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

A

aca() - Method in class RBNgui.LearnModule
 
accept(File) - Method in class RBNgui.Filter_bif
 
accept(File) - Method in class RBNgui.Filter_db
 
accept(File) - Method in class RBNgui.Filter_dne
 
accept(File) - Method in class RBNgui.Filter_foil
 
accept(File) - Method in class RBNgui.Filter_mln
 
accept(File) - Method in class RBNgui.Filter_net
 
accept(File) - Method in class RBNgui.Filter_pl
 
accept(File) - Method in class RBNgui.Filter_rbn
 
accept(File) - Method in class RBNgui.Filter_rdef
 
accept(File) - Method in class RBNgui.Filter_rst
 
aceStateChange(Control) - Method in class RBNgui.EvidenceModule
interface Control.ACEControlListener
actionPerformed(ActionEvent) - Method in class RBNgui.Bavaria
 
actionPerformed(ActionEvent) - Method in class RBNgui.EvidenceModule
 
actionPerformed(ActionEvent) - Method in class RBNgui.LearnModule
 
actionPerformed(ActionEvent) - Method in class RBNgui.LearnSettings
 
actionPerformed(ActionEvent) - Method in class RBNgui.NodeWindow
 
actionPerformed(ActionEvent) - Method in class RBNgui.Primula
 
actionPerformed(ActionEvent) - Method in class RBNgui.Settings
 
add(double) - Method in class mymath.DoubleVector
 
add(int) - Method in class mymath.IntVector
 
add(int, int) - Method in class mymath.IntVector
 
add(RelDataForOneInput) - Method in class RBNLearning.RelData
 
add(Rel, int[]) - Method in class RBNpackage.AtomList
 
add(Rel, int[], String) - Method in class RBNpackage.AtomList
 
add(Atom, int, String) - Method in class RBNpackage.Instantiation
 
add(Atom, boolean, String) - Method in class RBNpackage.Instantiation
 
add(Rel, int[], boolean, String) - Method in class RBNpackage.Instantiation
 
add(Rel, int[][], boolean, String) - Method in class RBNpackage.Instantiation
 
add(int[], boolean, int) - Method in class RBNpackage.OneRelData
 
add(OneRelData) - Method in class RBNpackage.OneStrucData
 
add(Atom, int, String) - Method in class RBNpackage.OneStrucData
 
add(Atom, boolean, String) - Method in class RBNpackage.OneStrucData
 
add(Rel, int[], boolean, String) - Method in class RBNpackage.OneStrucData
Returns 1 if r,tuple,tv was not already in the data; 0 otherwise.
add(Rel, int[][], boolean, String) - Method in class RBNpackage.OneStrucData
 
add(double) - Method in class RBNutilities.DoubleVector
 
add(double[], double[]) - Static method in class RBNutilities.SmallDouble
 
add_escapes(String) - Method in exception RBNio.ParseException
Used to convert raw characters to their escaped version when these raw version cannot be used as part of an ASCII string literal.
addACE(String) - Method in class RBNgui.QueryTableModel
 
addArgument(String) - Method in class MLNParser.ParsedRelation
 
addAtomsToElement(Element, RelStruc) - Method in class RBNpackage.OneStrucData
 
addCandidateType(Rel) - Method in class RBNio.AtomListReader
 
addCase(OneStrucData) - Method in class RBNLearning.RelDataForOneInput
 
addDomainDec(Element) - Method in class RBNpackage.RelStruc
 
addElement(String, String) - Method in class RBNio.AtomListReader
 
addEscapes(String) - Static method in error RBNio.TokenMgrError
Replaces unprintable characters by their escaped (or unicode escaped) equivalents in the given string
addMaxProb(String) - Method in class RBNgui.QueryTableModel
 
addMinProb(String) - Method in class RBNgui.QueryTableModel
 
addNewRelToNodeWindow(Rel) - Method in class RBNgui.EditPanel
 
addNewRelToNodeWindow(Rel) - Method in class RBNgui.NodeWindow
 
addNode(int, int) - Method in class RBNgui.Bavaria
 
addNode(SimpleBNNode, int, int) - Method in interface RBNinference.BayesNetInt
 
addNode(SimpleBNNode, int[], int) - Method in interface RBNinference.BayesNetInt
Add node to the network.
addNode(SimpleBNNode, int, int) - Method in class RBNinference.BayesNetIntBIF
 
addNode(SimpleBNNode, int[], int) - Method in class RBNinference.BayesNetIntBIF
 
addNode(SimpleBNNode, int, int) - Method in class RBNinference.BayesNetIntHuginNet
 
addNode(SimpleBNNode, int[], int) - Method in class RBNinference.BayesNetIntHuginNet
 
addNode(SimpleBNNode, int, int) - Method in class RBNinference.BayesNetIntNeticaDnet
 
addNode(SimpleBNNode, int[], int) - Method in class RBNinference.BayesNetIntNeticaDnet
 
addNode(SimpleBNNode, int) - Method in class RBNinference.BayesNetIntXMLBIF
 
addNode(SimpleBNNode, boolean, int) - Method in class RBNinference.BayesNetIntXMLBIF
 
addNode(SimpleBNNode, int[]) - Method in class RBNinference.BayesNetIntXMLBIF
 
addNode(SimpleBNNode, int[], boolean) - Method in class RBNinference.BayesNetIntXMLBIF
 
addNode() - Method in class RBNpackage.RelStruc
 
addNode(String) - Method in class RBNpackage.RelStruc
 
addNode(String, int, int) - Method in class RBNpackage.RelStruc
 
addNode(int, int) - Method in class RBNpackage.RelStruc
 
addOrRenameElementName() - Method in class RBNgui.EvidenceModule
 
addOrRenameEvidenceModuleNode() - Method in class RBNgui.Primula
 
addProb(String) - Method in class RBNgui.QueryTableModel
 
addProb(LinkedList) - Method in class RBNgui.QueryTableModel
 
addQuery(String) - Method in class RBNgui.QueryTableModel
 
addQuery(LinkedList) - Method in class RBNgui.QueryTableModel
 
addRelation(Rel) - Method in class RBNgui.Bavaria
 
addRelation(String, Vector<String>) - Method in class RBNio.AtomListReader
 
addRelation(Rel, String) - Method in class RBNpackage.OneStrucData
 
addRelation(Rel) - Method in class RBNpackage.OrdStruc
 
addRelation(Rel) - Method in class RBNpackage.RelStruc
 
addRelation(Rel) - Method in class RBNpackage.SparseRelStruc
 
addRelData(Element, RelStruc) - Method in class RBNpackage.OneRelData
 
addRelHeader(Element, String, String) - Method in class RBNpackage.Rel
Adds to root an element containing the header information for this Rel
addSorted(double) - Method in class mymath.DoubleVector
 
addSorted(int) - Method in class mymath.IntVector
 
addSorted(double) - Method in class RBNutilities.DoubleVector
 
addToChildren(BNNode) - Method in class RBNinference.BNNode
Adds newchild to children if not in children list already
addToChildren(GradientGraphProbFormNode, boolean) - Method in class RBNLearning.GradientGraphLikelihoodNode
 
addToChildren(GradientGraphProbFormNode, GradientGraphIndicatorNode) - Method in class RBNLearning.GradientGraphLikelihoodNode
 
addToChildren(GradientGraphProbFormNode) - Method in class RBNLearning.GradientGraphNode
 
addToElement(Element) - Method in class RBNLearning.RelDataForOneInput
 
addToIndicators(GradientGraphIndicatorNode) - Method in class RBNLearning.GradientGraph
 
addToParents(BNNode) - Method in class RBNinference.BNNode
 
addToParents(GradientGraphNode) - Method in class RBNLearning.GradientGraphNode
 
addToTruesampleweight(double[], int) - Method in class RBNinference.PFNetworkNode
 
addTuple(Rel) - Method in class RBNgui.Bavaria
 
addTuple(Rel, int[], String) - Method in class RBNgui.Bavaria
 
addTuple(String, Vector<String>, boolean) - Method in class RBNio.AtomListReader
 
addTuple(Rel, int[]) - Method in class RBNpackage.RelStruc
 
addTuple(Rel, String[]) - Method in class RBNpackage.RelStruc
 
addTupleToNodeWindow(Rel, int[]) - Method in class RBNgui.EditPanel
 
addTupleToNodeWindow(Rel, int[]) - Method in class RBNgui.NodeWindow
 
addVar(String) - Method in class RBNgui.QueryTableModel
 
adjustBeginLineColumn(int, int) - Method in class RBNio.SimpleCharStream
Method to adjust line and column numbers for the start of a token.
allArgTuples(Rel) - Method in class RBNpackage.RelStruc
 
allAtoms() - Method in class RBNpackage.AtomList
 
allElements(Type) - Method in class RBNpackage.RelStruc
Returns all elements in the domain of type rtype.
allElements(RelStruc) - Method in class RBNpackage.TypeDomain
Returns integer vector [0,1,...,dom-1] where dom is the domainsize of rs
allElements(int) - Method in class RBNpackage.TypeInteger
Returns integer vector [0,1,...,maxindex]
allElements(RelStruc) - Method in class RBNpackage.TypeRel
Returns all elements in the domain of rs that are of this type.
allFalse(Rel) - Method in class RBNpackage.Instantiation
Returns all tuples that are instantiated to false in relation r Tuples represented as integer arrays, using the internal indices of objects
allFalse(Rel, RelStruc) - Method in class RBNpackage.Instantiation
Returns all tuples that are instantiated to false in relation r Tuples represented as string arrays, using the names of objects as defined in A
allFalse() - Method in class RBNpackage.OneRelData
Returns all the atoms instantiated to false as a vector of int[].
allFalse(RelStruc) - Method in class RBNpackage.OneRelData
Returns all the atoms instantiated to false as a vector of strings.
allFalse(Rel) - Method in class RBNpackage.OneStrucData
Returns all tuples that are instantiated to false in relation r Tuples represented as integer arrays, using the internal indices of objects
allFalse(Rel, RelStruc) - Method in class RBNpackage.OneStrucData
Returns all tuples that are instantiated to false in relation r Tuples represented as string arrays, using the names of objects as defined in A
allInstAtoms() - Method in class RBNpackage.Instantiation
 
allInstAtoms() - Method in class RBNpackage.OneStrucData
 
allnodesSize() - Method in class RBNinference.PFNetwork
 
allsampleweight() - Method in class RBNinference.PFNetwork
 
allSatisfyingTuples(String[], int[], String[], TreeSet, int) - Static method in class RBNutilities.rbnutilities
Inserts into ts all integer tuples 'ints' of length vars.length, such that mixedvec[vars/ints]=intvec.
allTrue(Rel) - Method in class RBNpackage.Instantiation
Returns all tuples that are instantiated to true in relation r Tuples represented as integer arrays, using the internal indices of objects
allTrue() - Method in class RBNpackage.OneRelData
Returns all the atoms instantiated to true as a vector of int[].
allTrue(RelStruc) - Method in class RBNpackage.OneRelData
Returns all the atoms instantiated to true as a vector of strings.
allTrue(Rel) - Method in class RBNpackage.OneStrucData
Returns all tuples that are instantiated to true in relation r Tuples represented as integer arrays, using the internal indices of objects
allTrue(Rel, RelStruc) - Method in class RBNpackage.OneStrucData
Returns all tuples that are instantiated to true in relation r Tuples represented as string arrays, using the names of objects as defined in A
allTrue(CConstr, String[]) - Method in class RBNpackage.OrdStruc
 
allTrue(CConstr, String[]) - Method in class RBNpackage.RelStruc
 
allTrue(Rel) - Method in class RBNpackage.RelStruc
 
allTrue(CConstr, String[]) - Method in class RBNpackage.SparseRelStruc
 
allTrueAsTreeSet(CConstr, String[]) - Method in class RBNpackage.SparseRelStruc
 
allTypedTuples(Type[]) - Method in class RBNpackage.RelStruc
Returns an array of integer tuples of length types.length.
allUnInstantiated(int) - Method in class RBNpackage.OneRelData
Returns all the atoms which are not instantiated to either true or false.
ancestors() - Method in class RBNLearning.GradientGraphNode
Returns the set of all ancestors of this node in the Graph
appendMessage(String) - Static method in class RBNgui.Primula
 
appendMessageThis(String) - Method in class RBNgui.Primula
 
ArbitraryPanel - Class in RBNgui
 
ArbitraryPanel(Bavaria) - Constructor for class RBNgui.ArbitraryPanel
 
args - Variable in class RBNpackage.Atom
 
args() - Method in class RBNpackage.Atom
 
args(Rel) - Method in class RBNpackage.RBN
Returns the argument tuple for the ProbForm for r
ArgsAt(int) - Method in class RBNpackage.RBN
 
argsIfGround() - Method in class RBNpackage.ProbFormIndicator
Returns the arguments as an array of integers if formula represents a ground atom.
arguments - Variable in class RBNpackage.ProbFormIndicator
 
argumentsAt(int) - Method in class RBNpackage.RBN
 
arity - Variable in class RBNpackage.Rel
 
ARRAY_OPTIONS - Static variable in class RBNinference.BayesNetIntSamIam
 
arrayAdd(double[], double[]) - Static method in class mymath.MyMathOps
 
arrayCompare(int[], int[]) - Static method in class RBNutilities.rbnutilities
 
arrayConcat(double[], double[]) - Static method in class mymath.MyMathOps
 
arrayContains(int[], int) - Static method in class RBNutilities.rbnutilities
 
arrayEquals(int[], int[]) - Static method in class RBNutilities.rbnutilities
 
arraymerge(String[], String[]) - Static method in class RBNutilities.rbnutilities
 
arraymerge(Rel[], Rel[]) - Static method in class RBNutilities.rbnutilities
 
arrayNormalize(double[]) - Static method in class mymath.MyMathOps
 
arrayNormalizeEuclid(double[]) - Static method in class mymath.MyMathOps
 
arrayScalMult(double[], double) - Static method in class mymath.MyMathOps
 
arrayShiftArgs(int[], int) - Static method in class RBNutilities.rbnutilities
 
arraysubstraction(String[], String[]) - Static method in class RBNutilities.rbnutilities
 
arraysubstraction(Rel[], Rel[]) - Static method in class RBNutilities.rbnutilities
 
arrayToString(double[], String, String) - Static method in class myio.StringOps
 
arrayToString(double[], int, String, String) - Static method in class myio.StringOps
 
arrayToString(int[], String, String) - Static method in class myio.StringOps
 
arrayToString(String[], String, String) - Static method in class myio.StringOps
 
arrayToString(String[]) - Static method in class RBNutilities.rbnutilities
 
arrayToString(int[]) - Static method in class RBNutilities.rbnutilities
 
arrayToString(int[], String) - Static method in class RBNutilities.rbnutilities
prefixes every integer in the tuple with 'prefix'
arrayToString(double[]) - Static method in class RBNutilities.rbnutilities
 
arrayToString(Rel[]) - Static method in class RBNutilities.rbnutilities
 
arrayToStringParenth(String[], String, String) - Static method in class myio.StringOps
 
asArray() - Method in class mymath.DoubleVector
 
asArray() - Method in class mymath.IntVector
 
asArray() - Method in class RBNutilities.DoubleVector
 
asJFrame() - Method in class RBNgui.Primula
 
asString() - Method in class RBNpackage.Atom
 
asString(RelStruc) - Method in class RBNpackage.Atom
 
asString() - Method in class RBNpackage.CConstr
 
asString(RelStruc) - Method in class RBNpackage.CConstr
 
asString() - Method in class RBNpackage.CConstrAnd
 
asString(RelStruc) - Method in class RBNpackage.CConstrAnd
 
asString() - Method in class RBNpackage.CConstrAtom
 
asString(RelStruc) - Method in class RBNpackage.CConstrAtom
 
asString() - Method in class RBNpackage.CConstrEmpty
 
asString(RelStruc) - Method in class RBNpackage.CConstrEmpty
 
asString() - Method in class RBNpackage.CConstrEq
 
asString(RelStruc) - Method in class RBNpackage.CConstrEq
 
asString() - Method in class RBNpackage.CConstrNeg
 
asString(RelStruc) - Method in class RBNpackage.CConstrNeg
 
asString() - Method in class RBNpackage.CConstrOr
 
asString(RelStruc) - Method in class RBNpackage.CConstrOr
 
asString(int) - Method in class RBNpackage.ProbForm
 
asString() - Method in class RBNpackage.ProbForm
 
asString(int, RelStruc) - Method in class RBNpackage.ProbForm
 
asString(RelStruc) - Method in class RBNpackage.ProbForm
 
asString(int) - Method in class RBNpackage.ProbFormCombFunc
 
asString() - Method in class RBNpackage.ProbFormCombFunc
 
asString(int, RelStruc) - Method in class RBNpackage.ProbFormCombFunc
 
asString(RelStruc) - Method in class RBNpackage.ProbFormCombFunc
 
asString(int) - Method in class RBNpackage.ProbFormConstant
 
asString() - Method in class RBNpackage.ProbFormConstant
 
asString(int, RelStruc) - Method in class RBNpackage.ProbFormConstant
 
asString(RelStruc) - Method in class RBNpackage.ProbFormConstant
 
asString(int) - Method in class RBNpackage.ProbFormConvComb
 
asString() - Method in class RBNpackage.ProbFormConvComb
 
asString(RelStruc) - Method in class RBNpackage.ProbFormConvComb
 
asString(int, RelStruc) - Method in class RBNpackage.ProbFormConvComb
 
asString(int) - Method in class RBNpackage.ProbFormIndicator
 
asString() - Method in class RBNpackage.ProbFormIndicator
 
asString(int, RelStruc) - Method in class RBNpackage.ProbFormIndicator
 
asString(RelStruc) - Method in class RBNpackage.ProbFormIndicator
 
asString(int) - Method in class RBNpackage.ProbFormSFormula
 
asString(int, RelStruc) - Method in class RBNpackage.ProbFormSFormula
 
asString() - Method in class RBNpackage.ProbFormSFormula
 
asString(RelStruc) - Method in class RBNpackage.ProbFormSFormula
 
Atom - Class in RBNpackage
 
Atom() - Constructor for class RBNpackage.Atom
 
Atom(Rel, int[]) - Constructor for class RBNpackage.Atom
 
Atom(Rel, int[], String) - Constructor for class RBNpackage.Atom
 
atom() - Method in class RBNpackage.ProbFormIndicator
Returns the ground atom if this ProbForm represents a ground atom; otherwise returns null;
atomAt(int) - Method in class RBNinference.PFNetwork
 
atomAt(int) - Method in class RBNpackage.AtomList
 
AtomList - Class in RBNpackage
 
AtomList() - Constructor for class RBNpackage.AtomList
Creates new AtomList
AtomList(AtomList) - Constructor for class RBNpackage.AtomList
 
