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

A

addOutcome(String) - Method in class Variable
 
addParent(int) - Method in class Variable
 
addXBIFProbability(Node) - Method in class BayesNet
Finds CPTs and adds them to the DOM tree.
addXBIFVariable(int, Node) - Method in class BayesNet
Finds the definitions of random variables and adds them to the DOM tree.
addXMLBIFDefinition(Node) - Method in class BayesNet
Finds CPTs and adds them to the DOM tree.
addXMLBIFEvidence(int, Node) - Method in class BayesNet
Finds evidences and adds them to the DOM tree.
addXMLBIFVariable(int, Node) - Method in class BayesNet
Finds the definitions of random variables and adds them to the DOM tree.
adjTab - Variable in class BayesNet
Directed adjacency table that specifies the network structure of the BN.
array - Variable in class VArray
Bit array.
ATT_BIF_VERSION - Static variable in class BayesNet
 
ATT_VARIABLE_TYPE - Static variable in class BayesNet
 

B

B2PException - Exception in <Unnamed>
A wrapper class for exceptions.
B2PException() - Constructor for exception B2PException
 
B2PException(String) - Constructor for exception B2PException
 
B2PHandler - Class in <Unnamed>
A wrapper class for the exception handler used in the XML parser.
B2PHandler() - Constructor for class B2PHandler
 
basename - Variable in class BayesNet
Basename of the input file.
basename - Variable in class BNSetting
Basename of the input file.
BayesNet - Class in <Unnamed>
A Bayesian network.
BayesNet(BNSetting, Document, Document) - Constructor for class BayesNet
 
bayesNet - Variable in class VArray
Target Bayesian network.
BayesNet.VisitResult - Class in <Unnamed>
Immutable class containing a result of a visit in sorting a bucket.
BayesNet.VisitResult() - Constructor for class BayesNet.VisitResult
 
BayesNet.VisitResult(boolean, int) - Constructor for class BayesNet.VisitResult
 
BayesNet.VStat - Enum in <Unnamed>
Enum for the flags in topological sorting.
BayesNet.VStat() - Constructor for enum BayesNet.VStat
 
BN2Prism - Class in <Unnamed>
The main class of the translator.
BN2Prism() - Constructor for class BN2Prism
The default setting will be set.
BNSetting - Class in <Unnamed>
A setting for the translator.
BNSetting(String) - Constructor for class BNSetting
Several default settings are also made.
bucketList - Variable in class BayesNet
List of buckets, where each buckets contains cluster nodes, CPT nodes and instanciation nodes.
buildBN() - Method in class BN2Prism
Parse the input XMLBIF file, and store the information to the intermediate data structure.
buildElimOrder() - Method in class BayesNet
Builds the minimum deficiency order (MDO) using adjacency tables and return it.
buildInitialBuckets() - Method in class BayesNet
Builds the initial buckets.
buildModes() - Method in class BayesNet
Determines the input/output modes of cluster nodes and CPT nodes.
buildModes() - Method in class CPTNode
Adds the input/output modes for all variables in the CPT.

C

checkHasEvid() - Method in class BayesNet
Checks if there are evidences specified in the input.
checkTableEntries(Variable) - Method in class BayesNet
Checks if the CPT entries are normalized.
checkTableSize(Variable) - Method in class BayesNet
Checks the size of each CPT.
closeStreams() - Method in class BayesNet
Closes the output streams.
Cluster - Class in <Unnamed>
A cluster used in the bucket-tree algorithm.
Cluster() - Constructor for class Cluster
 
ClusterNode - Class in <Unnamed>
A cluster node used in the bucket-tree method.
ClusterNode(int, VArray) - Constructor for class ClusterNode
 
computeWidth(VArray) - Method in class Cluster
 
copy() - Method in class VArray
Returns a copy of this object.
CPTNode - Class in <Unnamed>
A CPT node used in the bucket-tree method.
CPTNode(int, VArray) - Constructor for class CPTNode
 

E

elimOrder - Variable in class BayesNet
Elimination order.
error(SAXParseException) - Method in class B2PHandler
 
evidence - Variable in class Variable
The index of an outcome that were observed as an evidence.
evidLevel - Variable in class BayesNet
Evidence levels used for generating random evidences.
evidPsm - Variable in class BayesNet
Output stream for Prism evidences.

