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

A

AbsoluteDataPoint - Class in uk.co.agena.minerva.util.model
This class represents DataPoints that have an absolute number (e.g.
AbsoluteDataPoint() - Constructor for class uk.co.agena.minerva.util.model.AbsoluteDataPoint
Default constructor.
AbsoluteDataPoint(double, int, double) - Constructor for class uk.co.agena.minerva.util.model.AbsoluteDataPoint
Constructs and AbsoluteDataPoint with the supplied "y" value, connected object ID and "x" value.
AbsoluteDataPoint(String, double, int, double) - Constructor for class uk.co.agena.minerva.util.model.AbsoluteDataPoint
Constructs and AbsoluteDataPoint with the supplied label, "y" value, connected object ID and "x" value.
actOnMarginalsChangedEvent - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This is the number of times that this object will act on a Marginals changed event.
add(int, int, int, int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Adds a new link with the specified child/parent ExtendedBN/ExtendedNode IDs to this MessagePassingLinks object.
addAbsoluteDataPoint(double) - Method in class uk.co.agena.minerva.util.model.DataSet
Adds a new absolute (i.e.
addBooleanNode(String, String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Creates a new Boolean node with the specified name and with the default states "False" and "True".
addChild(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Call this to add a child to an ExtendedNode, this connects the core nodes, then updated the parent list in this object and the function type.
addChild(QueryObjectNode) - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
addConnection(List, Connectable) - Method in class uk.co.agena.minerva.util.model.ConnectionProcessor
Adds the specified connetable to the connectables list
addContinuousIntervalNode(String, String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Creates a new Continuous Interval node with the specified name and with default states 0.0 - 10.0, 10.0 - 20.0, 20.0 - 30.0, 30.0 - 40.0 and 40.0 - 50.0.
addCoreBNListeners() - Method in class uk.co.agena.minerva.model.Propagation
Adds this as a Listener to each of the CoreBN's associated with the ExtendedBN's in the current models ExtendedBNList.
addDataPoint(DataPoint) - Method in class uk.co.agena.minerva.util.model.DataSet
Adds the supplied DataPoint to the DataSet.
addDataPoint(DataPoint, int) - Method in class uk.co.agena.minerva.util.model.DataSet
Adds the supplied DataPoint to the DataSet at the specified order postion.
addDataSet(DataSet) - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Adds the supplied DataSet to the DataSetGrouping.
addDataSet(DataSet, int) - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Adds the supplied DataSet to the DataSetGrouping at the specified order position.
addDataSetVars(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.ExpressionParser
Adds list of strings as variables to parser with string or double value.
addDDRelativeSumWidthEntropyError(double) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Add the argument entropy error value to the end of the list and moves the rest along by one, removing the oldest.
addDiscreteRealNode(String, String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Creates a new Discrete Real node with the specified name and with default states 1.0, 2.0, 3.0, 4.0 and 5.0.
addExpressionVariable(ExtendedNode, String, double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Adds a new Variable with the specified name and default value to the VariableList for the specified ExtendedNode.
addExpressionVariable(String, double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Adds a new Variable to the VariableList with the specified name and default value.
addExtendedBN(ExtendedBN, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Adds the supplied ExtendedBN to this ExtendedBNList.
addExtendedBN(ExtendedBN) - Method in class uk.co.agena.minerva.model.Model
Adds the supplied ExtendedBN to the Model.
addExtendedBN(String, String) - Method in class uk.co.agena.minerva.model.Model
Creates an empty BN with the supplied name and description and adds it to this model's list.
addExtendedBN(ExtendedBN, boolean) - Method in class uk.co.agena.minerva.model.Model
Adds the supplied ExtendedBN to the Model's ExtendedBNList and compiles it (if required and if it is not already compiled).
addExtendedBN(ExtendedBN, boolean, boolean) - Method in class uk.co.agena.minerva.model.Model
Adds the supplied ExtendedBN to the Model's ExtendedBNList and compiles it (if required and if if it is not already compiled).
addExtendedBNListener(ExtendedBNListener) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Adds an object interested in ExtendedBNEvents to the List of ExtendedBNListeners (actually held by an internal ExtendedBNEventGenerator).
addExtendedBNs(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Adds the supplied ExtendedBNs to this ExtendedBNList.
addExtendedBNs(List, boolean) - Method in class uk.co.agena.minerva.model.Model
Adds the supplied List of ExtendedBNs to this Model's List of ExtendedBNs and compiles them (if required and if if they are not already compiled).
addExtendedBNs(List, boolean, boolean) - Method in class uk.co.agena.minerva.model.Model
Adds the supplied List of ExtendedBNs to this Model's List of ExtendedBNs and compiles them (if required and if if they are not already compiled).
addExtendedNode(ExtendedNode, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Adds the specified ExtendedNode to the ExtendedBN's List.
addExtendedNode(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Adds the supplied node the Extended BN.
addExtendedNodeListener(ExtendedNodeListener) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Adds an object interested in ExtendedNodeEvents to the List of ExtendedNodeListeners (actually held by an internal ExtendedNodeEventGenerator).
addExtendedState(ExtendedState, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Adds an ExtendedState to this ExtendedNode's List of ExtendedStates.
addExtendedState(ExtendedState, boolean, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Adds an ExtendedState to this ExtendedNode's List of ExtendedStates.
addExtendedStateListener(ExtendedStateListener) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Adds an object interested in ExtendedStateEvents to the List of ExtendedStateListeners (actually held by an internal ExtendedStateEventGenerator).
addExtendedStates(List, int, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Adds the supplied states at the specified index in the list.
addHardEvidenceObservation(int, int, int) - Method in class uk.co.agena.minerva.model.scenario.Scenario
 