AtomListParser - Class in RBNio
 
AtomListParser(InputStream) - Constructor for class RBNio.AtomListParser
Constructor with InputStream.
AtomListParser(InputStream, String) - Constructor for class RBNio.AtomListParser
Constructor with InputStream and supplied encoding
AtomListParser(Reader) - Constructor for class RBNio.AtomListParser
Constructor.
AtomListParser(AtomListParserTokenManager) - Constructor for class RBNio.AtomListParser
Constructor with generated Token Manager.
AtomListParserConstants - Interface in RBNio
Token literal values and constants.
AtomListParserTokenManager - Class in RBNio
Token Manager.
AtomListParserTokenManager(SimpleCharStream) - Constructor for class RBNio.AtomListParserTokenManager
Constructor.
AtomListParserTokenManager(SimpleCharStream, int) - Constructor for class RBNio.AtomListParserTokenManager
Constructor.
AtomListReader - Class in RBNio
 
AtomListReader() - Constructor for class RBNio.AtomListReader
 
AttributesPanel - Class in RBNgui
 
AttributesPanel(Bavaria) - Constructor for class RBNgui.AttributesPanel
 
Averages - Class in mymath
 
Averages() - Constructor for class mymath.Averages
 

B

backup(int) - Method in class RBNio.SimpleCharStream
Backup a number of characters.
BadArityException - Exception in MLNExceptions
 
BadArityException() - Constructor for exception MLNExceptions.BadArityException
Creates a new instance of BadArityException without detail message.
BadArityException(String) - Constructor for exception MLNExceptions.BadArityException
Constructs an instance of BadArityException with the specified detail message.
Bavaria - Class in RBNgui
 
Bavaria(SparseRelStruc, Primula, boolean) - Constructor for class RBNgui.Bavaria
 
Bavaria(SparseRelStruc, File, Primula, boolean) - Constructor for class RBNgui.Bavaria
 
bavaria - Variable in class RBNgui.Primula
 
BayesConstructor - Class in RBNinference
 
BayesConstructor() - Constructor for class RBNinference.BayesConstructor
Creates new BayesConstructor
BayesConstructor(RBN, RelStruc, Instantiation, AtomList, File) - Constructor for class RBNinference.BayesConstructor
 
BayesConstructor(RBN, RelStruc, Instantiation, AtomList) - Constructor for class RBNinference.BayesConstructor
 
BayesConstructor(RBN, RelStruc, Instantiation, AtomList, Primula) - Constructor for class RBNinference.BayesConstructor
 
BayesConstructor(Primula, Instantiation, AtomList) - Constructor for class RBNinference.BayesConstructor
 
BayesConstructor(RBN, RelStruc, Instantiation, AtomList, String, Primula) - Constructor for class RBNinference.BayesConstructor
 
BayesConstructor(Primula, Instantiation, AtomList, String) - Constructor for class RBNinference.BayesConstructor
 
BayesConstructor.WeightComparator - Class in RBNinference
 
BayesNetInt - Interface in RBNinference
 
BayesNetIntBIF - Class in RBNinference
 
BayesNetIntBIF(File) - Constructor for class RBNinference.BayesNetIntBIF
Creates new BayesNetIntXMLBIF
BayesNetIntHuginNet - Class in RBNinference
 
BayesNetIntHuginNet(File) - Constructor for class RBNinference.BayesNetIntHuginNet
Creates new BayesNetIntHuginNet
BayesNetIntHuginNet() - Constructor for class RBNinference.BayesNetIntHuginNet
 
BayesNetIntNeticaDnet - Class in RBNinference
 
BayesNetIntNeticaDnet(File) - Constructor for class RBNinference.BayesNetIntNeticaDnet
Creates new BayesNetIntNeticaDnet
BayesNetIntSamIam - Class in RBNinference
 
BayesNetIntSamIam(Primula, String) - Constructor for class RBNinference.BayesNetIntSamIam
Creates new BayesNetIntSamIam
BayesNetIntXMLBIF - Class in RBNinference
 
BayesNetIntXMLBIF(String) - Constructor for class RBNinference.BayesNetIntXMLBIF
Creates new BayesNetIntXMLBIF
beginColumn - Variable in class RBNio.Token
The column number of the first character of this Token.
beginLine - Variable in class RBNio.Token
The line number of the first character of this Token.
BeginToken() - Method in class RBNio.SimpleCharStream
Start.
bif - Static variable in class RBNgui.Filter_bif
 
BinaryOptimizable - Interface in mymath
Represents a function that can be optimized by binary search.
binaryOptimization(BinaryOptimizable, Double, Double, double, double) - Static method in class mymath.BinaryOptimizer
find maximum of func insice [leftbound,rightbound] using binary search.
BinaryOptimizer - Class in mymath
 
BinaryOptimizer() - Constructor for class mymath.BinaryOptimizer
 
BinaryPanel - Class in RBNgui
 
BinaryPanel(Bavaria) - Constructor for class RBNgui.BinaryPanel
 
BLP_FORMAT - Static variable in class RBNpackage.RelStruc
 
BNNode - Class in RBNinference
 
BNNode() - Constructor for class RBNinference.BNNode
Creates new BNNode
BNNode(String) - Constructor for class RBNinference.BNNode
 
BNNode(String, int) - Constructor for class RBNinference.BNNode
 
BNNode(String, LinkedList, LinkedList) - Constructor for class RBNinference.BNNode
 
bnoutfile - Variable in class RBNgui.Primula
 
bnsystem - Variable in class RBNgui.Primula
 
BoolNode - Class in RBNinference
 
BoolNode() - Constructor for class RBNinference.BoolNode
Creates new BayesNetNode
BoolNode(String, BoolNode[]) - Constructor for class RBNinference.BoolNode
 
bufcolumn - Variable in class RBNio.SimpleCharStream
 
buffer - Variable in class RBNio.SimpleCharStream
 
bufline - Variable in class RBNio.SimpleCharStream
 
bufpos - Variable in class RBNio.SimpleCharStream
Position in buffer.
buildNodeStack() - Method in class RBNinference.BNNode
 

C

cartesProd(Vector) - Static method in class RBNutilities.rbnutilities
 
caseAt(int) - Method in class RBNLearning.RelData
 
CConstr - Class in RBNpackage
 
CConstr() - Constructor for class RBNpackage.CConstr
 
cconstr - Variable in class RBNpackage.ProbFormCombFunc
 
CConstrAnd - Class in RBNpackage
 
CConstrAnd(CConstr, CConstr) - Constructor for class RBNpackage.CConstrAnd
Creates new CConstrAnd
CConstrAtom - Class in RBNpackage
 
CConstrAtom(Rel, String[]) - Constructor for class RBNpackage.CConstrAtom
Creates new CConstrAtom
CConstrEmpty - Class in RBNpackage
 
CConstrEmpty() - Constructor for class RBNpackage.CConstrEmpty
Creates new CConstrEmpty
CConstrEq - Class in RBNpackage
 
CConstrEq(String, String) - Constructor for class RBNpackage.CConstrEq
Creates new CConstrAtom
CConstrNeg - Class in RBNpackage
 
CConstrNeg(CConstr) - Constructor for class RBNpackage.CConstrNeg
Creates new CConstrNeg
CConstrOr - Class in RBNpackage
 
CConstrOr(CConstr, CConstr) - Constructor for class RBNpackage.CConstrOr
Creates new CConstrAnd
ce(double[], double[]) - Static method in class mymath.MyMathOps
 
centerGraph(double, double) - Method in class RBNgui.Bavaria
 
centerView() - Method in class RBNgui.Bavaria
 
CF_ESUM - Static variable in class RBNgui.Primula
 
CF_INVSUM - Static variable in class RBNgui.Primula
 
CF_MEAN - Static variable in class RBNgui.Primula
 
CF_NOR - Static variable in class RBNgui.Primula
 
changeIndex() - Method in class RBNgui.NodeWindow
 
characterize(Instantiation) - Method in class RBNpackage.Instantiation
 
children - Variable in class RBNinference.BNNode
 
childrenSize() - Method in class RBNLearning.GradientGraphNode
 
chooseAttributeColor() - Method in class RBNpackage.Rel
 
chooseBinaryColor() - Method in class RBNpackage.Rel
 
clearSelections() - Method in class RBNgui.ArbitraryPanel
 
clearSelections() - Method in class RBNgui.AttributesPanel
 
clearSelections(int) - Method in class RBNgui.Bavaria
 
clearSelections() - Method in class RBNgui.BinaryPanel
 
clone() - Method in class RBNpackage.OrdStruc
 
clone() - Method in class RBNpackage.RelStruc
 
clone() - Method in class RBNpackage.SparseRelStruc
 
clonearray(int[]) - Static method in class RBNutilities.rbnutilities
 
clonearray(double[]) - Static method in class RBNutilities.rbnutilities
 
cloneDomain(Boolean) - Method in class RBNpackage.SparseRelStruc
Returns a new SparseRelStruc containing all the objects of this SparseRelStruc.
clonevector(Vector) - Static method in class RBNutilities.rbnutilities
Clones vector vec without cloning the components of the vector
closeAllNodeWindows() - Method in class RBNgui.EditPanel
 
closeNodeWindow(NodeWindow) - Method in class RBNgui.EditPanel
 
ClosePar - Static variable in interface RBNio.AtomListParserConstants
RegularExpression Id.
color - Variable in class RBNpackage.Rel
 
COLOR_BLUE - Static variable in class RBNgui.Primula
 
COLOR_BLUE_SELECTED - Static variable in class RBNgui.Primula
 
COLOR_GREEN - Static variable in class RBNgui.Primula
 
COLOR_GREEN_SELECTED - Static variable in class RBNgui.Primula
 
COLOR_RED - Static variable in class RBNgui.Primula
 
COLOR_RED_SELECTED - Static variable in class RBNgui.Primula
 
COLOR_YELLOW - Static variable in class RBNgui.Primula
 
COLOR_YELLOW_SELECTED - Static variable in class RBNgui.Primula
 
column - Variable in class RBNio.SimpleCharStream
 
CombFunc - Class in RBNpackage
 
CombFunc() - Constructor for class RBNpackage.CombFunc
 
CombFuncESum - Class in RBNpackage
 
CombFuncESum() - Constructor for class RBNpackage.CombFuncESum
Creates new CombFuncESum
CombFuncInvsum - Class in RBNpackage
 
CombFuncInvsum() - Constructor for class RBNpackage.CombFuncInvsum
Creates new CombFuncInvsum
CombFuncMean - Class in RBNpackage
 
CombFuncMean() - Constructor for class RBNpackage.CombFuncMean
Creates new CombFuncMean
CombFuncNOr - Class in RBNpackage
 
CombFuncNOr() - Constructor for class RBNpackage.CombFuncNOr
Creates new CombFuncNOr
combineAtomVecs(Vector, Vector) - Static method in class RBNutilities.rbnutilities
 
compare(Object, Object) - Method in class RBNinference.BayesConstructor.WeightComparator
 
compare(Object, Object) - Method in class RBNutilities.DoubleArrayComparatorByComponent
Returns 0 if arr1 and arr2 are equal -1 if arr1.length < arr2.length or arr1.length = arr2.length and arr1 > arr2 in lexical order 1 otherwise
compare(Object, Object) - Method in class RBNutilities.IntArrayComparator
Returns 0 if arr1 and arr2 are equal -1 if arr1.length < arr2.length or arr1.length = arr2.length and arr1 < arr2 in lexical order 1 otherwise
compare(Object, Object) - Method in class RBNutilities.SmallDouble
 
compare(Object, Object) - Method in class RBNutilities.SmallDoubleArrayComparatorByComponent
 
compareSD(Object, Object) - Static method in class RBNutilities.SmallDouble
 
compareTo(GradientGraphNode) - Method in class RBNLearning.GradientGraphNode
 
ComplexBNGroundAtomNode - Class in RBNinference
 
ComplexBNGroundAtomNode() - Constructor for class RBNinference.ComplexBNGroundAtomNode
Creates new ComplexBNGroundAtomlNode
ComplexBNGroundAtomNode(Atom, ProbForm) - Constructor for class RBNinference.ComplexBNGroundAtomNode
 
ComplexBNGroundAtomNode(Atom, ProbForm, int) - Constructor for class RBNinference.ComplexBNGroundAtomNode
 
ComplexBNGroundAtomNode(Rel, int[], ProbForm) - Constructor for class RBNinference.ComplexBNGroundAtomNode
 
ComplexBNGroundAtomNode(Atom, String, ProbForm) - Constructor for class RBNinference.ComplexBNGroundAtomNode
 
ComplexBNGroundAtomNode(Rel, String, int[], ProbForm) - Constructor for class RBNinference.ComplexBNGroundAtomNode
 
ComplexBNGroundAtomNode(Atom, ProbForm, LinkedList, LinkedList) - Constructor for class RBNinference.ComplexBNGroundAtomNode
 
ComplexBNGroundAtomNode(Rel, int[], ProbForm, LinkedList, LinkedList) - Constructor for class RBNinference.ComplexBNGroundAtomNode
 
ComplexBNNode - Class in RBNinference
 
ComplexBNNode() - Constructor for class RBNinference.ComplexBNNode
Creates new ComplexBNNode
ComplexBNNode(String, ProbForm) - Constructor for class RBNinference.ComplexBNNode
 
ComplexBNNode(String, ProbForm, int) - Constructor for class RBNinference.ComplexBNNode
 
ComplexBNNode(String, ProbForm, LinkedList, LinkedList) - Constructor for class RBNinference.ComplexBNNode
 
ComplexBNNodeInt - Interface in RBNinference
 
ComplexPFNetworkNode - Class in RBNinference
 
ComplexPFNetworkNode(ComplexBNGroundAtomNode) - Constructor for class RBNinference.ComplexPFNetworkNode
 
ComplexPFNetworkNode(Rel, String, int[], ProbForm) - Constructor for class RBNinference.ComplexPFNetworkNode
 
computeCombFunc(int, double[]) - Method in class RBNLearning.GradientGraph
 
computeCorrespondingIndex(int, int, int) - Static method in class RBNutilities.rbnutilities
computes index of 0,1-vector in list of all 0,1-vectors of length 'size' that has the same components as vector at 'index', except in coordinate 'pos' 0 <= pos < size Example: 000 0 001 1 010 2 011 3 100 4 101 5 110 6 111 7 computeCorrespondingIndex(3,1,4)=6
computeLikelihood(LearnThread) - Method in class RBNLearning.GradientGraph
Computes the likelihood value given the current parameter setting by Gibbs sampling.
computePermutedIndex(int, int[], int, int) - Static method in class RBNutilities.rbnutilities
computes the index of permutation of tuple with index ind Example perm = (2,3,1), ind=5, range =2, dim = 3: tuple represented by index: (1,0,0) Permuted tuple: (0,0,1) Index: 2
conditionalsampleweightsfalse - Variable in class RBNinference.SimplePFNetworkNode
conditionalsampleweightsfalse[i]: sum of all weights of samples in which i'th parent configuration was sampled and this node was sampled false (in a run of importance sampling).
conditionalsampleweightsfalse() - Method in class RBNinference.SimplePFNetworkNode
 
conditionalsampleweightsfalse_subsample - Variable in class RBNinference.SimplePFNetworkNode
array of dimensions 2 x num_parentconfig x num_samples conditionalsampleweightsfalse_subsample[i][j] contains the sum of weights (represented as SmallDouble) of all samples assigned to the jth subsample with parentconfig i where this node is sampled false
conditionalsampleweightstrue - Variable in class RBNinference.SimplePFNetworkNode
conditionalsampleweightstrue[i]: sum of all weights of samples in which i'th parent configuration was sampled and this node was sampled true (in a run of importance sampling).
conditionalsampleweightstrue() - Method in class RBNinference.SimplePFNetworkNode
 
conditionalsampleweightstrue_subsample - Variable in class RBNinference.SimplePFNetworkNode
array of dimensions 2 x num_parentconfig x num_samples conditionalsampleweightstrue_subsample[i][j] contains the sum of weights (represented as SmallDouble) of all samples assigned to the jth subsample with parentconfig i where this node is sampled true
conditionEvidence(RelStruc, Instantiation) - Method in class RBNpackage.ProbForm
Simplify ProbForm by substituting values of instantiated R-atoms and evaluating subformulas no longer dependent on any uninstantiated R-atom.
conditionEvidence(Instantiation) - Method in class RBNpackage.ProbForm
 
conditionEvidence(Instantiation) - Method in class RBNpackage.ProbFormCombFunc
 
conditionEvidence(RelStruc, Instantiation) - Method in class RBNpackage.ProbFormCombFunc
 
conditionEvidence(RelStruc, Instantiation) - Method in class RBNpackage.ProbFormConstant
 
conditionEvidence(Instantiation) - Method in class RBNpackage.ProbFormConstant
 
conditionEvidence(RelStruc, Instantiation) - Method in class RBNpackage.ProbFormConvComb
 
conditionEvidence(Instantiation) - Method in class RBNpackage.ProbFormConvComb
 
conditionEvidence(RelStruc, Instantiation) - Method in class RBNpackage.ProbFormIndicator
 
conditionEvidence(Instantiation) - Method in class RBNpackage.ProbFormIndicator
 
conditionEvidence(RelStruc, Instantiation) - Method in class RBNpackage.ProbFormSFormula
 
conditionEvidence(Instantiation) - Method in class RBNpackage.ProbFormSFormula
 
condProb(RelStruc, Hashtable, Instantiation, long[]) - Method in class RBNinference.ComplexPFNetworkNode
 
confirm(String, int) - Method in class RBNgui.Bavaria
 
confirm(String) - Method in class RBNgui.Primula
 
Constant - Static variable in interface RBNio.AtomListParserConstants
RegularExpression Id.
constructCPTNetwork(int, int, int, int, int, int) - Method in class RBNinference.BayesConstructor
 
constructGGPFN(GradientGraph, ProbForm, Hashtable<String, GradientGraphNode>, RelStruc, Instantiation, int, int) - Static method in class RBNLearning.GradientGraphProbFormNode
 
constructPFNetwork(int, int, int) - Method in class RBNinference.BayesConstructor
 
contains(Rel, int[], String) - Method in class RBNpackage.AtomList
 
contains(Atom) - Method in class RBNpackage.AtomList
 
contains(Rel, int[]) - Method in class RBNpackage.AtomList
 
containsAll(Instantiation) - Method in class RBNpackage.Instantiation
 
copy() - Method in class RBNpackage.Instantiation
 
copy() - Method in class RBNpackage.OneStrucData
 
CorrArraySubstraction(String[], String[], int[]) - Static method in class RBNutilities.rbnutilities
 