F

failed() - Method in class BayesNet.VisitResult
 
fatalError(SAXParseException) - Method in class B2PHandler
 
format - Variable in class BayesNet
Format of the XML input.
format - Variable in class BNSetting
Format of the XML input.
Format - Enum in <Unnamed>
Enum for file formats.
Format() - Constructor for enum Format
 

G

get(int) - Method in class VArray
Returns the i-th element of the bit array.
getAdjacencyTable() - Method in class BayesNet
Builds the directed adjacency table and return it.
getArray() - Method in class VArray
 
getBaseName() - Method in class BNSetting
 
getCleanTextContent(Node) - Method in class BayesNet
Cleans up the text contents by replacing all space symbols by white spaces and perform triming.
getElimOrder() - Method in class BayesNet
Gets the elimination order.
getEvidence() - Method in class Variable
 
getEvidLevel() - Method in class BayesNet
Computes the evidence levels for all variables in the BN.
getExternalElimOrder() - Method in class BayesNet
Retrieves the elimination order from the file named BASENAME.num.
getFirstNetworkNode(Document) - Method in class BayesNet
Gets the first DOM tree of the BN specification.
getFormat() - Method in class BNSetting
 
getHasExtElimOrder() - Method in class BNSetting
 
getHasTrCPT() - Method in class BNSetting
 
getId() - Method in class Cluster
 
getId() - Method in class Variable
 
getIndex() - Method in class BayesNet.VisitResult
 
getInstAry() - Method in class Cluster
 
getInverseTotalOrder() - Method in class BayesNet
Builds the inverse mapping of order[].
getModeAry() - Method in class Cluster
 
getModeDepTable(int, List<Cluster>) - Method in class BayesNet
Gets the table on input/output dependencies.
getModeEvid() - Method in class BNSetting
 
getModeNormalize() - Method in class BNSetting
 
getModeRandom() - Method in class BNSetting
 
getModeVerbose() - Method in class BNSetting
 
getModeZeroComp() - Method in class BNSetting
 
getName() - Method in class Variable
 
getNodeString(Node) - Method in class BN2Prism
Get the string which denotes the contents of a node.
getNumberOfVariables() - Method in class BayesNet
Returns the number of variables in the BN.
getOffset() - Method in class Cluster
 
getOrder() - Method in class Variable
 
getOutcomeList() - Method in class Variable
 
getOutcomeSize() - Method in class Variable
 
getParentList() - Method in class Variable
 
getPrimaryCluster() - Method in class BayesNet
Gets the primary clusters for all variables.
getSetting() - Method in class BN2Prism
Returns the current setting of the translator.
getTable() - Method in class Variable
 
getTotalOrder() - Method in class BayesNet
Gets the total order of variables by topological sorting.
getUndirectedAdjacencyTable() - Method in class BayesNet
Converts a directed adjacency table to the undirected one.
getVarAry() - Method in class Cluster
 
getVariable(int) - Method in class BayesNet
Returns the i-th variable in the BN.
getVersion() - Method in class BNSetting
 
getWidth() - Method in class Cluster
 
getXBIFFirstNetworkNode(Document) - Method in class BayesNet
Gets the DOM tree of the XBIF specification of a BN.
getXMLBIFFirstNetworkNode(Document) - Method in class BayesNet
Gets the DOM tree of the XMLBIF specification of a BN.
growBuckets() - Method in class BayesNet
Grows the buckets one by one.

H

hasEvid - Variable in class BayesNet
Flag indicating wheter the translator has some evidence file.
hasExtElimOrder - Variable in class BayesNet
Flag indicating whether we have an external file (BASENAME.num) which specifies the elimination order.
hasExtElimOrder - Variable in class BNSetting
Flag indicating whether we have an external file (BASENAME.num) which specifies the elimination order.
hasTrCPT - Variable in class BayesNet
Flag indicating whether the CPTs given in the input file are transposed.
hasTrCPT - Variable in class BNSetting
Flag indicating whether the CPTs given in the input file are transposed.
headAry - Variable in class BayesNet
List of cluster nodes that lead to be heads of the translated Prism clauses.

