static variable in class UaiMpeMain
 

Z

ZCEngine - Class in edu.ucla.belief.inference
 
ZCEngine(BeliefNetwork, Dynamator) - Constructor for class ZCEngine
 
ZCEngine(BeliefNetwork, Dynamator, List) - Constructor for class ZCEngine
 
ZCEngine(BeliefNetwork, Dynamator, EliminationOrders.JT) - Constructor for class ZCEngine
 
ZCEngine(BeliefNetwork, Collection, Map, Dynamator) - Constructor for class ZCEngine
 
ZCEngineGenerator - Class in edu.ucla.belief.inference
 
ZCEngineGenerator() - Constructor for class ZCEngineGenerator
 
ZCWrapper - Class in edu.ucla.belief.inference
 
ZCWrapper(BeliefNetwork) - Constructor for class ZCWrapper
 
ZCWrapper(BeliefNetwork, Collection, Map) - Constructor for class ZCWrapper
 
ZCWrapper(BeliefNetwork, List) - Constructor for class ZCWrapper
 
ZCWrapper(BeliefNetwork, EliminationOrders.JT) - Constructor for class ZCWrapper
 
ZCWrapper(BeliefNetwork, EliminationOrders.JT, QuantitativeDependencyHandler) - Constructor for class ZCWrapper
 
zero(Dimension) - Static method in class Macros
 
ZERO - Static variable in class Table
 
zeroConciousDivideRelevantInto(double[], boolean[]) - Method in class Table
 
zeroConciousMakeReal(boolean[]) - Method in class Table
 
zeroConciousMultiplyInto(Table, boolean[]) - Method in class Table
 
zeroConciousMultiplyVarIndicators(int, int, boolean[]) - Method in class Table
 
zeroConciousProjectInto(Table, boolean[], boolean[]) - Method in class Table
 
zeroConciousProjectOnto(int, boolean[], boolean[]) - Method in class Table
 
zeroConciousRealProjectInto(Table, boolean[]) - Method in class Table
 
zeroConciousRealProjectOnto(int, boolean[]) - Method in class Table
 
zeroConditional(FiniteVariable) - Method in class Macros.Bridge
 

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