CorrArraySubstraction(String[], String[], String[]) - Static method in class RBNutilities.rbnutilities
 
createCoords() - Method in class RBNpackage.RelStruc
 
createTab(Rel, Vector) - Method in class RBNgui.NodeWindow
 
createValidNetID(String) - Static method in class RBNinference.BayesNetIntSamIam
 
curChar - Variable in class RBNio.AtomListParserTokenManager
 
currentfile - Variable in class RBNio.SparseRelStrucReader
 
currentLikelihood() - Method in class RBNLearning.GradientGraph
 
currentParameters() - Method in class RBNLearning.GradientGraph
 
currentToken - Variable in exception RBNio.ParseException
This is the last token that has been consumed successfully.
cval - Variable in class RBNpackage.ProbFormConstant
 

D

data() - Method in class RBNpackage.Instantiation
 
dataAt(int) - Method in class RBNpackage.OneStrucData
 
db - Static variable in class RBNgui.Filter_db
 
debugStream - Variable in class RBNio.AtomListParserTokenManager
Debug output.
DeclaredType - Class in MLNParser
 
DeclaredType(TypeRel) - Constructor for class MLNParser.DeclaredType
 
decomposemode - Variable in class RBNgui.Primula
 
DEFAULT - Static variable in interface RBNio.AtomListParserConstants
Lexical state.
delete(Rel, int[]) - Method in class RBNpackage.AtomList
 
delete(String) - Method in class RBNpackage.AtomList
 
delete(int) - Method in class RBNpackage.AtomList
 
delete(Atom) - Method in class RBNpackage.Instantiation
 
delete(Rel, int[]) - Method in class RBNpackage.Instantiation
 
delete(Rel, int[], boolean) - Method in class RBNpackage.Instantiation
 
delete(int) - Method in class RBNpackage.OneRelData
Delete all atoms containing a
delete(int[], boolean) - Method in class RBNpackage.OneRelData
 
delete(int[][], boolean) - Method in class RBNpackage.OneRelData
 
delete(Atom) - Method in class RBNpackage.OneStrucData
 
delete(Rel, int[]) - Method in class RBNpackage.OneStrucData
 
delete(Rel, int[], boolean) - Method in class RBNpackage.OneStrucData
 
delete(Rel) - Method in class RBNpackage.OneStrucData
delete all instantiations of the relation relname
deleteElementFromEvidenceModule(int) - Method in class RBNgui.Primula
 
deleteElementName(int) - Method in class RBNgui.EvidenceModule
 
deleteNode(int) - Method in class RBNgui.Bavaria
 
deleteNode(int) - Method in class RBNpackage.SparseRelStruc
 
deleteRelation(Rel) - Method in class RBNgui.Bavaria
 
deleteRelation(Rel) - Method in class RBNpackage.RelStruc
 
deleteRelFromNodeWindow(Rel) - Method in class RBNgui.EditPanel
 
deleteRelFromNodeWindow(Rel) - Method in class RBNgui.NodeWindow
 
deleteShift(int) - Method in class RBNpackage.Instantiation
 
deleteShift(int) - Method in class RBNpackage.OneStrucData
Delete all atoms containing a and subtract 1 from all elements with index > a
deleteTuple(Rel, int[]) - Method in class RBNgui.Bavaria
 
deleteTuple(Rel, int[]) - Method in class RBNpackage.RelStruc
 
dependsOn(int) - Method in class RBNLearning.GradientGraphProbFormNode
 
dependsOn(String, RelStruc, Instantiation) - Method in class RBNpackage.ProbForm
Checks whether this prob.form depends on the unknown parameter 'variable' when prob.form is evaluated over input structure A and relative to instantiation (data) data.
dependsOn(String, RelStruc, Instantiation) - Method in class RBNpackage.ProbFormCombFunc
 
dependsOn(String, RelStruc, Instantiation) - Method in class RBNpackage.ProbFormConstant
 
dependsOn(String, RelStruc, Instantiation) - Method in class RBNpackage.ProbFormConvComb
 
dependsOn(String, RelStruc, Instantiation) - Method in class RBNpackage.ProbFormIndicator
 
dependsOn(String, RelStruc, Instantiation) - Method in class RBNpackage.ProbFormSFormula
 
dependsOnParam - Variable in class RBNLearning.GradientGraphProbFormNode
dependsOnParam[i] is true if the probform of this node depends on the i'th parameter, as given by the order defined by gg
depth - Variable in class RBNinference.BNNode
 
depth() - Method in class RBNinference.BNNode
 
DifferentTypesException - Exception in MLNExceptions
 
DifferentTypesException() - Constructor for exception MLNExceptions.DifferentTypesException
Creates a new instance of DifferentTypesException without detail message.
DifferentTypesException(Type, Rel, String) - Constructor for exception MLNExceptions.DifferentTypesException
 
DifferentTypesException(String) - Constructor for exception MLNExceptions.DifferentTypesException
Constructs an instance of DifferentTypesException with the specified detail message.
disable_tracing() - Method in class RBNio.AtomListParser
Disable tracing.
disposeNodeWindow() - Method in class RBNgui.NodeWindow
 
Distance - Class in mymath
 
Distance() - Constructor for class mymath.Distance
 
divide(double[], double[]) - Static method in class RBNutilities.SmallDouble
computes sd1/sd2
divide(double[], double) - Static method in class RBNutilities.SmallDouble
 
divide(double[], int) - Static method in class RBNutilities.SmallDouble
 
dne - Static variable in class RBNgui.Filter_dne
 
dom - Variable in class RBNpackage.RelStruc
 
domSize() - Method in class RBNpackage.RelStruc
 
Done() - Method in class RBNio.SimpleCharStream
Reset buffer when finished.
DoubleArrayComparatorByComponent - Class in RBNutilities
Compares two double arrays according to their value in component 'index'
DoubleArrayComparatorByComponent(int) - Constructor for class RBNutilities.DoubleArrayComparatorByComponent
 
doubleConverter(String) - Static method in class myio.StringOps
 
doubleConverter(double) - Static method in class myio.StringOps
 
DoubleVector - Class in mymath
 
DoubleVector() - Constructor for class mymath.DoubleVector
 
DoubleVector - Class in RBNutilities
 
DoubleVector() - Constructor for class RBNutilities.DoubleVector
 
drawGrid(Graphics2D, int) - Method in class RBNgui.EditPanel
 
drawLine(Graphics2D, Vector[], Vector) - Method in class RBNgui.EditPanel
 
drawPie(Graphics2D, int, int, Vector) - Method in class RBNgui.EditPanel
 
DummyBNNode - Class in RBNinference
 
DummyBNNode() - Constructor for class RBNinference.DummyBNNode
Creates new DummyBNNode
DummyBNNode(int) - Constructor for class RBNinference.DummyBNNode
 
dv() - Method in class RBNpackage.OneRelData
 
dvAt(int) - Method in class RBNpackage.OneStrucData
 

E

EditPanel - Class in RBNgui
 
EditPanel(Bavaria) - Constructor for class RBNgui.EditPanel
 
edu - package edu
 
elementAt(int) - Method in class mymath.DoubleVector
 
elementAt(int) - Method in class mymath.IntVector
 
elementAt(int) - Method in class RBNLearning.RelData
 
elementAt(int) - Method in class RBNutilities.DoubleVector
 
elements() - Method in class RBNpackage.RBN
 
empty() - Method in class RBNgui.ArbitraryPanel
 
empty() - Method in class RBNgui.AttributesPanel
 
empty() - Method in class RBNgui.BinaryPanel
 
emptyFunction() - Method in class RBNgui.Bavaria
 
emptyRelationLists() - Method in class RBNgui.Bavaria
 
enable_tracing() - Method in class RBNio.AtomListParser
Enable tracing.
endColumn - Variable in class RBNio.Token
The column number of the last character of this Token.
endLine - Variable in class RBNio.Token
The line number of the last character of this Token.
EndLiteral - Static variable in interface RBNio.AtomListParserConstants
RegularExpression Id.
EOF - Static variable in interface RBNio.AtomListParserConstants
End of File.
EOL - Static variable in interface RBNio.AtomListParserConstants
RegularExpression Id.
eol - Variable in exception RBNio.ParseException
The end of line string for this machine.
equals(GradientGraphNode) - Method in class RBNLearning.GradientGraphNode
 
equals(Atom) - Method in class RBNpackage.Atom
 
equals(Object) - Method in class RBNpackage.InstAtom
 
equals(ProbFormIndicator) - Method in class RBNpackage.ProbFormIndicator
 
equals(Rel) - Method in class RBNpackage.Rel
 
equals(RelName) - Method in class RBNpackage.RelName
 
equivArray(int[], int[], int[]) - Static method in class RBNutilities.rbnutilities
Tests whether ar1 and ar2 are equivalent modulo base in the following sense: ar1 and ar2 have the same length, and every number appearing in base appear only in identical places in ar1 and ar2.
equivAtoms(Atom, Atom, int[]) - Static method in class RBNutilities.rbnutilities
 
ESUM - Static variable in class RBNpackage.ProbFormCombFunc
 
euclDist(double[], double[]) - Static method in class mymath.MyMathOps
Computes the Euclidean distance between a and b (must be of same length)
evalSample(RelStruc, Hashtable, Instantiation, long[]) - Method in class RBNpackage.ProbForm
Evaluate this probform over RelStruc A.
evalSample(RelStruc, Hashtable, Instantiation, long[]) - Method in class RBNpackage.ProbFormCombFunc
 
evalSample(RelStruc, Hashtable, Instantiation, long[]) - Method in class RBNpackage.ProbFormConstant
 
evalSample(RelStruc, Hashtable, Instantiation, long[]) - Method in class RBNpackage.ProbFormConvComb
 
evalSample(RelStruc, Hashtable, Instantiation, long[]) - Method in class RBNpackage.ProbFormIndicator
 
evalSample(RelStruc, Hashtable, Instantiation, long[]) - Method in class RBNpackage.ProbFormSFormula
 
evaluate() - Method in class RBNLearning.GradientGraphCombFuncNode
 
evaluate() - Method in class RBNLearning.GradientGraphConstantNode
 
evaluate() - Method in class RBNLearning.GradientGraphConvCombNode
 
evaluate() - Method in class RBNLearning.GradientGraphIndicatorNode
 
evaluate() - Method in class RBNLearning.GradientGraphLikelihoodNode
Computes the likelihood (ignoring those terms that are not dependent on unknown atoms or parameters) Returns the likelihood[0] component.
evaluate() - Method in class RBNLearning.GradientGraphNode
Evaluate this GradientGraphNode using current values of parameters and the current instantiation for unobserved atoms.
evaluate(double[]) - Method in class RBNpackage.CombFunc
 
evaluate(double[]) - Method in class RBNpackage.CombFuncESum
 
evaluate(double[]) - Method in class RBNpackage.CombFuncInvsum
 
evaluate(double[]) - Method in class RBNpackage.CombFuncMean
 
evaluate(double[]) - Method in class RBNpackage.CombFuncNOr
 
evaluate(RelStruc, Instantiation, String[], int[], boolean) - Method in class RBNpackage.ProbForm
Evaluate this ProbForm for input structure A, instantiation inst, under the substitution tuple for vars.
evaluate(RelStruc, Instantiation, String[], int[], boolean) - Method in class RBNpackage.ProbFormCombFunc
 
evaluate(RelStruc, Instantiation, String[], int[], boolean) - Method in class RBNpackage.ProbFormConstant
 
evaluate(RelStruc, Instantiation, String[], int[], boolean) - Method in class RBNpackage.ProbFormConvComb
 
evaluate(RelStruc, Instantiation, String[], int[], boolean) - Method in class RBNpackage.ProbFormIndicator
 
evaluate(RelStruc, Instantiation, String[], int[], boolean) - Method in class RBNpackage.ProbFormSFormula
 
evaluate(RelStruc, String[], int[]) - Method in class RBNpackage.ProbFormSFormula
 
evaluate(RelStruc) - Method in class RBNpackage.ProbFormSFormula
 
evaluateBounds() - Method in class RBNLearning.GradientGraph
 
evaluateBounds() - Method in class RBNLearning.GradientGraphCombFuncNode
 
evaluateBounds() - Method in class RBNLearning.GradientGraphConstantNode
 
evaluateBounds() - Method in class RBNLearning.GradientGraphConvCombNode
 
evaluateBounds() - Method in class RBNLearning.GradientGraphIndicatorNode
 
evaluateBounds() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
evaluateBounds() - Method in class RBNLearning.GradientGraphNode
 
evaluateGrad(int) - Method in class RBNLearning.GradientGraphCombFuncNode
 
evaluateGrad(int) - Method in class RBNLearning.GradientGraphConstantNode
 
evaluateGrad(int) - Method in class RBNLearning.GradientGraphConvCombNode
 
evaluateGrad(int) - Method in class RBNLearning.GradientGraphIndicatorNode
 
evaluateGrad(int) - Method in class RBNLearning.GradientGraphLikelihoodNode
for compatibility with GradientGraphNode ....
evaluateGrad(int) - Method in class RBNLearning.GradientGraphNode
 
evaluateGradients() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
evaluateLikelihoodAndPartDerivs(boolean) - Method in class RBNLearning.GradientGraph
Computes the empirical likelihood and empirical partial derivatives of the current sample.
evaluatesTo(RelStruc, Instantiation, boolean, Hashtable) - Method in class RBNinference.ComplexPFNetworkNode
 
evaluatesTo(RelStruc, Instantiation, boolean, Hashtable) - Method in class RBNinference.PFNetworkNode
 
evaluatesTo(RelStruc, Instantiation, boolean, Hashtable) - Method in class RBNinference.SimplePFNetworkNode
 
evaluatesTo(boolean) - Method in class RBNinference.SimplePFNetworkNode
 
evaluatesTo(int[]) - Method in class RBNpackage.CombFunc
 
evaluatesTo(int[]) - Method in class RBNpackage.CombFuncESum
 
evaluatesTo(int[]) - Method in class RBNpackage.CombFuncInvsum
 
evaluatesTo(int[]) - Method in class RBNpackage.CombFuncMean
 
evaluatesTo(int[]) - Method in class RBNpackage.CombFuncNOr
 
evaluatesTo(RelStruc, Instantiation, boolean, Hashtable) - Method in class RBNpackage.ProbForm
Returns 0 if this probform evaluates to zero over structure A and with respect to instantiation inst, but irrespective of any instantiation of other probabilistic atoms.
evaluatesTo(RelStruc) - Method in class RBNpackage.ProbForm
 
evaluatesTo(RelStruc, Instantiation, boolean, Hashtable) - Method in class RBNpackage.ProbFormCombFunc
 
evaluatesTo(RelStruc) - Method in class RBNpackage.ProbFormCombFunc
 
evaluatesTo(RelStruc) - Method in class RBNpackage.ProbFormConstant
 
evaluatesTo(RelStruc, Instantiation, boolean, Hashtable) - Method in class RBNpackage.ProbFormConstant
 
evaluatesTo(RelStruc) - Method in class RBNpackage.ProbFormConvComb
 
evaluatesTo(RelStruc, Instantiation, boolean, Hashtable) - Method in class RBNpackage.ProbFormConvComb
 
evaluatesTo(RelStruc) - Method in class RBNpackage.ProbFormIndicator
 
evaluatesTo(RelStruc, Instantiation, boolean, Hashtable) - Method in class RBNpackage.ProbFormIndicator
 
evaluatesTo(RelStruc) - Method in class RBNpackage.ProbFormSFormula
 
evaluatesTo(RelStruc, Instantiation, boolean, Hashtable) - Method in class RBNpackage.ProbFormSFormula
 
evidencemode - Variable in class RBNgui.Primula
 
evidencemode() - Method in class RBNgui.Primula
 
EvidenceModule - Class in RBNgui
 
EvidenceModule(Primula) - Constructor for class RBNgui.EvidenceModule
 
evidenceModule - Variable in class RBNgui.Primula
 
exitProgram() - Method in class RBNgui.Primula
 
ExpandBuff(boolean) - Method in class RBNio.SimpleCharStream
 
expectedTokenSequences - Variable in exception RBNio.ParseException
Each entry in this array is an array of integers.