I

id - Variable in class Cluster
ID of the cluster.
id - Variable in class Variable
ID of the variable
index - Variable in class BayesNet.VisitResult
 
InstanciateNode - Class in <Unnamed>
An instanciation node, a special node which is newly introduced in the BN2Prism translator.
InstanciateNode(int) - Constructor for class InstanciateNode
 
instAry - Variable in class Cluster
Bit array that indicates the existences of the instanciation nodes in the same bucket.
intersect(VArray) - Method in class VArray
Takes the bit-wise intersection of the bit array and va.
intersect(VArray, VArray) - Static method in class VArray
Returns the bit-wise exclusive OR of va1 and va2.
invOrder - Variable in class BayesNet
Inverse mapping of order[] (the total order).

M

main(String[]) - Static method in class BN2Prism
Main method.
matchName(String, String) - Method in class BayesNet
Matches two strings ignoring the case.
MAX_NVAR_NAIVE - Static variable in class BayesNet
Max.
modeAry - Variable in class Cluster
Bit array that indicates the input/output modes of the variables in the cluster.
modeEvid - Variable in class BayesNet
Flag for generating random evidences.
modeEvid - Variable in class BNSetting
Flag for generating random evidences.
modeNormalize - Variable in class BayesNet
Flag for normalizing CPT entries.
modeNormalize - Variable in class BNSetting
Flag for normalizing CPT entries.
modeRandom - Variable in class BayesNet
Flag for assigning random parameters.
modeRandom - Variable in class BNSetting
Flag for assigning random parameters.
modeVerbose - Variable in class BayesNet
Flag for the verbose mode.
modeVerbose - Variable in class BNSetting
Flag for the verbose mode.
modeZeroComp - Variable in class BayesNet
Flag for zero-compression of CPTs.
modeZeroComp - Variable in class BNSetting
Flag for zero-compression of CPTs.

N

name - Variable in class Variable
Original variable name in the XML specification.
NON_TINY_PROB - Static variable in class BayesNet
Threshold by which we judge the non-tininess of a float-point number.
NUM_EVID_LEVEL - Static variable in class BayesNet
Number of levels for random evidences.

O

offset - Variable in class Cluster
Temporary variable used for breaking a loop of input/output dependency
order - Variable in class BayesNet
Total order of the variables in the BN.
order - Variable in class Variable
The position of the variable in the total (topological) order.
origTable - Variable in class Variable
Original CPT.
outcomeList - Variable in class Variable
Original names of the outcomes in the XML specification.

P

parentList - Variable in class Variable
List of IDs of parent variables.
parseArgs(String[]) - Method in class BN2Prism
 