F

f1() - Method in class RBNpackage.ProbFormConvComb
 
f2() - Method in class RBNpackage.ProbFormConvComb
 
f3() - Method in class RBNpackage.ProbFormConvComb
 
familyXcenter() - Method in class RBNinference.BNNode
Computes the mean of the (current) xcoords of parents and children.
FileIO - Class in myio
 
FileIO() - Constructor for class myio.FileIO
Creates new OpenInputFile
FileIO - Class in RBNio
 
FileIO() - Constructor for class RBNio.FileIO
Creates new OpenInputFile
FillBuff() - Method in class RBNio.SimpleCharStream
 
Filter_bif - Class in RBNgui
 
Filter_bif() - Constructor for class RBNgui.Filter_bif
 
Filter_db - Class in RBNgui
 
Filter_db(boolean) - Constructor for class RBNgui.Filter_db
 
Filter_dne - Class in RBNgui
 
Filter_dne() - Constructor for class RBNgui.Filter_dne
 
Filter_foil - Class in RBNgui
 
Filter_foil() - Constructor for class RBNgui.Filter_foil
 
Filter_mln - Class in RBNgui
 
Filter_mln() - Constructor for class RBNgui.Filter_mln
 
Filter_net - Class in RBNgui
 
Filter_net() - Constructor for class RBNgui.Filter_net
 
Filter_pl - Class in RBNgui
 
Filter_pl() - Constructor for class RBNgui.Filter_pl
 
Filter_rbn - Class in RBNgui
 
Filter_rbn() - Constructor for class RBNgui.Filter_rbn
 
Filter_rdef - Class in RBNgui
 
Filter_rdef() - Constructor for class RBNgui.Filter_rdef
 
Filter_rst - Class in RBNgui
 
Filter_rst() - Constructor for class RBNgui.Filter_rst
 
find(String) - Method in class RBNpackage.OneStrucData
Finds the OneRelData with name relname
find(Rel) - Method in class RBNpackage.OneStrucData
 
FLAG_DEBUG - Static variable in class RBNgui.Primula
 
focusGained(FocusEvent) - Method in class RBNgui.ArbitraryPanel
 
focusLost(FocusEvent) - Method in class RBNgui.ArbitraryPanel
 
foilextension - Static variable in class RBNgui.Filter_foil
 
forgetAll() - Method in class RBNgui.EvidenceModule
 
forgetAll() - Method in class RBNgui.Primula
 
forInclusion(boolean, boolean) - Static method in enum RBNpackage.Instantiation.SetRelationship
 
freevars() - Method in class RBNpackage.CConstr
 
freevars() - Method in class RBNpackage.CConstrAnd
 
freevars() - Method in class RBNpackage.CConstrAtom
 
freevars() - Method in class RBNpackage.CConstrEmpty
 
freevars() - Method in class RBNpackage.CConstrEq
 
freevars() - Method in class RBNpackage.CConstrNeg
 
freevars() - Method in class RBNpackage.CConstrOr
 
freevars() - Method in class RBNpackage.ProbForm
returns the free variables of the formula
freevars() - Method in class RBNpackage.ProbFormCombFunc
 
freevars() - Method in class RBNpackage.ProbFormConstant
 
freevars() - Method in class RBNpackage.ProbFormConvComb
 
freevars() - Method in class RBNpackage.ProbFormIndicator
 
freevars() - Method in class RBNpackage.ProbFormSFormula
 

G

generateParseException() - Method in class RBNio.AtomListParser
Generate ParseException.
getACEControl() - Method in class RBNgui.EvidenceModule
 
getAdaptiveMode() - Method in class RBNgui.EvidenceModule
 
getArbitraryNames(Vector<Rel>) - Method in class RBNgui.ArbitraryPanel
 
getArbitraryRelations() - Method in class RBNpackage.OneStrucData
returns all the relations with arity >=3
getArbitraryRelations() - Method in class RBNpackage.RelStruc
 
getArguments() - Method in class MLNParser.ParsedRelation
 
getArgumentsArray() - Method in class MLNParser.ParsedRelation
 
getArity() - Method in class RBNpackage.Rel
 
getAttributes() - Method in class RBNpackage.OneStrucData
returns all the relations with arity 1
getAttributes() - Method in class RBNpackage.RelStruc
 
getAttributesColors(int) - Method in class RBNgui.Bavaria
 
getAttributesColors(int) - Method in class RBNpackage.RelStruc
 
getAttributesNames(Vector<Rel>) - Method in class RBNgui.AttributesPanel
 
getAttrRelsAndTuples(int) - Method in class RBNgui.Bavaria
 
getAttrRelsAndTuples(int) - Method in class RBNpackage.SparseRelStruc
returns this node's attributes and tuples
getBadType() - Method in exception MLNExceptions.DifferentTypesException
 
getBeginColumn() - Method in class RBNio.SimpleCharStream
Get token beginning column number.
getBeginLine() - Method in class RBNio.SimpleCharStream
Get token beginning line number.
getBinaryColors(int) - Method in class RBNgui.Bavaria
 
getBinaryColors(int) - Method in class RBNpackage.RelStruc
Returns the binary relation tuples from this node to some other node and the colors of the relations
getBinaryRelations() - Method in class RBNpackage.OneStrucData
returns all the relations with arity 2
getBinaryRelations() - Method in class RBNpackage.RelStruc
 
getBinaryrelsNames(Vector<Rel>) - Method in class RBNgui.BinaryPanel
 
getBinDirs(int) - Method in class RBNpackage.OneRelData
Returns the binary tuples from the specified node to some other node This method is usable ONLY with binary relations
getColor() - Method in class RBNpackage.Rel
 
getColumn() - Method in class RBNio.SimpleCharStream
Deprecated.  
getColumnCount() - Method in class RBNgui.ParameterTableModel
 
getColumnCount() - Method in class RBNgui.QueryTableModel
 
getConstants() - Method in class MLNParser.DeclaredType
 
getCoords() - Method in class RBNgui.Bavaria
 
getCoords() - Method in class RBNpackage.RelStruc
 
getCPTParents() - Method in class RBNgui.EvidenceModule
 
getCurrentInst() - Method in class RBNLearning.GradientGraphIndicatorNode
 
getCurrentParamVal() - Method in class RBNLearning.GradientGraphConstantNode
 
getCval() - Method in class RBNpackage.ProbFormConstant
 
getData() - Method in class RBNpackage.RelStruc
 
getDescription() - Method in class RBNgui.Filter_bif
 
getDescription() - Method in class RBNgui.Filter_db
 
getDescription() - Method in class RBNgui.Filter_dne
 
getDescription() - Method in class RBNgui.Filter_foil
 
getDescription() - Method in class RBNgui.Filter_mln
 
getDescription() - Method in class RBNgui.Filter_net
 
getDescription() - Method in class RBNgui.Filter_pl
 
getDescription() - Method in class RBNgui.Filter_rbn
 
getDescription() - Method in class RBNgui.Filter_rdef
 
getDescription() - Method in class RBNgui.Filter_rst
 
getEndColumn() - Method in class RBNio.SimpleCharStream
Get token end column number.
getEndLine() - Method in class RBNio.SimpleCharStream
Get token end line number.
getEstimates() - Method in class RBNgui.ParameterTableModel
 
getGradDistThresh() - Method in class RBNgui.LearnModule
 
getIcon(String) - Method in class RBNgui.Primula
 
GetImage() - Method in class RBNio.SimpleCharStream
Get token literal value.
getIndex() - Method in class RBNgui.NodeWindow
 
getIndexes(String[]) - Method in class RBNpackage.RelStruc
 
getInstantiation() - Method in class MLNParser.MLNParserFacade
 
getInstantiation() - Method in class RBNgui.Primula
 
getLine() - Method in class RBNio.SimpleCharStream
Deprecated.  
getLineDistThresh() - Method in class RBNgui.LearnModule
 
getLineLikThresh() - Method in class RBNgui.LearnModule
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class RBNgui.MyListCellRenderer
 
getLogfilename() - Method in class RBNgui.EvidenceModule
 
getMaxFails() - Method in class RBNgui.LearnModule
 
getMaximumXandY() - Method in class RBNgui.Bavaria
 
getMaxIterations() - Method in class RBNgui.LearnModule
 
getMaxProbs() - Method in class RBNinference.SampleProbs
 
getMessage() - Method in exception RBNio.ParseException
This method has the standard behavior when this object has been created using the standard constructors.
getMessage() - Method in error RBNio.TokenMgrError
You can also modify the body of this method to customize your error messages.
getMinimumXandY() - Method in class RBNgui.Bavaria
 
getMinProbs() - Method in class RBNinference.SampleProbs
 
getName() - Method in class RBNpackage.Type
 
getName() - Method in class RBNpackage.TypeDomain
 
getName() - Method in class RBNpackage.TypeInteger
 
getName() - Method in class RBNpackage.TypeRel
 
getNames() - Method in class RBNgui.Bavaria
 
getNames() - Method in class RBNpackage.RelStruc
 
getNextToken() - Method in class RBNio.AtomListParser
Get the next Token.
getNextToken() - Method in class RBNio.AtomListParserTokenManager
Get the next Token.
getNumChains() - Method in class RBNgui.LearnModule
 
getNumSubsamples_adapt() - Method in class RBNgui.EvidenceModule
 
getNumSubsamples_minmax() - Method in class RBNgui.EvidenceModule
 
getOtherRelsAndTuples(int) - Method in class RBNgui.Bavaria
 
getOtherRelsAndTuples(int) - Method in class RBNpackage.SparseRelStruc
returns binary and arbitrary relations and corresponding tuples which include this node
getOwner() - Method in class RBNpackage.Atom
 
getParameters() - Method in class RBNgui.ParameterTableModel
 
getParameters() - Method in class RBNLearning.GradientGraph
 
getParamName() - Method in class RBNpackage.ProbFormConstant
 
getParamratiothresh() - Method in class RBNgui.LearnModule
 
getPreferences() - Method in class RBNgui.Primula
 
getProbRels() - Method in class RBNLearning.RelDataForOneInput
 
getProbs() - Method in class RBNinference.SampleProbs
 
getProgress() - Method in class RBNinference.BayesConstructor
 
getProgressMax() - Method in class RBNinference.BayesConstructor
 
getQuery() - Method in class RBNgui.QueryTableModel
 
getRBN() - Method in class MLNParser.MLNParserFacade
 
getRBN() - Method in class RBNgui.Primula
 
getRel() - Method in class RBNpackage.TypeRel
 
getRelation() - Method in exception MLNExceptions.DifferentTypesException
 
getRelationName() - Method in class MLNParser.ParsedRelation
 
getRels() - Method in class RBNgui.Primula
 
getRels() - Method in class RBNpackage.OneStrucData
The RelStruc argument is used to save the data using the real names for the objects.
getRels() - Method in class RBNpackage.RelStruc
 
getRelStruc() - Method in class MLNParser.MLNParserFacade
 
getRestarts() - Method in class RBNgui.LearnModule
 
getRowCount() - Method in class RBNgui.ParameterTableModel
 
getRowCount() - Method in class RBNgui.QueryTableModel
 
getSamiamManager() - Method in class RBNgui.Primula
 
getSamIamUIInstanceThis() - Method in class RBNgui.Primula
 
getSampleLikelihood(int) - Method in class RBNLearning.GradientGraphLikelihoodNode
 
getSampleLikelihoods() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
getSampleLogMode() - Method in class RBNgui.EvidenceModule
 
getSampleLogMode(int) - Method in class RBNgui.EvidenceModule
 
getSampleOrdMode() - Method in class RBNgui.EvidenceModule
 
getSize() - Method in class RBNinference.SampleProbs
 
getSize() - Method in class RBNpackage.RelStruc
 
getSmallgradient() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
GetStrings(String) - Method in class RBNio.RBNReader
Returns the contents of file as an array of strings.
GetSuffix(int) - Method in class RBNio.SimpleCharStream
Get the suffix.
getTabSize(int) - Method in class RBNio.SimpleCharStream
 
getToken(int) - Method in class RBNio.AtomListParser
Get the specific Token.
getType() - Method in class MLNParser.DeclaredType
 
getTypes() - Method in class RBNpackage.Rel
 
getTypesAsString() - Method in class RBNpackage.Rel
 
getValue() - Method in class RBNio.Token
An optional attribute value of the Token.
getValueAt(int, int) - Method in class RBNgui.ParameterTableModel
 
getValueAt(int, int) - Method in class RBNgui.QueryTableModel
 
getVar() - Method in class RBNinference.SampleProbs
 
getVariable() - Method in exception MLNExceptions.DifferentTypesException
 
getWeight() - Method in class RBNinference.SampleProbs
 
getWindowSize() - Method in class RBNgui.LearnModule
 
getZoom() - Method in class RBNgui.EditPanel
 
gibbsSample(int, LearnThread) - Method in class RBNLearning.GradientGraph
Performs one round of Gibbs sampling.
gradient() - Method in class RBNLearning.GradientGraphNode
 
gradientAsDouble() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
gradientAsDouble(int) - Method in class RBNLearning.GradientGraphLikelihoodNode
Returns the gradient (scaled to fit double precision) with all components where zeros[i]=1 set to 0 Corresponds to taking partial derivatives, ignoring parameters with index i.
GradientGraph - Class in RBNLearning
Main class for RBN parameter learning.
GradientGraph(Primula, RelData, LearnModule) - Constructor for class RBNLearning.GradientGraph
 
GradientGraphCombFuncNode - Class in RBNLearning
 
GradientGraphCombFuncNode(GradientGraph, ProbForm, Hashtable, RelStruc, Instantiation, int, int) - Constructor for class RBNLearning.GradientGraphCombFuncNode
 
GradientGraphConstantNode - Class in RBNLearning
 
GradientGraphConstantNode(GradientGraph, ProbForm, RelStruc, Instantiation) - Constructor for class RBNLearning.GradientGraphConstantNode
 
GradientGraphConvCombNode - Class in RBNLearning
In a GradientGraphConvCombNode the children vector has exactly 3 elements, one for each of the three subformulas An element is set to null if the formula does not actually need to be contained in this vector.
GradientGraphConvCombNode(GradientGraph, ProbForm, Hashtable<String, GradientGraphNode>, RelStruc, Instantiation, int, int) - Constructor for class RBNLearning.GradientGraphConvCombNode
pf must be a ground ProbForm !
GradientGraphIndicatorNode - Class in RBNLearning
 
GradientGraphIndicatorNode(GradientGraph, ProbForm, RelStruc, Instantiation, int, int) - Constructor for class RBNLearning.GradientGraphIndicatorNode
 
GradientGraphLikelihoodNode - Class in RBNLearning
 
GradientGraphLikelihoodNode(GradientGraph) - Constructor for class RBNLearning.GradientGraphLikelihoodNode
 
GradientGraphNode - Class in RBNLearning
 
GradientGraphNode(GradientGraph) - Constructor for class RBNLearning.GradientGraphNode
 
GradientGraphProbFormNode - Class in RBNLearning
 
GradientGraphProbFormNode(GradientGraph, ProbForm, RelStruc, Instantiation) - Constructor for class RBNLearning.GradientGraphProbFormNode
 
gradientsumAsDouble() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
gradientsumAsDouble(int) - Method in class RBNLearning.GradientGraphLikelihoodNode
 
GroundAtomNodeInt - Interface in RBNinference
 

H

hashCode() - Method in class RBNpackage.Atom
 
hashCodeImpl() - Method in class RBNpackage.Atom
 
hashCodeImpl() - Method in class RBNpackage.InstAtom
 
horizontalIP(double, double, double, double, double, double, boolean) - Method in class RBNgui.EditPanel
 

I

image - Variable in class RBNio.Token
The string image of the token.
inArgument(int) - Method in class RBNpackage.Atom
 
inArray(Rel[], Rel) - Static method in class RBNutilities.rbnutilities
 
inArray(int[], int) - Static method in class RBNutilities.rbnutilities
 
inBuf - Variable in class RBNio.SimpleCharStream
 
incrementBitVector(int[]) - Static method in class RBNutilities.rbnutilities
bv is a 0-1 vector representing integer n Method turns it into vector representing n+1 (if n+1 < 2^bv.length, otherwise throws exception)
indexInArray(String[], String) - Static method in class RBNutilities.rbnutilities
Returns the index of the (first occurrence) of s in sarray; Returns -1 if s not in sarray
indexOf(double) - Method in class mymath.DoubleVector
 
indexOf(int) - Method in class mymath.IntVector
 
indexOf(double) - Method in class RBNutilities.DoubleVector
 
indexto01array(int, int) - Static method in class mymath.MyMathOps
 
indexToTuple(int, int, int) - Static method in class myio.StringOps
 
indexToTuple(int, int, int) - Static method in class RBNutilities.rbnutilities
returns the tuple i_0,i_2,...,i_(dim-1) that occurs in place 'ind' in a lexicographic enumeration of all 'dim'-tuples of integers in the range [0..range-1] 0 <= ind <= range^dim
initializeForNextSample() - Method in class RBNinference.PFNetworkNode
 
initializeForSampling(int, int, AtomList, int, int) - Method in class RBNinference.ComplexPFNetworkNode
 
initializeForSampling(int, int, AtomList, int, int) - Method in class RBNinference.PFNetworkNode
 
initializeForSampling(int, int, AtomList, int, int) - Method in class RBNinference.SimplePFNetworkNode
 
initIndicators(LearnThread) - Method in class RBNLearning.GradientGraph
 
initSampledVals(int) - Method in class RBNLearning.GradientGraphIndicatorNode
initializes sampledVals to an array of size 'size'
initSampleLikelihoods(int) - Method in class RBNLearning.GradientGraphLikelihoodNode
 
innerProduct(double[], double[]) - Static method in class mymath.MyMathOps
 
input_stream - Variable in class RBNio.AtomListParserTokenManager
 
inputcaseno() - Method in class RBNLearning.GradientGraphIndicatorNode
 
inputDomain() - Method in class RBNLearning.RelDataCase
 
inputDomain() - Method in class RBNLearning.RelDataForOneInput
 
inputStream - Variable in class RBNio.SimpleCharStream
 
InsertArguments(String[], int) - Method in class RBNpackage.RBN
 
insertCompNetwork(LinkedList, SimpleBNNode, int) - Method in class RBNpackage.CombFuncMean
 
insertCompNetwork(LinkedList, SimpleBNNode, int) - Method in class RBNpackage.CombFuncNOr
 
insertCompNetwork(LinkedList, SimpleBNNode, int) - Method in class RBNpackage.MultLinCombFunc
 
insertConstant(String) - Method in class MLNParser.DeclaredType
 
InsertProbForm(ProbForm, int) - Method in class RBNpackage.RBN
 
insertRel(Rel, int) - Method in class RBNpackage.RBN
 
inst - Variable in class RBNgui.Primula
 
INSTANCE - Static variable in class RBNinference.BayesConstructor.WeightComparator
 
instantiate(int) - Method in class RBNinference.BNNode
 
instantiated - Variable in class RBNinference.BNNode
 
instantiatedTo() - Method in class RBNinference.BNNode
 
Instantiation - Class in RBNpackage
 
Instantiation() - Constructor for class RBNpackage.Instantiation
Creates new Instantiation
Instantiation(Instantiation) - Constructor for class RBNpackage.Instantiation
 
Instantiation(OneStrucData) - Constructor for class RBNpackage.Instantiation
 
Instantiation.SetRelationship - Enum in RBNpackage
 
InstAtom - Class in RBNpackage
 
InstAtom() - Constructor for class RBNpackage.InstAtom
Creates new InstAtom
InstAtom(Rel, int[], boolean) - Constructor for class RBNpackage.InstAtom
 
instContainsAll(Instantiation) - Method in class RBNgui.Primula
 
instValAt(int) - Method in class RBNinference.PFNetwork
 
intarrayadd(int[], int[]) - Static method in class mymath.MyMathOps
 
IntArrayComparator - Class in RBNutilities
 
IntArrayComparator() - Constructor for class RBNutilities.IntArrayComparator
 
intArrayToDoubleArray(int[]) - Static method in class myio.StringOps
 
intArrVecToString(Vector) - Static method in class RBNutilities.rbnutilities
Formats a vector of int[] as String
integerMatch(String[], int[]) - Static method in class RBNutilities.rbnutilities
Checks whether all the components in sarray that are integers match the integers in iarray at the same position
intPow(int, int) - Static method in class mymath.MyMathOps
 
IntPow(int, int) - Static method in class RBNutilities.rbnutilities
 
IntVector - Class in mymath
 
IntVector() - Constructor for class mymath.IntVector
 
InvalidTypeArgumentsException - Exception in MLNExceptions
 
InvalidTypeArgumentsException() - Constructor for exception MLNExceptions.InvalidTypeArgumentsException
Creates a new instance of InvalidTypeArgumentsException without detail message.
InvalidTypeArgumentsException(String) - Constructor for exception MLNExceptions.InvalidTypeArgumentsException
Constructs an instance of InvalidTypeArgumentsException with the specified detail message.
INVSUM - Static variable in class RBNpackage.ProbFormCombFunc
 
isCombFuncName(String) - Static method in class RBNpackage.CombFunc
 
isConstantInType(String) - Method in class MLNParser.DeclaredType
 
isDetEquivalent(SimpleBNNode) - Method in class RBNinference.SimpleBNNode
returns true if this and sbnn are equivalent deterministic nodes, i.e.
isEmpty() - Method in class RBNpackage.AtomList
 
isEmpty() - Method in class RBNpackage.Instantiation
 
isEmpty() - Method in class RBNpackage.OneStrucData
 
isGround() - Method in class RBNpackage.ProbFormIndicator
 
isIdenticalTo(Atom) - Method in class RBNpackage.Atom
 
isInstEmpty() - Method in class RBNgui.Primula
 
IsInteger(String) - Static method in class RBNutilities.rbnutilities
 
isIsolatedZeroNode(RelStruc) - Method in class RBNinference.ComplexBNNode
 
isIsolatedZeroNode(RelStruc) - Method in interface RBNinference.ComplexBNNodeInt
 
isIsolatedZeroNode(RelStruc) - Method in class RBNinference.ComplexPFNetworkNode
 
isIsolatedZeroNode() - Method in class RBNinference.SimpleBNNode
 
isIsolatedZeroNode(RelStruc) - Method in class RBNinference.SimplePFNetworkNode
 
isLocallyConsistent(RelStruc, Instantiation, boolean, Hashtable, int) - Method in class RBNinference.PFNetworkNode
 
isolatedzeronodesmode - Variable in class RBNgui.Primula
 
isOrdRel(Rel) - Method in class RBNpackage.RelStruc
Returns true if r is one of the OrdRels
isQueryatomsEmpty() - Method in class RBNgui.Primula
 
isstopped() - Method in class RBNLearning.LearnThread
 
isSubset() - Method in enum RBNpackage.Instantiation.SetRelationship
 
isSuperset() - Method in enum RBNpackage.Instantiation.SetRelationship
 
isSystemExitEnabled() - Method in class RBNgui.Primula
 
itemStateChanged(ItemEvent) - Method in class RBNgui.LearnSettings
 
itemStateChanged(ItemEvent) - Method in class RBNgui.Primula
 
itemStateChanged(ItemEvent) - Method in class RBNgui.Settings
 

J

jj_nt - Variable in class RBNio.AtomListParser
Next token.
jjFillToken() - Method in class RBNio.AtomListParserTokenManager
 
jjnewLexState - Static variable in class RBNio.AtomListParserTokenManager
Lex State array.
jjstrLiteralImages - Static variable in class RBNio.AtomListParserTokenManager
Token literal values.

K

keyPressed(KeyEvent) - Method in class RBNgui.ArbitraryPanel
 
keyPressed(KeyEvent) - Method in class RBNgui.AttributesPanel
 
keyPressed(KeyEvent) - Method in class RBNgui.BinaryPanel
 
keyPressed(KeyEvent) - Method in class RBNgui.NodeWindow
 
keyPressed(KeyEvent) - Method in class RBNgui.Primula
 
keyReleased(KeyEvent) - Method in class RBNgui.ArbitraryPanel
 
keyReleased(KeyEvent) - Method in class RBNgui.AttributesPanel
 
keyReleased(KeyEvent) - Method in class RBNgui.BinaryPanel
 
keyReleased(KeyEvent) - Method in class RBNgui.NodeWindow
 
keyReleased(KeyEvent) - Method in class RBNgui.Primula
 
keyTyped(KeyEvent) - Method in class RBNgui.ArbitraryPanel
 
keyTyped(KeyEvent) - Method in class RBNgui.AttributesPanel
 
keyTyped(KeyEvent) - Method in class RBNgui.BinaryPanel
 
keyTyped(KeyEvent) - Method in class RBNgui.NodeWindow
 
keyTyped(KeyEvent) - Method in class RBNgui.Primula
 
kind - Variable in class RBNio.Token
An integer that describes the kind of this token.

L

layoutmode - Variable in class RBNgui.Primula
 
LearnModule - Class in RBNgui
 
LearnModule(Primula) - Constructor for class RBNgui.LearnModule
 
learnModule - Variable in class RBNgui.Primula
 
learnParameters(LearnThread) - Method in class RBNLearning.GradientGraph
 
LearnSettings - Class in RBNgui
 
LearnSettings(LearnModule) - Constructor for class RBNgui.LearnSettings
 
LearnThread - Class in RBNLearning
 
LearnThread(Primula, RelData, ParameterTableModel, JTable, JTextField, LearnModule) - Constructor for class RBNLearning.LearnThread
 
legalRelName(String) - Static method in class RBNpackage.RelName
 
LexicalError(boolean, int, int, int, String, char) - Static method in error RBNio.TokenMgrError
Returns a detailed message for the Error when it is thrown by the token manager to indicate a lexical error.
lexStateNames - Static variable in class RBNio.AtomListParserTokenManager
Lexer state names.
likelihood() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
likelihoodsum() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
line - Variable in class RBNio.SimpleCharStream
 
linkedListToVector(LinkedList) - Static method in class RBNutilities.rbnutilities
 
Literal(AtomListReader) - Method in class RBNio.AtomListParser
 
loadFunction() - Method in class RBNgui.Bavaria
 
LoadMLN(File, File, File) - Method in class RBNgui.Primula
 
loadRBNFunction(File) - Method in class RBNgui.Primula
 
loadSparseRelFile(File) - Method in class RBNgui.Primula
 
lowerBound() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
lowerBound() - Method in class RBNLearning.GradientGraphProbFormNode
 

M

main(String[]) - Static method in class mymath.Averages
 
main(String[]) - Static method in class mymath.Distance
 
main(String[]) - Static method in class mymath.Normalize
 
main(String[]) - Static method in class mymath.RandomGenerator
 
main(String[]) - Static method in class RBNgui.Primula
 
main(String[]) - Static method in class RBNLearning.SampleMain
 
makeAlternateName() - Method in class RBNgui.Primula
 
makeCitationGraph(int, double, double, double) - Method in class RBNLearning.Sampler
Build a structure representing authors, papers and citations numauthors: number of authors posauthors: probability of an author being a positive example (high h number)
makeCPT(ProbForm, RelStruc, Instantiation, Vector) - Static method in class RBNinference.BayesConstructor
 
makeIDFromDisplayName(String) - Static method in class RBNinference.BayesNetIntHuginNet
 
makeNetName(String) - Static method in class RBNinference.BayesNetIntHuginNet
 
makeNetworkName() - Method in class RBNgui.Primula
 
makeParentVec(RelStruc) - Method in class RBNpackage.ProbForm
returns the vector of (ground!) Atoms on which the evaluation of the probform depends
makeParentVec(RelStruc, Instantiation) - Method in class RBNpackage.ProbForm
same as previous but with respect to the given truth values in the Instantiation argument
makeParentVec(RelStruc) - Method in class RBNpackage.ProbFormCombFunc
 
makeParentVec(RelStruc, Instantiation) - Method in class RBNpackage.ProbFormCombFunc
 
makeParentVec(RelStruc) - Method in class RBNpackage.ProbFormConstant
 
makeParentVec(RelStruc, Instantiation) - Method in class RBNpackage.ProbFormConstant
 
makeParentVec(RelStruc) - Method in class RBNpackage.ProbFormConvComb
 
makeParentVec(RelStruc, Instantiation) - Method in class RBNpackage.ProbFormConvComb
 
makeParentVec(RelStruc) - Method in class RBNpackage.ProbFormIndicator
 
makeParentVec(RelStruc, Instantiation) - Method in class RBNpackage.ProbFormIndicator
 
makeParentVec(RelStruc) - Method in class RBNpackage.ProbFormSFormula
 
makeParentVec(RelStruc, Instantiation) - Method in class RBNpackage.ProbFormSFormula
 
makeRandomColoredGraph(int, double, double, double) - Method in class RBNLearning.Sampler
Constructs a random graph (given by binary relation 'edge') over 'size' nodes.
makeRandomGraph(int, double, boolean, int) - Method in class RBNLearning.Sampler
Constructs a random graph (given by binary relation 'edge') over 'size' nodes.
makeRandomPedigree(int, double) - Method in class RBNLearning.Sampler
Constructs a random pedigree-like structure: nodes have either two or zero parents
makeRandomTypedDomain(int, String[], double[]) - Method in class RBNLearning.Sampler
Constructs a domain of size 'size' with objects of types 'types'.
makeSampleStruc(Primula) - Method in class RBNLearning.Sampler
 
makeSlotchainBase(int, int, int, int, int) - Method in class RBNLearning.Sampler
Constructs a random structure for investigating slotchain like dependencies: domain consists of 'numtypes' different types of objects; 'numoftype' objects of each type.
matrixToString(int[][], String, String) - Static method in class myio.StringOps
 
matrixToString(double[][], String, String) - Static method in class myio.StringOps
 
MatrixToString(int[][]) - Static method in class RBNutilities.rbnutilities
 
maxNextCharInd - Variable in class RBNio.SimpleCharStream
 
MEAN - Static variable in class RBNpackage.ProbFormCombFunc
 
mergeSorted(DoubleVector) - Method in class mymath.DoubleVector
 
mergeSorted(IntVector) - Method in class mymath.IntVector
 
mergeSorted(DoubleVector) - Method in class RBNutilities.DoubleVector
 
mln - Static variable in class RBNgui.Filter_mln
 
MLN_FORMAT - Static variable in class RBNpackage.RelStruc
 
MLNExceptions - package MLNExceptions
 
MLNParser - package MLNParser
 
MLNParserFacade - Class in MLNParser
 
MLNParserFacade() - Constructor for class MLNParser.MLNParserFacade
 
mouseClicked(MouseEvent) - Method in class RBNgui.ArbitraryPanel
 
mouseClicked(MouseEvent) - Method in class RBNgui.AttributesPanel
 
mouseClicked(MouseEvent) - Method in class RBNgui.BinaryPanel
 
mouseClicked(MouseEvent) - Method in class RBNgui.EditPanel
 
mouseClicked(MouseEvent) - Method in class RBNgui.EvidenceModule
 
mouseClicked(MouseEvent) - Method in class RBNgui.NodeWindow
 
mouseDragged(MouseEvent) - Method in class RBNgui.EditPanel
 
mouseEntered(MouseEvent) - Method in class RBNgui.ArbitraryPanel
 
mouseEntered(MouseEvent) - Method in class RBNgui.AttributesPanel
 
mouseEntered(MouseEvent) - Method in class RBNgui.BinaryPanel
 
mouseEntered(MouseEvent) - Method in class RBNgui.EditPanel
 
mouseEntered(MouseEvent) - Method in class RBNgui.EvidenceModule
 
mouseEntered(MouseEvent) - Method in class RBNgui.NodeWindow
 
mouseExited(MouseEvent) - Method in class RBNgui.ArbitraryPanel
 
mouseExited(MouseEvent) - Method in class RBNgui.AttributesPanel
 
mouseExited(MouseEvent) - Method in class RBNgui.BinaryPanel
 
mouseExited(MouseEvent) - Method in class RBNgui.EditPanel
 
mouseExited(MouseEvent) - Method in class RBNgui.EvidenceModule
 
mouseExited(MouseEvent) - Method in class RBNgui.NodeWindow
 
mouseMoved(MouseEvent) - Method in class RBNgui.EditPanel
 
mousePressed(MouseEvent) - Method in class RBNgui.ArbitraryPanel
 
mousePressed(MouseEvent) - Method in class RBNgui.AttributesPanel
 
mousePressed(MouseEvent) - Method in class RBNgui.BinaryPanel
 
mousePressed(MouseEvent) - Method in class RBNgui.EditPanel
 
mousePressed(MouseEvent) - Method in class RBNgui.EvidenceModule
 
mousePressed(MouseEvent) - Method in class RBNgui.NodeWindow
 
mouseReleased(MouseEvent) - Method in class RBNgui.ArbitraryPanel
 
mouseReleased(MouseEvent) - Method in class RBNgui.AttributesPanel
 
mouseReleased(MouseEvent) - Method in class RBNgui.BinaryPanel
 
mouseReleased(MouseEvent) - Method in class RBNgui.EditPanel
 
mouseReleased(MouseEvent) - Method in class RBNgui.EvidenceModule
 
mouseReleased(MouseEvent) - Method in class RBNgui.NodeWindow
 
moveView(double, double) - Method in class RBNgui.Bavaria
 
multiply(double[], double[]) - Static method in class RBNutilities.SmallDouble
 
multiply(double[], double) - Static method in class RBNutilities.SmallDouble
 
MultLinCombFunc - Class in RBNpackage
 
MultLinCombFunc() - Constructor for class RBNpackage.MultLinCombFunc
 
multlinOnly() - Method in class RBNpackage.ProbForm
returns true if ProbForm only contains multilinear combination functions
multlinOnly() - Method in class RBNpackage.ProbFormCombFunc
 
multlinOnly() - Method in class RBNpackage.ProbFormConstant
 
multlinOnly() - Method in class RBNpackage.ProbFormConvComb
 
multlinOnly() - Method in class RBNpackage.ProbFormIndicator
 
multlinOnly() - Method in class RBNpackage.ProbFormSFormula
 
multlinOnly() - Method in class RBNpackage.RBN
 
multRandInt(int, int, int) - Static method in class RBNutilities.randomGenerators
Returns an array of num random integers between min and max without repetitions Very inefficient implementation unless num << max-min
myatom() - Method in class RBNinference.ComplexBNGroundAtomNode
 
myatom() - Method in interface RBNinference.GroundAtomNodeInt
 
myatom - Variable in class RBNinference.PFNetworkNode
 
myatom() - Method in class RBNinference.PFNetworkNode
 
myatom - Variable in class RBNinference.SimpleBNGroundAtomNode
 
myatom() - Method in class RBNinference.SimpleBNGroundAtomNode
 
myatom() - Method in class RBNLearning.GradientGraphIndicatorNode
 
mycomb - Variable in class RBNpackage.ProbFormCombFunc
 
mycombInt - Variable in class RBNpackage.ProbFormCombFunc
 
myCombInt() - Method in class RBNpackage.ProbFormCombFunc
Returns the combination function used in this probform according to the integer encoding: N-or = 1 (= static int ProbFormCombFunc.NOR); Mean = 2 (= static int ProbFormCombFunc.MEAN); InvSum = 3 (= static int ProbFormCombFunc.INVSUM); ESUM = 3 (= static int ProbFormCombFunc.INVSUM);
mycpt() - Method in class RBNinference.SimplePFNetworkNode
 
myio - package myio
 
MyListCellRenderer - Class in RBNgui
 
MyListCellRenderer() - Constructor for class RBNgui.MyListCellRenderer
 
mymath - package mymath
 
MyMathOps - Class in mymath
 
MyMathOps() - Constructor for class mymath.MyMathOps
 
MyRandom - Class in mymath
 
MyRandom() - Constructor for class mymath.MyRandom
 

N

name - Variable in class RBNinference.BNNode
 
Name - Static variable in interface RBNio.AtomListParserConstants
RegularExpression Id.
name() - Method in class RBNLearning.GradientGraphLikelihoodNode
The name of this node.
name() - Method in class RBNLearning.GradientGraphNode
The name of this node.
name() - Method in class RBNLearning.GradientGraphProbFormNode
The name of this node.
name - Variable in class RBNpackage.CombFunc
 
name - Variable in class RBNpackage.Rel
 
name - Variable in class RBNpackage.RelName
 
name - Variable in class RBNpackage.Type
 
nameAt(int) - Method in class RBNgui.Bavaria
 
nameAt(int) - Method in class RBNpackage.OrdStruc
 
NameAt(int) - Method in class RBNpackage.RBN
 
nameAt(int) - Method in class RBNpackage.RelStruc
 
namesAt(int[]) - Method in class RBNpackage.RelStruc
 
namesAtAsArray(int[]) - Method in class RBNpackage.RelStruc
 
net - Static variable in class RBNgui.Filter_net
 
newAdaptiveMode(int) - Method in class RBNgui.EvidenceModule
 
newElementNames() - Method in class RBNgui.EvidenceModule
 
newOrdStruc(int) - Method in class RBNgui.Primula
 
newSampleordMode(int) - Method in class RBNgui.EvidenceModule
 
newToken(int, String) - Static method in class RBNio.Token
Returns a new Token object, by default.
newToken(int) - Static method in class RBNio.Token
 
NewVariables(String[], int) - Static method in class RBNutilities.rbnutilities
 
next - Variable in class RBNio.Token
A reference to the next regular (non-special) token from the input stream.
nodeClicked(long, long) - Method in class RBNgui.EditPanel
 
NodeWindow - Class in RBNgui
 
NodeWindow(Bavaria, EditPanel, int) - Constructor for class RBNgui.NodeWindow
 
nodeWindowNodeDeleted(int) - Method in class RBNgui.EditPanel
 
nodeWindowNodeDeleted(int) - Method in class RBNgui.NodeWindow
 
NonIntOnly(String[]) - Static method in class RBNutilities.rbnutilities
 
NOR - Static variable in class RBNpackage.ProbFormCombFunc
 
Normalize - Class in mymath
 
Normalize() - Constructor for class mymath.Normalize
 
NoSuchRelationException - Exception in MLNExceptions
 
NoSuchRelationException() - Constructor for exception MLNExceptions.NoSuchRelationException
Creates a new instance of NoSuchRelationException without detail message.
NoSuchRelationException(String) - Constructor for exception MLNExceptions.NoSuchRelationException
Constructs an instance of NoSuchRelationException with the specified detail message.
Not - Static variable in interface RBNio.AtomListParserConstants
RegularExpression Id.
nthRoot(double[], double) - Static method in class RBNutilities.SmallDouble
 
numberOfEdges() - Method in class RBNLearning.GradientGraph
Returns the number of links in the graph
numberOfIndicators() - Method in class RBNLearning.GradientGraph
Returns the number of indicator nodes in the graph
numberOfNodes() - Method in class RBNLearning.GradientGraph
Returns the number of nodes in the graph
numberOfParameters() - Method in class RBNLearning.GradientGraph
 
numChildren() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
numfalse() - Method in class RBNpackage.OneRelData
 
numfalsesamples - Variable in class RBNinference.SimplePFNetworkNode
numtruesamples[i]: number of samples in which i'th parent configuration was sampled and this node was sampled false (in a run of importance sampling).
numfalsesamples_subsample - Variable in class RBNinference.SimplePFNetworkNode
 
numObservations() - Method in class RBNLearning.RelDataForOneInput
 
numPFargs() - Method in class RBNpackage.ProbFormCombFunc
Returns the number of probability formulas in the argument of this formula's combination function
NumPFs() - Method in class RBNpackage.RBN
 
numRels() - Method in class RBNpackage.OneStrucData
 
numtrue() - Method in class RBNpackage.OneRelData
 
numtruesamples - Variable in class RBNinference.SimplePFNetworkNode
numtruesamples[i]: number of samples in which i'th parent configuration was sampled and this node was sampled true (in a run of importance sampling).
numtruesamples_subsample - Variable in class RBNinference.SimplePFNetworkNode
 