parseXBIFNetwork(Document) - Method in class BayesNet
Traverses and collects information on the DOM of XBIF network file.
parseXMLBIFEvidence(Document) - Method in class BayesNet
Traverses and collects information on the DOM of XMLBIF _evidence_ file.
parseXMLBIFNetwork(Document) - Method in class BayesNet
Traverses and collects information on the DOM of XMLBIF _network_ file.
postCheckNetwork() - Method in class BayesNet
Performs post checking and post processing of the network specification.
primCluster - Variable in class BayesNet
Primary clusters for variables.
primClusterWidth - Variable in class BayesNet
The widths of primary clusters.
printAdjacencyTable() - Method in class BayesNet
Prints the directed adjacency table.
printBuckets() - Method in class BayesNet
Prints buckets (the base method).
printDocument(Document) - Method in class BN2Prism
Display the contents in a DOM tree.
printElimOrder() - Method in class BayesNet
Prints the elimination order.
printFinalBuckets() - Method in class BayesNet
Prints the buckets finally obtained by the bucket-tree method.
printInitialBuckets() - Method in class BayesNet
Prints the initial buckets.
printModedBuckets() - Method in class BayesNet
Prints the buckets added the input/output modes.
printPrismBuckets() - Method in class BayesNet
Writes the modeling part to the outoput.
printPrismCPT() - Method in class BayesNet
Writes the definition of the cpt predicate.
printPrismDecls() - Method in class BayesNet
Writes the declaration part to the outoput.
printPrismDistrib() - Method in class BayesNet
Writes the naive version of the modeling part.
printPrismModes() - Method in class BayesNet
Writes the mode declarations to the outoput.
printPrismNaiveBN() - Method in class BayesNet
Writes the naive version of the modeling part.
printPrismNames() - Method in class BayesNet
Writes the predicates that relate the names systematically given by the translator to the original ones given in the XML input.
printPrismRanges() - Method in class BayesNet
Writes definitions of range/2 into the output according to the value of modeZeroComp.
printPrismRanges2() - Method in class BayesNet
Writes definitions of range/2 into the output without zero compression.
printPrismRanges3() - Method in class BayesNet
Writes definitions of range/3 into the output with zero compression.
printPrismSampler() - Method in class BayesNet
Writes the routine for sampling.
printPrismSetSwitches() - Method in class BayesNet
Writes the routine for parameter settings.
printPrismVersion() - Method in class BayesNet
Writes the version number to the outoput.
printPsmEvid() - Method in class BayesNet
Writes the evidences.
printPsmRandomEvid() - Method in class BayesNet
Writes the random evidences.
printTotalOrder() - Method in class BayesNet
Writes the total order of the variables in the BN.
printUndirectedAdjacencyTable() - Method in class BayesNet
Prints the undirected adjacency table.
printVariables() - Method in class BayesNet
Writes the variables in the BN.
psm - Variable in class BayesNet
Output stream for the translated Prism program.

R

randEvidPsm - Variable in class BayesNet
Output streams for random Prism evidences.
replaceRandomTable() - Method in class Variable
Replaces the original CPT with a randomly generated one.

S

set(int, boolean) - Method in class VArray
Sets the i-th element of the bit array as b.
setAll(boolean) - Method in class VArray
Sets all elements of the bit array as b.
setArray(boolean[]) - Method in class VArray
Makes a deep copy of a to the bit array.
setBaseName(String) - Method in class BNSetting
 
setEvidence(int) - Method in class Variable
 
setFormat(Format) - Method in class BNSetting
 
setHasExtElimOrder(boolean) - Method in class BNSetting
 
setHasTrCPT(boolean) - Method in class BNSetting
 
setId(int) - Method in class Variable
 
setInstAry(VArray) - Method in class Cluster
 
setModeAry(VArray) - Method in class Cluster
 
setModeEvid(boolean) - Method in class BNSetting
 
setModeNormalize(boolean) - Method in class BNSetting
 
setModeRandom(boolean) - Method in class BNSetting
 
setModeVerbose(boolean) - Method in class BNSetting
 
setModeZeroComp(boolean) - Method in class BNSetting
 
setName(String) - Method in class Variable
 
setOffset(int) - Method in class Cluster
 
setOrder(int) - Method in class Variable
 
setOutcomeList(List<String>) - Method in class Variable
 
setParentList(List<Integer>) - Method in class Variable
 
setTable(double[]) - Method in class Variable
 
setting - Variable in class BN2Prism
Settings for the translator.
size() - Method in class VArray
Returns the size of the bit array.
sortBuckets() - Method in class BayesNet
Orders the elements in each bucket according to the input/output modes.
succ - Variable in class BayesNet.VisitResult
 

T

table - Variable in class Variable
CPT.
TAG_BIF - Static variable in class BayesNet
 