O

observcaseno() - Method in class RBNLearning.GradientGraphIndicatorNode
 
observedAtoms() - Method in class RBNLearning.RelDataCase
 
observedAtoms() - Method in class RBNLearning.RelDataForOneInput
 
omitRounds() - Method in class RBNgui.LearnModule
 
OneRelData - Class in RBNpackage
An object of the class OneRelData represents one observation of all or some atoms of one probabilistic relation for one given input domain.
OneRelData(Rel, String) - Constructor for class RBNpackage.OneRelData
 
OneStrucData - Class in RBNpackage
An object of the class OneStrucData represents one (partial) observation of a given set of relations for one given input domain.
OneStrucData() - Constructor for class RBNpackage.OneStrucData
 
OneStrucData(Vector<OneRelData>) - Constructor for class RBNpackage.OneStrucData
 
oneStrucDataAt(int) - Method in class RBNLearning.RelDataForOneInput
 
open() - Method in interface RBNinference.BayesNetInt
 
open() - Method in class RBNinference.BayesNetIntBIF
 
open() - Method in class RBNinference.BayesNetIntHuginNet
 
open() - Method in class RBNinference.BayesNetIntNeticaDnet
 
open() - Method in class RBNinference.BayesNetIntSamIam
 
open() - Method in class RBNinference.BayesNetIntXMLBIF
 
openInputFile(String) - Static method in class myio.FileIO
 
openInputFile(String) - Static method in class RBNio.FileIO
 
openNodeWindow(int) - Method in class RBNgui.EditPanel
 
openOutputFile(String) - Static method in class myio.FileIO
 
openOutputFile(File) - Static method in class myio.FileIO
 
openOutputFile(String) - Static method in class RBNio.FileIO
 
OpenPar - Static variable in interface RBNio.AtomListParserConstants
RegularExpression Id.
openWorld - Variable in class RBNgui.Filter_db
 
OPTION_DECOMPOSE - Static variable in class RBNgui.Primula
 
OPTION_DECOMPOSE_DETERMINISTIC - Static variable in class RBNgui.Primula
 
OPTION_ELIMINATE_ISOLATED_ZERO_NODES - Static variable in class RBNgui.Primula
 
OPTION_EVIDENCE_CONDITIONED - Static variable in class RBNgui.Primula
 
OPTION_HUGIN - Static variable in class RBNgui.Primula
 
OPTION_JAVABAYES - Static variable in class RBNgui.Primula
 
OPTION_LAYOUT - Static variable in class RBNgui.Primula
 
OPTION_NETICA - Static variable in class RBNgui.Primula
 
OPTION_NO_LAYOUT - Static variable in class RBNgui.Primula
 
OPTION_NOT_DECOMPOSE - Static variable in class RBNgui.Primula
 
OPTION_NOT_ELIMINATE_ISOLATED_ZERO_NODES - Static variable in class RBNgui.Primula
 
OPTION_NOT_EVIDENCE_CONDITIONED - Static variable in class RBNgui.Primula
 
OPTION_NOT_QUERY_SPECIFIC - Static variable in class RBNgui.Primula
 
OPTION_NOT_SAMPLE_ADAPTIVE - Static variable in class RBNgui.EvidenceModule
 
OPTION_QUERY_SPECIFIC - Static variable in class RBNgui.Primula
 
OPTION_SAMIAM - Static variable in class RBNgui.Primula
 
OPTION_SAMPLE_ADAPTIVE - Static variable in class RBNgui.EvidenceModule
 
OPTION_SAMPLEORD_FORWARD - Static variable in class RBNgui.EvidenceModule
 
OPTION_SAMPLEORD_RIPPLE - Static variable in class RBNgui.EvidenceModule
 
OrdStruc - Class in RBNpackage
 
OrdStruc(int) - Constructor for class RBNpackage.OrdStruc
 
OrdStruc(OrdStruc) - Constructor for class RBNpackage.OrdStruc
 

P

paintComponent(Graphics) - Method in class RBNgui.EditPanel
 
parameterAt(int) - Method in class RBNLearning.GradientGraph
 
parameters() - Method in class RBNLearning.GradientGraph
 
parameters() - Method in class RBNpackage.ProbForm
Returns all the parameters that this ProbForm depends on
parameters() - Method in class RBNpackage.ProbFormCombFunc
 
parameters() - Method in class RBNpackage.ProbFormConstant
 
parameters() - Method in class RBNpackage.ProbFormConvComb
 
parameters() - Method in class RBNpackage.ProbFormIndicator
 
parameters() - Method in class RBNpackage.ProbFormSFormula
 
parameters() - Method in class RBNpackage.RBN
Returns all the parameters contained in probability formulas in the RBN.
ParameterTableModel - Class in RBNgui
 
ParameterTableModel() - Constructor for class RBNgui.ParameterTableModel
 
paramname() - Method in class RBNLearning.GradientGraphConstantNode
 
parentConfig() - Method in class RBNinference.SimplePFNetworkNode
 
parents - Variable in class RBNinference.BNNode
 
parents() - Method in class RBNLearning.GradientGraphNode
 
parentsSubset(BNNode) - Method in class RBNinference.BNNode
returns true if this.parents is subset of bnn.parents
ParsedRelation - Class in MLNParser
 
ParsedRelation() - Constructor for class MLNParser.ParsedRelation
 
ParsedRelation(String) - Constructor for class MLNParser.ParsedRelation
 
ParseException - Exception in RBNio
This exception is thrown when parse errors are encountered.
ParseException(Token, int[][], String[]) - Constructor for exception RBNio.ParseException
This constructor is used by the method "generateParseException" in the generated parser.
ParseException() - Constructor for exception RBNio.ParseException
The following constructors are for use by you for whatever purpose you can think of.
ParseException(String) - Constructor for exception RBNio.ParseException
Constructor with message.
permuteTuple(int[], int[]) - Static method in class RBNutilities.rbnutilities
Example: tup=(4,2,9), perm=(3,1,2) returns (9,4,2)
pfargs - Variable in class RBNpackage.ProbFormCombFunc
 
PFNetwork - Class in RBNinference
 
PFNetwork() - Constructor for class RBNinference.PFNetwork
 
PFNetwork(Primula, Vector, RelStruc, Instantiation) - Constructor for class RBNinference.PFNetwork
 
PFNetworkNode - Class in RBNinference
 
PFNetworkNode(Atom) - Constructor for class RBNinference.PFNetworkNode
 
pl - Static variable in class RBNgui.Filter_pl
 
pluckNameFromPath(String) - Static method in class RBNgui.Primula
 
prepareForSampling(int, int, boolean[], int, AtomList, int, int, BufferedWriter) - Method in class RBNinference.PFNetwork
 
prevCharIsCR - Variable in class RBNio.SimpleCharStream
 
prevCharIsLF - Variable in class RBNio.SimpleCharStream
 
Primula - Class in RBNgui
 
Primula() - Constructor for class RBNgui.Primula
 
printarray(String[]) - Static method in class RBNutilities.rbnutilities
 
printarray(int[]) - Static method in class RBNutilities.rbnutilities
 
printarray(double[]) - Static method in class RBNutilities.rbnutilities
 
printarray(Rel[]) - Static method in class RBNutilities.rbnutilities
 
printAsString(RelStruc, String) - Method in class RBNpackage.Instantiation
 
printAsString(RelStruc, String) - Method in class RBNpackage.OneRelData
 
printAsString(RelStruc, String) - Method in class RBNpackage.OneStrucData
 
printname() - Method in class RBNpackage.Rel
 
printSummary() - Method in class RBNpackage.OneStrucData
 
probform() - Method in class RBNinference.ComplexBNNode
 
probform() - Method in interface RBNinference.ComplexBNNodeInt
 
probform() - Method in class RBNinference.ComplexPFNetworkNode
 
ProbForm - Class in RBNpackage
 
ProbForm() - Constructor for class RBNpackage.ProbForm
 
probForm(Rel) - Method in class RBNpackage.RBN
Returns the probability formula for relation r
probformAt(int) - Method in class RBNpackage.ProbFormCombFunc
Returns the i'th probability formula in the argument of this formula's combination function
ProbFormAt(int) - Method in class RBNpackage.RBN
 
ProbFormCombFunc - Class in RBNpackage
 
ProbFormCombFunc() - Constructor for class RBNpackage.ProbFormCombFunc
 
ProbFormCombFunc(CombFunc, ProbForm[], String[], CConstr) - Constructor for class RBNpackage.ProbFormCombFunc
Creates new ProbFormCombFunc
ProbFormCombFunc(String, ProbForm[], String[], CConstr) - Constructor for class RBNpackage.ProbFormCombFunc
 
ProbFormConstant - Class in RBNpackage
A ProbFormConstant represents a probability constant.
ProbFormConstant() - Constructor for class RBNpackage.ProbFormConstant
 
ProbFormConstant(double) - Constructor for class RBNpackage.ProbFormConstant
 
ProbFormConstant(String) - Constructor for class RBNpackage.ProbFormConstant
 
ProbFormConvComb - Class in RBNpackage
 
ProbFormConvComb() - Constructor for class RBNpackage.ProbFormConvComb
 
ProbFormConvComb(ProbForm, ProbForm, ProbForm) - Constructor for class RBNpackage.ProbFormConvComb
Creates new ProbFormConvComb
ProbFormIndicator - Class in RBNpackage
 
ProbFormIndicator() - Constructor for class RBNpackage.ProbFormIndicator
 
ProbFormIndicator(Rel) - Constructor for class RBNpackage.ProbFormIndicator
 
ProbFormIndicator(Rel, String[]) - Constructor for class RBNpackage.ProbFormIndicator
Creates new ProbFormIndicator
ProbFormIndicator(Rel, int[]) - Constructor for class RBNpackage.ProbFormIndicator
 
ProbFormSFormula - Class in RBNpackage
 
ProbFormSFormula() - Constructor for class RBNpackage.ProbFormSFormula
Creates new ProbFormSFormula
ProbFormSFormula(CConstr) - Constructor for class RBNpackage.ProbFormSFormula
 
propagateDeterministic(Vector, RelStruc, boolean) - Method in class RBNinference.PFNetwork
 
propagateDeterministic(RelStruc, Instantiation, Vector, boolean, Hashtable) - Method in class RBNinference.PFNetworkNode
 

Q

quantvars - Variable in class RBNpackage.ProbFormCombFunc
 
quantvars() - Method in class RBNpackage.ProbFormCombFunc
Returns the quantvars of this combination function
queryatoms - Variable in class RBNgui.Primula
 
querymode - Variable in class RBNgui.Primula
 
QueryTableModel - Class in RBNgui
 
QueryTableModel() - Constructor for class RBNgui.QueryTableModel
...

R

randInt(int, int) - Static method in class RBNutilities.randomGenerators
Returns a random integer between min and max (inclusive)
randomCPTRow(int) - Static method in class mymath.MyRandom
 
RandomGenerator - Class in mymath
 
RandomGenerator() - Constructor for class mymath.RandomGenerator
 
randomGenerators - Class in RBNutilities
 
randomGenerators() - Constructor for class RBNutilities.randomGenerators
 
randomIntArray(int, int) - Static method in class mymath.MyRandom
 
randomInteger(int) - Static method in class mymath.MyRandom
 
randomInteger(long) - Static method in class mymath.MyRandom
 
randomPoisson(double) - Static method in class mymath.MyRandom
 
randSeqToFile(double, String, int) - Static method in class mymath.MyRandom
 
rbn - Static variable in class RBNgui.Filter_rbn
 
rbn - Variable in class RBNgui.Primula
 
RBN - Class in RBNpackage
 
RBN() - Constructor for class RBNpackage.RBN
Creates new RBN
RBN(int) - Constructor for class RBNpackage.RBN
 
RBN(String) - Constructor for class RBNpackage.RBN
 
RBN(RBN) - Constructor for class RBNpackage.RBN
 
RBNBadSampleException - Exception in RBNExceptions
 
RBNBadSampleException() - Constructor for exception RBNExceptions.RBNBadSampleException
Creates new RBNBadSampleException without detail message.
RBNBadSampleException(String) - Constructor for exception RBNExceptions.RBNBadSampleException
Constructs an RBNBadSampleException with the specified detail message.
RBNCompatibilityException - Exception in RBNExceptions
 
RBNCompatibilityException() - Constructor for exception RBNExceptions.RBNCompatibilityException
Creates new RBNCompatibilityException without detail message.
RBNCompatibilityException(String) - Constructor for exception RBNExceptions.RBNCompatibilityException
Constructs an RBNCompatibilityException with the specified detail message.
RBNCyclicException - Exception in RBNExceptions
 
RBNCyclicException() - Constructor for exception RBNExceptions.RBNCyclicException
Creates new RBNCyclicException without detail message.
RBNCyclicException(String) - Constructor for exception RBNExceptions.RBNCyclicException
Constructs an RBNCyclicException with the specified detail message.
RBNExceptions - package RBNExceptions
 
rbnfile - Variable in class RBNgui.Primula
 
RBNgui - package RBNgui
 
RBNIllegalArgumentException - Exception in RBNExceptions
 
RBNIllegalArgumentException() - Constructor for exception RBNExceptions.RBNIllegalArgumentException
Creates new RBNIllegalArgumentException without detail message.
RBNIllegalArgumentException(String) - Constructor for exception RBNExceptions.RBNIllegalArgumentException
Constructs an RBNIllegalArgumentException with the specified detail message.
RBNInconsistentEvidenceException - Exception in RBNExceptions
 
RBNInconsistentEvidenceException() - Constructor for exception RBNExceptions.RBNInconsistentEvidenceException
Creates new RBNInconsistentEvidenceException without detail message.
RBNInconsistentEvidenceException(String) - Constructor for exception RBNExceptions.RBNInconsistentEvidenceException
Constructs an RBNInconsistentEvidenceException with the specified detail message.
RBNinference - package RBNinference
 
RBNio - package RBNio
 
RBNioException - Exception in RBNExceptions
 
RBNioException() - Constructor for exception RBNExceptions.RBNioException
Creates new RBNBadSampleException without detail message.
RBNioException(String) - Constructor for exception RBNExceptions.RBNioException
Constructs an RBNBadSampleException with the specified detail message.
RBNLearning - package RBNLearning
 
RBNpackage - package RBNpackage
 
RBNReader - Class in RBNio
 
RBNReader() - Constructor for class RBNio.RBNReader
Creates new RBNReader
RBNRuntimeException - Exception in RBNExceptions
 
RBNRuntimeException() - Constructor for exception RBNExceptions.RBNRuntimeException
Creates new RBNBadSampleException without detail message.
RBNRuntimeException(String) - Constructor for exception RBNExceptions.RBNRuntimeException
Constructs an RBNBadSampleException with the specified detail message.
RBNSyntaxException - Exception in RBNExceptions
 
RBNSyntaxException() - Constructor for exception RBNExceptions.RBNSyntaxException
Creates new RBNSyntaxException without detail message.
RBNSyntaxException(String) - Constructor for exception RBNExceptions.RBNSyntaxException
Constructs an RBNSyntaxException with the specified detail message.
RBNutilities - package RBNutilities
 
rbnutilities - Class in RBNutilities
 
rbnutilities() - Constructor for class RBNutilities.rbnutilities
 
rdef - Static variable in class RBNgui.Filter_rdef
 
RDEFReader - Class in RBNio
 
RDEFReader() - Constructor for class RBNio.RDEFReader
 
readAL(File) - Method in class RBNio.AtomListReader
 
readALFile(AtomListReader) - Method in class RBNio.AtomListParser
 
readChar() - Method in class RBNio.SimpleCharStream
Read a character.
readDouble(String, BufferedReader, double, double) - Static method in class myio.SystemIO
 
readDouble(String, BufferedReader, double, double) - Static method in class RBNutilities.SystemIO
 
readInt(String, BufferedReader, int, int) - Static method in class myio.SystemIO
 
readInt(String, BufferedReader, int, int) - Static method in class RBNutilities.SystemIO
 
ReadMLN(File, File, File) - Method in class MLNParser.MLNParserFacade
 
READONESTRUC - Static variable in class RBNio.RDEFReader
 
ReadRBNfromFile(String) - Method in class RBNio.RBNReader
 
readRBNRelations() - Method in class RBNgui.EvidenceModule
 
readRDEF(String, RelStruc) - Method in class RBNio.RDEFReader
RelData primarily stores information on observed probabilistic relations.
READRELDATA - Static variable in class RBNio.RDEFReader
 
readSparseRelStrucFromFile(String) - Method in class RBNio.SparseRelStrucReader
 
reEvaluateUpstream() - Method in class RBNLearning.GradientGraphNode
Re-evaluates all ancestor nodes of this node.
ReInit(InputStream) - Method in class RBNio.AtomListParser
Reinitialise.
ReInit(InputStream, String) - Method in class RBNio.AtomListParser
Reinitialise.
ReInit(Reader) - Method in class RBNio.AtomListParser
Reinitialise.
ReInit(AtomListParserTokenManager) - Method in class RBNio.AtomListParser
Reinitialise.
ReInit(SimpleCharStream) - Method in class RBNio.AtomListParserTokenManager
Reinitialise parser.
ReInit(SimpleCharStream, int) - Method in class RBNio.AtomListParserTokenManager
Reinitialise parser.
ReInit(Reader, int, int, int) - Method in class RBNio.SimpleCharStream
Reinitialise.
ReInit(Reader, int, int) - Method in class RBNio.SimpleCharStream
Reinitialise.
ReInit(Reader) - Method in class RBNio.SimpleCharStream
Reinitialise.
ReInit(InputStream, String, int, int, int) - Method in class RBNio.SimpleCharStream
Reinitialise.
ReInit(InputStream, int, int, int) - Method in class RBNio.SimpleCharStream
Reinitialise.
ReInit(InputStream, String) - Method in class RBNio.SimpleCharStream
Reinitialise.
ReInit(InputStream) - Method in class RBNio.SimpleCharStream
Reinitialise.
ReInit(InputStream, String, int, int) - Method in class RBNio.SimpleCharStream
Reinitialise.
ReInit(InputStream, int, int) - Method in class RBNio.SimpleCharStream
Reinitialise.
rel - Variable in class RBNpackage.Atom
 
rel() - Method in class RBNpackage.Atom
returns the Rel of this atom
rel() - Method in class RBNpackage.OneRelData
 
Rel - Class in RBNpackage
 
Rel() - Constructor for class RBNpackage.Rel
 
Rel(String, int) - Constructor for class RBNpackage.Rel
 
Rel(String, int, Type[]) - Constructor for class RBNpackage.Rel
 
relAt(int) - Method in class RBNinference.PFNetwork
 
relAt(int) - Method in class RBNpackage.OneStrucData
 
relAt(int) - Method in class RBNpackage.RBN
 
Relation - Static variable in interface RBNio.AtomListParserConstants
RegularExpression Id.
relation - Variable in class RBNpackage.ProbFormIndicator
 
relationalStructureEdited() - Method in class RBNgui.EvidenceModule
 
RelData - Class in RBNLearning
RelData consists of pairs of input structures and (vectors of) OneStrucData representing observations of the probabilistic relations, i.e.
RelData() - Constructor for class RBNLearning.RelData
 
RelDataCase - Class in RBNLearning
represents an observation of an input domain and the values of probabilistic relations.
RelDataCase(RelStruc, OneStrucData) - Constructor for class RBNLearning.RelDataCase
 
RelDataForOneInput - Class in RBNLearning
 
RelDataForOneInput() - Constructor for class RBNLearning.RelDataForOneInput
 
RelDataForOneInput(RelStruc) - Constructor for class RBNLearning.RelDataForOneInput
 
relname() - Method in class RBNpackage.Atom
Returns the name of the relation of this atom
RelName - Class in RBNpackage
 
RelName() - Constructor for class RBNpackage.RelName
Creates new RelName
RelName(String) - Constructor for class RBNpackage.RelName
 
rels - Variable in class RBNgui.Primula
 
Rels() - Method in class RBNpackage.RBN
 
RelStruc - Class in RBNpackage
 
RelStruc() - Constructor for class RBNpackage.RelStruc
Creates new RelStruc
RelStruc(int) - Constructor for class RBNpackage.RelStruc
Creates new RelStruc with a domain of n elements
RelStruc(Vector, OneStrucData, Vector) - Constructor for class RBNpackage.RelStruc
 
RelStruc(RelStruc) - Constructor for class RBNpackage.RelStruc
 
removeAllQueries() - Method in class RBNgui.QueryTableModel
 
removeQuery(int) - Method in class RBNgui.QueryTableModel
 
rename(String) - Static method in class RBNinference.BayesNetIntSamIam
 
replaceInChildrenList(BNNode, BNNode) - Method in class RBNinference.BNNode
 
replaceInParentList(BNNode, BNNode) - Method in class RBNinference.BNNode
 
reset() - Method in class RBNgui.EditPanel
 
reset() - Method in class RBNgui.QueryTableModel
 
reset() - Method in class RBNpackage.AtomList
 
reset() - Method in class RBNpackage.Instantiation
 
resetACE() - Method in class RBNgui.QueryTableModel
 
resetBounds() - Method in class RBNLearning.GradientGraph
Resets to [-1,-1] the bounds in all nodes
resetBounds() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
resetBounds() - Method in class RBNLearning.GradientGraphProbFormNode
 
resetGradient() - Method in class RBNLearning.GradientGraphNode
 
resetGradientSum() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
resetLikelihoodSum() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
resetMaxProb() - Method in class RBNgui.QueryTableModel
 
resetMinProb() - Method in class RBNgui.QueryTableModel
 
resetParents() - Method in class RBNinference.BNNode
 
resetProb() - Method in class RBNgui.QueryTableModel
 
resetTheColorCounters() - Static method in class RBNpackage.Rel
 
resetValue() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
resetValue() - Method in class RBNLearning.GradientGraphNode
 
resetValues(boolean) - Method in class RBNLearning.GradientGraph
 
resetVar() - Method in class RBNgui.QueryTableModel
 
resetVisited(int) - Method in class RBNinference.BNNode
 
resetVisitedUpDownstream(int) - Method in class RBNinference.BNNode
 
resetVisitedUpstream(int) - Method in class RBNinference.BNNode
 
roundDouble(double, int) - Static method in class mymath.MyMathOps
 
rst - Static variable in class RBNgui.Filter_rst
 
RSymbs - Variable in class RBNpackage.ProbForm
 
run() - Method in class RBNinference.SampleThread
 
run() - Method in class RBNLearning.LearnThread
 

S

sample(RelStruc, Hashtable, Instantiation, int, int, long[], boolean) - Method in class RBNinference.PFNetworkNode
 
sampleBeta(double, double) - Static method in class mymath.MyRandom
Sample a parameter p in [0,1] according to a beta distribution that has mean e and variance v.
sampledepth - Variable in class RBNinference.PFNetworkNode
 
sampledepth() - Method in class RBNinference.PFNetworkNode
 
sampleForward(RelStruc, Hashtable, Instantiation, int, long[]) - Method in class RBNinference.ComplexPFNetworkNode
 
sampleForward(RelStruc, Hashtable, Instantiation, int, long[]) - Method in class RBNinference.PFNetworkNode
 
sampleForward(RelStruc, Hashtable, Instantiation, int, long[]) - Method in class RBNinference.SimplePFNetworkNode
 
sampleForward(RelStruc, int) - Method in class RBNinference.SimplePFNetworkNode
 
sampleindex - Variable in class RBNinference.SimplePFNetworkNode
 
sampleInst(int, boolean) - Method in class RBNinference.PFNetwork
Sample one instantiation; set instantiated field of the nodes accordingly
sampleinst - Variable in class RBNinference.PFNetworkNode
 
sampleinstantiate(int) - Method in class RBNinference.PFNetworkNode
 
sampleinstVal() - Method in class RBNinference.PFNetworkNode
 
SampleMain - Class in RBNLearning
 
SampleMain() - Constructor for class RBNLearning.SampleMain
 
sampleOneStrucData(double) - Method in class RBNLearning.Sampler
Samples OneStrucData with a percentage of pcmissing values missing (completely at random)
sampleparentconfig - Variable in class RBNinference.PFNetworkNode
 
SampleProbs - Class in RBNinference
 
SampleProbs(int) - Constructor for class RBNinference.SampleProbs
 
Sampler - Class in RBNLearning
 
Sampler() - Constructor for class RBNLearning.Sampler
 
sampleRipple(RelStruc, Hashtable, Instantiation, int, long[], boolean) - Method in class RBNinference.PFNetworkNode
 
SampleThread - Class in RBNinference
 
SampleThread(Observer, PFNetwork, AtomList, int, boolean[], BufferedWriter) - Constructor for class RBNinference.SampleThread
 
sampleValAt(int) - Method in class RBNinference.PFNetwork
 
saveFile(File) - Method in class RBNgui.Bavaria
 
saveFile(SparseRelStruc, File, Primula) - Static method in class RBNio.SparseRelStrucReader
 
saveToAtomFile(String, int) - Method in class RBNpackage.RelStruc
Saves the RelStruc into a file using the BLP or MLN syntax for logical specifications
saveToBLPDatFile(String, int) - Method in class RBNpackage.Instantiation
 
saveToBLPDatFile(String, int) - Method in class RBNpackage.OneStrucData
 
saveToFile(File) - Method in class RBNpackage.RBN
 
saveToFOIL(File) - Method in class RBNLearning.RelData
Saves first RelDataForOneInput into FOIL format
saveToFOIL(File) - Method in class RBNLearning.RelDataForOneInput
 
saveToMysql(String) - Method in class RBNpackage.RelStruc
Saves the RelStruc to a new MySQL database
saveToProximityText(String) - Method in class RBNpackage.RelStruc
Saves the RelStruc to a collection of text file in Proximity format path is a directory path
saveToRDEF(String) - Method in class RBNLearning.RelData
 
saveToRDEF(File) - Method in class RBNLearning.RelData
 
saveToRDEF(FileWriter) - Method in class RBNLearning.RelData
 
saveToRDEF(File, RelStruc) - Method in class RBNpackage.Instantiation
 
saveToRDEF(File) - Method in class RBNpackage.RelStruc
 
saveToTextFiles(String) - Method in class RBNpackage.RelStruc
Saves structure into collection of text files into directory path
scaleX(int) - Method in class RBNgui.Bavaria
 
scaleY(int) - Method in class RBNgui.Bavaria
 
set(int, double) - Method in class mymath.DoubleVector
 
set(int, int) - Method in class mymath.IntVector
 
set(int, double) - Method in class RBNutilities.DoubleVector
 
setA(RelStruc) - Method in class RBNLearning.RelDataForOneInput
 
setAca(boolean) - Method in class RBNgui.LearnModule
 
setAdaptiveMode(int) - Method in class RBNgui.EvidenceModule
 
setCanvasSize() - Method in class RBNgui.Bavaria
 
setColor(Color) - Method in class RBNpackage.Rel
 
setCPT(double[]) - Method in class RBNinference.SimpleBNNode
 
setCptEntry(int, double) - Method in class RBNinference.BoolNode
 
setCptEntry(int[], double) - Method in class RBNinference.BoolNode
 
setCPTParents(int) - Method in class RBNgui.EvidenceModule
 
setCurrentInst(int) - Method in class RBNLearning.GradientGraphIndicatorNode
Sets the current instantiation according to the value in the sno's sample
setCurrentInst(boolean) - Method in class RBNLearning.GradientGraphIndicatorNode
Sets the current instantiation according to the truth value tv
setCurrentParamVal(double) - Method in class RBNLearning.GradientGraphConstantNode
 
setData(Rel, int[], boolean) - Method in class RBNpackage.OneStrucData
 
setData(String, int[], boolean) - Method in class RBNpackage.OneStrucData
 
setData(OneStrucData) - Method in class RBNpackage.RelStruc
 
setDebugStream(PrintStream) - Method in class RBNio.AtomListParserTokenManager
Set debug output.
setDecomposeMode(int) - Method in class RBNgui.Primula
 
setDepth(int) - Method in class RBNinference.BNNode
 
setDistrProb(RelStruc, Hashtable, Instantiation, long[]) - Method in class RBNinference.ComplexPFNetworkNode
 
setDistrProb(RelStruc, Hashtable, Instantiation, long[]) - Method in class RBNinference.PFNetworkNode
 
setDistrProb(RelStruc, Hashtable, Instantiation, long[]) - Method in class RBNinference.SimplePFNetworkNode
 
setEstimates(double[]) - Method in class RBNgui.ParameterTableModel
 
setFrameTitle(String) - Method in class RBNgui.Bavaria
 
setGradDistThresh(double) - Method in class RBNgui.LearnModule
 
setGrid(boolean, int) - Method in class RBNgui.EditPanel
 
setInputFile(File) - Method in class RBNgui.Primula
 
setInst(Instantiation) - Method in class RBNgui.Primula
 
setIsBavariaOpen(boolean) - Static method in class RBNgui.Primula
 
setIsBavariaOpenThis(boolean) - Method in class RBNgui.Primula
 
setIsEdited(boolean) - Method in class RBNgui.Bavaria
 
setIsEvModuleOpen(boolean) - Static method in class RBNgui.Primula
 
setIsEvModuleOpenThis(boolean) - Method in class RBNgui.Primula
 
setIsLearnModuleOpen(boolean) - Static method in class RBNgui.Primula
 
setLearnSampleSize(Integer) - Method in class RBNgui.LearnModule
 
setLineDistThresh(double) - Method in class RBNgui.LearnModule
 
setLineLikThresh(double) - Method in class RBNgui.LearnModule
 
setLogfilename(String) - Method in class RBNgui.EvidenceModule
 
setMaxFails(Integer) - Method in class RBNgui.LearnModule
 
setMaxIterations(Integer) - Method in class RBNgui.LearnModule
 
setMaxProb(double, int) - Method in class RBNinference.SampleProbs
 
setMinProb(double, int) - Method in class RBNinference.SampleProbs
 
setMode(int) - Method in class RBNgui.ArbitraryPanel
 
setMode(int) - Method in class RBNgui.AttributesPanel
 
setMode(int) - Method in class RBNgui.BinaryPanel
 
setMode(int) - Method in class RBNgui.EditPanel
 
setName(String, int) - Method in class RBNgui.Bavaria
 
setName(String, int) - Method in class RBNpackage.RelStruc
 
setNumSubsamples_adapt(int) - Method in class RBNgui.EvidenceModule
 
setNumSubsamples_minmax(int) - Method in class RBNgui.EvidenceModule
 
setParameters(String[]) - Method in class RBNgui.ParameterTableModel
 
setParameters(double[]) - Method in class RBNLearning.GradientGraph
Sets the parameter values to thetas.
setParameters(String[], double[]) - Method in class RBNpackage.ProbForm
Sets all occurrences of parameters appearing in params to their corresponding value in values.
setParameters(String[], double[]) - Method in class RBNpackage.ProbFormCombFunc
 
setParameters(String[], double[]) - Method in class RBNpackage.ProbFormConstant
 
setParameters(String[], double[]) - Method in class RBNpackage.ProbFormConvComb
 
setParameters(String[], double[]) - Method in class RBNpackage.ProbFormIndicator
 
setParameters(String[], double[]) - Method in class RBNpackage.ProbFormSFormula
 
setParameters(String[], double[]) - Method in class RBNpackage.RBN
Sets all occurrences of parameters appearing in params to their corresponding value in values.
setParametersRandom() - Method in class RBNLearning.GradientGraph
 
setParametersUniform() - Method in class RBNLearning.GradientGraph
 
setParseNo(int) - Method in class RBNio.AtomListParser
 
setPause(boolean) - Method in class RBNinference.SampleThread
 
setProb(double, int) - Method in class RBNinference.SampleProbs
 
setProbs(double[]) - Method in class RBNinference.SampleProbs
 
setRel(Rel) - Method in class RBNgui.EditPanel
 
setRelationName(String) - Method in class MLNParser.ParsedRelation
 
setRelStruc(SparseRelStruc) - Method in class RBNgui.Bavaria
 
setRelStruc(RelStruc) - Method in class RBNgui.Primula
 
setRestarts(Integer) - Method in class RBNgui.LearnModule
 
setRunning(boolean) - Method in class RBNinference.SampleThread
 
setSampleDepth(int) - Method in class RBNinference.PFNetworkNode
 
setSampleLikelihood(int) - Method in class RBNLearning.GradientGraphLikelihoodNode
Sets the current likelihood value as the likelihood value for the i'th sample
setSampleLogMode(int, boolean) - Method in class RBNgui.EvidenceModule
 
setSampleOrdMode(int) - Method in class RBNgui.EvidenceModule
 
setSampleProb(double) - Method in class RBNinference.PFNetworkNode
 
setSampleProbs(SampleProbs, int, BufferedWriter) - Method in class RBNinference.PFNetwork
 
setSampleVal(int, boolean) - Method in class RBNLearning.GradientGraphIndicatorNode
Sets value in sno's sample to tv
setSampleVal(int) - Method in class RBNLearning.GradientGraphIndicatorNode
Sets value in sno's sample to current instantiation
setSettingsOpen(boolean) - Method in class RBNgui.EvidenceModule
 
setSettingsOpen(boolean) - Method in class RBNgui.LearnModule
 
setSize(int) - Method in class RBNinference.SampleProbs
 
setStopped() - Method in class RBNLearning.LearnThread
 
setStrucEdited(boolean) - Method in class RBNgui.Primula
 
setSystemExitEnabled(boolean) - Method in class RBNgui.Primula
 
setTabSize(int) - Method in class RBNio.SimpleCharStream
 
setTheSamIamUI(SamiamUIInt) - Method in class RBNgui.Primula
 
Settings - Class in RBNgui
 
Settings(EvidenceModule) - Constructor for class RBNgui.Settings
 
setTruthVals(int) - Method in class RBNLearning.GradientGraph
Sets the truthval fields in the ProbFormNodes corresponding to unobserved atoms to the truthvalues in the sno's sample If sno<0 do nothing!
setUpstreamOfEvidence(boolean) - Method in class RBNinference.PFNetworkNode
 
setVar(double, int) - Method in class RBNinference.SampleProbs
 
setVerbose(boolean) - Method in class RBNgui.LearnModule
 
setWeight(double) - Method in class RBNinference.SampleProbs
 
setWindowSize(Integer) - Method in class RBNgui.LearnModule
 
setXSize(int) - Method in class RBNgui.Bavaria
 
setXSize(int) - Method in class RBNgui.EditPanel
 
setYSize(int) - Method in class RBNgui.Bavaria
 
setYSize(int) - Method in class RBNgui.EditPanel
 
setZoom(double) - Method in class RBNgui.EditPanel
 
sEval(RelStruc) - Method in class RBNinference.ComplexPFNetworkNode
 
sEval(RelStruc) - Method in class RBNpackage.ProbForm
Returns a ProbForm in which the dependence on A is already pre-evaluated (substitution lists in combination functions, and values of ProbFormSFormula)
sEval(RelStruc) - Method in class RBNpackage.ProbFormCombFunc
 
sEval(RelStruc) - Method in class RBNpackage.ProbFormConstant
 
sEval(RelStruc) - Method in class RBNpackage.ProbFormConvComb
 
sEval(RelStruc) - Method in class RBNpackage.ProbFormIndicator
 
sEval(RelStruc) - Method in class RBNpackage.ProbFormSFormula
 
shiftArgs(int) - Method in class RBNpackage.AtomList
 
shiftArgs(int) - Method in class RBNpackage.Instantiation
 
shiftArgs(int) - Method in class RBNpackage.OneRelData
Replaces all arguments b of trueAtoms and falseAtoms lists by b-1 if b>a (needed after the deletion of node with index a from the underlying SparseRelStruc)
shiftArgs(int) - Method in class RBNpackage.OneStrucData
 
showAllLikelihoods(double) - Method in class RBNLearning.GradientGraph
Prints a list of likelihood values for all possible parameter settings obtained by varying each parameter from 0.0 to 1.0 using a stepsize of incr
showAllNodes(int, RelStruc) - Method in class RBNLearning.GradientGraph
 
showAllReachable() - Method in class RBNinference.BNNode
Prints names of all nodes connected to this one
showCoordinates(int, int) - Method in class RBNgui.Bavaria
 
showGraphInfo(int, RelStruc) - Method in class RBNLearning.GradientGraph
 
showInputDialog() - Method in class RBNgui.TypeSelectionPanel
 
showLikelihoodNode(RelStruc) - Method in class RBNLearning.GradientGraph
 
showMessage(String) - Method in class RBNgui.Bavaria
 
showMessage(String) - Static method in class RBNgui.Primula
 
showMessageThis(String) - Method in class RBNgui.Primula
 
showNodes() - Method in class RBNinference.PFNetwork
 
showNumFalse() - Method in class RBNinference.SimplePFNetworkNode
 
showNumTrue() - Method in class RBNinference.SimplePFNetworkNode
 
showSampleOrd(RelStruc, BufferedWriter) - Method in class RBNinference.PFNetwork
 
SimpleBNGroundAtomNode - Class in RBNinference
 
SimpleBNGroundAtomNode(String) - Constructor for class RBNinference.SimpleBNGroundAtomNode
Creates new SimpleBNGroundAtomlNode
SimpleBNGroundAtomNode(Atom) - Constructor for class RBNinference.SimpleBNGroundAtomNode
 