TAG_DEFINITION - Static variable in class BayesNet
 
TAG_EVIDENCE - Static variable in class BayesNet
 
TAG_FOR - Static variable in class BayesNet
 
TAG_GIVEN - Static variable in class BayesNet
 
TAG_NAME - Static variable in class BayesNet
 
TAG_NETWORK - Static variable in class BayesNet
 
TAG_OUTCOME - Static variable in class BayesNet
 
TAG_PROBABILITY - Static variable in class BayesNet
 
TAG_PROPERTY - Static variable in class BayesNet
 
TAG_TABLE - Static variable in class BayesNet
 
TAG_VALUE - Static variable in class BayesNet
 
TAG_VALUES - Static variable in class BayesNet
 
TAG_VARIABLE - Static variable in class BayesNet
 
TAG_VARIABLENAME - Static variable in class BayesNet
 
TINY_PROB - Static variable in class BayesNet
Threshold by which we judge the tininess of a float-point number.
toPrismModeString() - Method in class ClusterNode
Returns a mode declaration of the corresponding "node_xN" predicate.
toPrismModeString2() - Method in class ClusterNode
Returns a mode declaration of the corresponding "pot_xN" predicate.
toPrismString() - Method in class Cluster
 
toPrismString() - Method in class ClusterNode
Returns a string representation of the corresponding "node_xN" literal.
toPrismString() - Method in class CPTNode
Returns a string representation of the corresponding "cpt" literal.
toPrismString() - Method in class InstanciateNode
Returns a string representation of the corresponding "instanciate" literal.
toPrismString2() - Method in class Cluster
 
toPrismString2() - Method in class ClusterNode
Returns a string representation of the corresponding "pot_xN" literal.
toPrismString2() - Method in class CPTNode
The same as toPrismString().
toPrismString2() - Method in class InstanciateNode
The same as toPrismString().
toString() - Method in class BayesNet
Returns a string representation.
toString() - Method in class Cluster
 
toString() - Method in class ClusterNode
Returns an _internal_ string representation.
toString() - Method in class CPTNode
Returns an _internal_ string representation.
toString() - Method in class InstanciateNode
Returns an _internal_ string representation.
toString() - Method in class Variable
 
toString() - Method in class VArray
Returns a string representation of the bit array.
transposeCPT(Variable) - Method in class BayesNet
Transposes the transposed CPT.
traverse(Node, int) - Method in class BN2Prism
Display the contents of a DOM tree recursively.

U

uAdjTab - Variable in class BayesNet
Undirected adjacency table that specifies the network structure of the BN.
union(VArray) - Method in class VArray
Takes the bit-wise union of the bit array and va.
union(VArray, VArray) - Static method in class VArray
Returns the bit-wise union of va1 and va2.
USAGE - Static variable in class BN2Prism
Message on usage

V

valueOf(String) - Static method in enum BayesNet.VStat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum Format
Returns the enum constant of this type with the specified name.
values() - Static method in enum BayesNet.VStat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum Format
Returns an array containing the constants of this enum type, in the order they are declared.
varAry - Variable in class Cluster
Bit array that indicates the variables in the cluster.
Variable - Class in <Unnamed>
A variable in a Bayesian network.
Variable() - Constructor for class Variable
Create a BN variable with no operation.
varList - Variable in class BayesNet
List of the variables appearing in the BN.
varMap - Variable in class BayesNet
Hashtable for the variable names.
VArray - Class in <Unnamed>
A wrapper of a bit array related to the random variables in a Bayesian network.
VArray(BayesNet, boolean) - Constructor for class VArray
Initializes all bits as b.
VArray(BayesNet) - Constructor for class VArray
Initializes all bits as false.
VArray(BayesNet, Variable) - Constructor for class VArray
Sets true to the bits corresponding to the variables included in the CPT at which the variable v appears.
version - Variable in class BayesNet
Version number of the translator.
VERSION - Static variable in class BN2Prism
String representation of the version number
version - Variable in class BNSetting
Version number of the translator.
visit(int, int, int, BayesNet.VStat[]) - Method in class BayesNet
Visits each variable in the BN based on the direct adjacency table.
visitBucket(int, int, BayesNet.VisitResult, int[][], BayesNet.VStat[], List<Integer>) - Method in class BayesNet
Visit an element in a bucket recursively.

W

warning(SAXParseException) - Method in class B2PHandler
 
width - Variable in class Cluster
The width of the cluster.

X

xor(VArray) - Method in class VArray
Takes the bit-wise exclusive OR of the bit array and va.
xor(VArray, VArray) - Static method in class VArray
Returns the bit-wise exclusive OR of va1 and va2.

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