SimpleBNGroundAtomNode(Rel, int[]) - Constructor for class RBNinference.SimpleBNGroundAtomNode
 
SimpleBNGroundAtomNode(Atom, String) - Constructor for class RBNinference.SimpleBNGroundAtomNode
 
SimpleBNGroundAtomNode(Rel, String, int[]) - Constructor for class RBNinference.SimpleBNGroundAtomNode
 
SimpleBNGroundAtomNode(Atom, String, double[], LinkedList, LinkedList) - Constructor for class RBNinference.SimpleBNGroundAtomNode
 
SimpleBNGroundAtomNode(Rel, String, int[], double[], LinkedList, LinkedList) - Constructor for class RBNinference.SimpleBNGroundAtomNode
 
SimpleBNNode - Class in RBNinference
 
SimpleBNNode() - Constructor for class RBNinference.SimpleBNNode
Creates new SimpleBNNode
SimpleBNNode(String) - Constructor for class RBNinference.SimpleBNNode
 
SimpleBNNode(String, double[], LinkedList, LinkedList) - Constructor for class RBNinference.SimpleBNNode
 
SimpleCharStream - Class in RBNio
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 RBNio.SimpleCharStream
Constructor.
SimpleCharStream(Reader, int, int) - Constructor for class RBNio.SimpleCharStream
Constructor.
SimpleCharStream(Reader) - Constructor for class RBNio.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, String, int, int, int) - Constructor for class RBNio.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, int, int, int) - Constructor for class RBNio.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, String, int, int) - Constructor for class RBNio.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, int, int) - Constructor for class RBNio.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, String) - Constructor for class RBNio.SimpleCharStream
Constructor.
SimpleCharStream(InputStream) - Constructor for class RBNio.SimpleCharStream
Constructor.
SimplePFNetworkNode - Class in RBNinference
 
SimplePFNetworkNode(Atom) - Constructor for class RBNinference.SimplePFNetworkNode
 
SimplePFNetworkNode(ComplexPFNetworkNode, Instantiation, RelStruc) - Constructor for class RBNinference.SimplePFNetworkNode
 
size() - Method in class mymath.DoubleVector
 
size() - Method in class mymath.IntVector
 
size() - Method in class RBNLearning.RelData
 
size() - Method in class RBNpackage.AtomList
 
size() - Method in class RBNpackage.Instantiation
 
size() - Method in class RBNpackage.OneStrucData
 
size() - Method in class RBNutilities.DoubleVector
 
sizeFamily() - Method in class RBNinference.BNNode
 
SmallDouble - Class in RBNutilities
Provides static methods for handling very small double values d represented as pairs d[0],d[1].
SmallDouble() - Constructor for class RBNutilities.SmallDouble
 
SmallDoubleArrayComparatorByComponent - Class in RBNutilities
Compares two double arrays according to their components baseindex and factorindex, which are interpreted as a representation for a SmallDouble.
SmallDoubleArrayComparatorByComponent(int, int) - Constructor for class RBNutilities.SmallDoubleArrayComparatorByComponent
 
snapshot() - Method in class RBNgui.Primula
 
snapToGrid() - Method in class RBNgui.EditPanel
 
sortArray(double[]) - Static method in class myio.StringOps
 
sortArray(int[]) - Static method in class myio.StringOps
 
sortArrayCopy(double[]) - Static method in class myio.StringOps
 
SparseRelStruc - Class in RBNpackage
 
SparseRelStruc() - Constructor for class RBNpackage.SparseRelStruc
Creates new SparseRelStruc
SparseRelStruc(int) - Constructor for class RBNpackage.SparseRelStruc
Creates new SparseRelStruc with n elements
SparseRelStruc(Vector, OneStrucData, Vector) - Constructor for class RBNpackage.SparseRelStruc
 
SparseRelStruc(SparseRelStruc) - Constructor for class RBNpackage.SparseRelStruc
 
SparseRelStruc(RelStruc) - Constructor for class RBNpackage.SparseRelStruc
 
SparseRelStrucReader - Class in RBNio
 
SparseRelStrucReader() - Constructor for class RBNio.SparseRelStrucReader
Creates new SparseRelStrucReader
specialConstructor - Variable in exception RBNio.ParseException
This variable determines which constructor was used to create this object and thereby affects the semantics of the "getMessage" method (see below).
specialToken - Variable in class RBNio.Token
This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
splitOnCConstr(String) - Method in class RBNio.RBNReader
 
splitOnDelim(String, int) - Method in class RBNio.RBNReader
 
splitOnName(String) - Method in class RBNio.RBNReader
Splits string of the form with : valid name : first illegal character for names into and
splitOnProbForm(String) - Method in class RBNio.RBNReader
Splits string of the form into and
srsfile - Variable in class RBNgui.Primula
 
SSymbs - Variable in class RBNpackage.ProbForm
 
stateChanged(ChangeEvent) - Method in class RBNgui.NodeWindow
 
staticFlag - Static variable in class RBNio.SimpleCharStream
Whether parser is static.
STR_EMPTY - Static variable in class RBNgui.QueryTableModel
 
STR_FILE_EXTENSION_NET - Static variable in class RBNinference.BayesNetIntSamIam
 
STR_FILENAME_LOGO - Static variable in class RBNgui.Primula
 
STR_ID_DEFAULT - Static variable in class RBNinference.BayesNetIntSamIam
 
STR_OPTION_DEBUG - Static variable in class RBNgui.Primula
 
STR_PATTERN_DECIMAL_FORMAT - Static variable in class RBNinference.BayesNetIntSamIam
 
STR_RENAME_OPTION - Static variable in class RBNinference.BayesNetIntSamIam
 
STR_REPLACE_OPTION - Static variable in class RBNinference.BayesNetIntSamIam
 
stringArrayToIntArray(String[]) - Static method in class RBNutilities.rbnutilities
 
StringOps - Class in myio
 
StringOps() - Constructor for class myio.StringOps
 
stringToCConstr(String) - Method in class RBNio.RBNReader
Parses string into CConstr
stringToDoubleArray(String) - Static method in class myio.StringOps
 
stringToDoubleVector(String) - Static method in class myio.StringOps
 
stringToIntArray(String) - Static method in class myio.StringOps
 
stringToIntegerVector(String) - Static method in class myio.StringOps
 
stringToStringArray(String) - Static method in class myio.StringOps
 
subPF(int) - Method in class RBNpackage.ProbFormConvComb
 
substitute(String[], int[]) - Method in class RBNpackage.CConstr
 
substitute(String[], String[]) - Method in class RBNpackage.CConstr
 
substitute(String[], int[]) - Method in class RBNpackage.CConstrAnd
 
substitute(String[], String[]) - Method in class RBNpackage.CConstrAnd
 
substitute(String[], int[]) - Method in class RBNpackage.CConstrAtom
 
substitute(String[], String[]) - Method in class RBNpackage.CConstrAtom
 
substitute(String[], int[]) - Method in class RBNpackage.CConstrEmpty
 
substitute(String[], String[]) - Method in class RBNpackage.CConstrEmpty
 
substitute(String[], int[]) - Method in class RBNpackage.CConstrEq
 
substitute(String[], String[]) - Method in class RBNpackage.CConstrEq
 
substitute(String[], int[]) - Method in class RBNpackage.CConstrNeg
 
substitute(String[], String[]) - Method in class RBNpackage.CConstrNeg
 
substitute(String[], int[]) - Method in class RBNpackage.CConstrOr
 
substitute(String[], String[]) - Method in class RBNpackage.CConstrOr
 
substitute(String[], int[]) - Method in class RBNpackage.ProbForm
returns the formula obtained by substituting args for the vars in the formula.
substitute(String[], String[]) - Method in class RBNpackage.ProbForm
 
substitute(String[], int[]) - Method in class RBNpackage.ProbFormCombFunc
 
substitute(String[], String[]) - Method in class RBNpackage.ProbFormCombFunc
 
substitute(String[], int[]) - Method in class RBNpackage.ProbFormConstant
 
substitute(String[], String[]) - Method in class RBNpackage.ProbFormConstant
 
substitute(String[], int[]) - Method in class RBNpackage.ProbFormConvComb
 
substitute(String[], String[]) - Method in class RBNpackage.ProbFormConvComb
 
substitute(String[], int[]) - Method in class RBNpackage.ProbFormIndicator
 
substitute(String[], String[]) - Method in class RBNpackage.ProbFormIndicator
 
substitute(String[], int[]) - Method in class RBNpackage.ProbFormSFormula
 
substitute(String[], String[]) - Method in class RBNpackage.ProbFormSFormula
 
subtract(double[], double[]) - Static method in class RBNutilities.SmallDouble
 
SwitchTo(int) - Method in class RBNio.AtomListParserTokenManager
Switch to specified lex state.
SystemIO - Class in myio
 
SystemIO() - Constructor for class myio.SystemIO
 
SystemIO - Class in RBNutilities
 
SystemIO() - Constructor for class RBNutilities.SystemIO
 

T

tabSize - Variable in class RBNio.SimpleCharStream
 
thisdistrprob - Variable in class RBNinference.PFNetworkNode
 
thisdistrprob() - Method in class RBNinference.PFNetworkNode
 
thissampleprob - Variable in class RBNinference.PFNetworkNode
 
thissampleprob() - Method in class RBNinference.PFNetworkNode
 
toggleCurrentInst() - Method in class RBNLearning.GradientGraphIndicatorNode
 
toggleSampleVal(int) - Method in class RBNLearning.GradientGraphIndicatorNode
Toggles value in sno's sample
token - Variable in class RBNio.AtomListParser
Current token.
Token - Class in RBNio
Describes the input token stream.
Token() - Constructor for class RBNio.Token
No-argument constructor
Token(int) - Constructor for class RBNio.Token
Constructs a new token for the specified Image.
Token(int, String) - Constructor for class RBNio.Token
Constructs a new token for the specified Image and Kind.
token_source - Variable in class RBNio.AtomListParser
Generated Token Manager.
tokenImage - Static variable in interface RBNio.AtomListParserConstants
Literal token values.
tokenImage - Variable in exception RBNio.ParseException
This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.
TokenMgrError - Error in RBNio
Token Manager Error.
TokenMgrError() - Constructor for error RBNio.TokenMgrError
No arg constructor.
TokenMgrError(String, int) - Constructor for error RBNio.TokenMgrError
Constructor with message and reason.
TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error RBNio.TokenMgrError
Full Constructor.
toss(double) - Static method in class mymath.MyRandom
 
toStandardDouble(double[]) - Static method in class RBNutilities.SmallDouble
 
toStandardDoubleArray(double[][]) - Static method in class RBNutilities.SmallDouble
Takes an array sdarr of SmallDoubles and returns an array of doubles representing a scaled version of the vector represented by sdarr Example: sdarr= (1.2E-4,20.0) (4.3E-7,40.0) (6.4E-2,140.0) return toStandardDouble(1.2E-4,0)=1.2E-4 toStandardDouble(4.3E-7,20.0)=4.3E-27 toStandardDouble(6.4E-2,120)=0
toString() - Method in class RBNio.Token
Returns the image.
toString() - Method in class RBNpackage.InstAtom
 
toString() - Method in class RBNpackage.Rel
 
toStringWArity() - Method in class RBNpackage.Rel
 
trueCC(CConstr, String[], int[]) - Method in class RBNpackage.OrdStruc
 
trueCC(CConstr, String[], int[]) - Method in class RBNpackage.RelStruc
 
trueGroundCC(CConstr) - Method in class RBNpackage.OrdStruc
 
trueGroundCC(CConstr) - Method in class RBNpackage.RelStruc
 
trueodds_variance - Variable in class RBNinference.SimplePFNetworkNode
 
trueOrdAtom(CConstrAtom) - Method in class RBNpackage.RelStruc
 
trueOrdAtom(CConstrAtom, String[], int[]) - Method in class RBNpackage.RelStruc
 
truesampleweight - Variable in class RBNinference.PFNetworkNode
The sum of the likelihood weights of all samples in which this node was instantiated true; Represented as SmallDouble
truesampleweight() - Method in class RBNinference.PFNetworkNode
 
truesampleweight_subsample - Variable in class RBNinference.PFNetworkNode
The same but distributed over num_subsamples subsamples only used at querynodes
truesampleweight_subsample(int) - Method in class RBNinference.PFNetworkNode
 
trueSampleWeightAt(int) - Method in class RBNinference.PFNetwork
 
truthval - Variable in class RBNpackage.InstAtom
 
truthValueOf(Atom) - Method in class RBNpackage.Instantiation
Returns 1,0, or -1 according to whether at is true, false, or undefined according to this instantiation.
truthValueOf(Rel, int[]) - Method in class RBNpackage.Instantiation
Returns 1,0, or -1 according to whether r(tuple) is true, false, or undefined according to this instantiation.
truthValueOf(Atom) - Method in class RBNpackage.OneStrucData
Returns 1,0, or -1 according to whether at is true, false, or undefined according to this instantiation.
truthValueOf(Rel, int[]) - Method in class RBNpackage.OneStrucData
Returns 1,0, or -1 according to whether r(tuple) is true, false, or undefined according to this instantiation.
truthValueOf(Rel, int[]) - Method in class RBNpackage.RelStruc
 
tupleDeletedFromNodeWindow(Rel, int[]) - Method in class RBNgui.EditPanel
 
tupleDeletedFromNodeWindow(Rel, int[]) - Method in class RBNgui.NodeWindow
 
tuplesSatisfyingCConstr(RelStruc, String[], int[]) - Method in class RBNpackage.ProbFormCombFunc
Returns the set of all tuples in A that satisfy the CConstr of this formula after the substituion vars/tuple has been performed
tupleToIndex(int[], int) - Static method in class myio.StringOps
 
tupleToIndex(int[], int) - Static method in class RBNutilities.rbnutilities
 
tupleToIndex(int[], int[]) - Static method in class RBNutilities.rbnutilities
 
Type - Class in RBNpackage
 
Type() - Constructor for class RBNpackage.Type
 
TypeDomain - Class in RBNpackage
A "vacuous" type that represents all elements of a domain
TypeDomain() - Constructor for class RBNpackage.TypeDomain
 
TypeInteger - Class in RBNpackage
 
TypeInteger() - Constructor for class RBNpackage.TypeInteger
 
TypeRel - Class in RBNpackage
 
TypeRel(String) - Constructor for class RBNpackage.TypeRel
 
TypeRel(Rel) - Constructor for class RBNpackage.TypeRel
 
TypeSelectionPanel - Class in RBNgui
 
TypeSelectionPanel(Vector<String>) - Constructor for class RBNgui.TypeSelectionPanel
 

U

unset() - Method in class RBNLearning.GradientGraphIndicatorNode
Resets the currentInst field to -1, i.e.
update(Observable, Object) - Method in class RBNgui.EvidenceModule
 
updateACE(Map<String, double[]>) - Method in class RBNgui.QueryTableModel
 
updateconditionalsampleweights(RelStruc, double[]) - Method in class RBNinference.SimplePFNetworkNode
 
updateconditionalsampleweightsnew() - Method in class RBNinference.SimplePFNetworkNode
 
updateGradSum() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
updateInstantiationList() - Method in class RBNgui.EvidenceModule
 
updateLikelihoodSum() - Method in class RBNLearning.GradientGraphLikelihoodNode
updates the likelihoodsum field by adding value
UpdateLineColumn(char) - Method in class RBNio.SimpleCharStream
 
updateMessageArea() - Method in class RBNgui.Primula
 
updateNodeName(int) - Method in class RBNgui.EditPanel
 
updateNodeName(int) - Method in class RBNgui.NodeWindow
 
updateQueryatomsList() - Method in class RBNgui.EvidenceModule
 
updateRBNRelations() - Method in class RBNgui.EvidenceModule
 
upperBound() - Method in class RBNLearning.GradientGraphLikelihoodNode
 
upperBound() - Method in class RBNLearning.GradientGraphProbFormNode
 
upstreamofevidence - Variable in class RBNinference.PFNetworkNode
 
upstreamOfEvidence() - Method in class RBNinference.PFNetworkNode
 

V

value(double) - Method in interface mymath.BinaryOptimizable
 
value() - Method in class RBNLearning.GradientGraphNode
 
valueOf(String) - Static method in enum RBNpackage.Instantiation.SetRelationship
Returns the enum constant of this type with the specified name.
values() - Static method in enum RBNpackage.Instantiation.SetRelationship
Returns an array containing the constants of this enum type, in the order they are declared.
vectorToArray(Vector<String>) - Static method in class myio.StringOps
 
vectorToString(Vector<String>) - Static method in class myio.StringOps
 
verbose() - Method in class RBNgui.LearnModule
 
verticalIP(double, double, double, double, double, double, boolean) - Method in class RBNgui.EditPanel
 

W

WithinComment - Static variable in interface RBNio.AtomListParserConstants
Lexical state.
writeTruthValue(int) - Method in class RBNinference.BayesNetIntHuginNet
 

X

xSum(Collection<BNNode>) - Static method in class RBNinference.BNNode
 

Y

ynQuestion(String, BufferedReader) - Static method in class myio.SystemIO
 
ynQuestion(String, BufferedReader) - Static method in class RBNutilities.SystemIO
 

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