addIntegerIntervalNode(String, String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Creates a new Integer Interval node with the specified name and with default states 0 - 10, 10 - 20, 20 - 30, 30 - 40 and 40 - 50.
addIntegerObservation(int, int, int) - Method in class uk.co.agena.minerva.model.scenario.Scenario
 
addIntervalDataPoint(double, double) - Method in class uk.co.agena.minerva.util.model.DataSet
Adds a new interval data point to the DataSet.
addLabelledDataPoint(String) - Method in class uk.co.agena.minerva.util.model.DataSet
Adds a new labelled DataPoint to the DataSet.
addLabelledNode(String, String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Creates a new Labelled node with the specified name and with the default states "State_1", "State_2" and "State_3".
addLog(NameDescription) - Method in class uk.co.agena.minerva.util.model.ModificationLog
Adds a modifiatcion item to the log, and returns it
addMessageParseLink(ExtendedNode, ExtendedNode) - Method in class uk.co.agena.minerva.model.Model
This method will add the specified message parssing link to the model.
addMessageParseLink(ExtendedNode, ExtendedBN) - Method in class uk.co.agena.minerva.model.Model
This method will create a new message parse link from the specified source node, and the selected target BN a Clone of the source node will be created and added to the target BN in order to create the link.
addMessagePassingLinks(List, boolean) - Method in class uk.co.agena.minerva.model.Model
Adds the supplied MessagePassingLinks objects to the Model's List.
addModelListener(ModelListener) - Method in class uk.co.agena.minerva.model.Model
Adds an object interested in ModelEvents to the List of ModelListeners (actually held by an internal ModelEventGenerator).
addModificationLogItem(NameDescription) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Convience method adds a new modification log top the extended BN
addNote(Note) - Method in class uk.co.agena.minerva.util.model.Notes
Add a note to the notes collection
addNote(List) - Method in class uk.co.agena.minerva.util.model.Notes
Adds all the notes in the specified list of notes
addNote(String, String) - Method in class uk.co.agena.minerva.util.model.Notes
Adds a note with the specified text
addObjectsToView(MinervaMainFrame, QueryObjectNode) - Method in class uk.co.agena.minerva.model.querymodel.StructureElement
Creates new MetaDataItems corresponding to each node in the Query Object tree.
addObservation(Observation, boolean) - Method in class uk.co.agena.minerva.model.scenario.Scenario
Adds the supplied Observation to the end of the List of Observations.
addObservations(MinervaMainFrame, QueryObjectNode) - Method in class uk.co.agena.minerva.model.querymodel.StructureElement
 
addParent(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Call this to add a parent to an ExtendedNode, this connects the core nodes, then updated tha parent list in this object and the function type.
addPropagationListener(PropagationListener) - Method in class uk.co.agena.minerva.model.Propagation
Adds an object interested in PropagationEvents to the List of PropagationListeners (actually held by an internal PropagationEventGenerator).
addQuestionnaire(Questionnaire) - Method in class uk.co.agena.minerva.model.Model
Adds the supplied Questionnaire to the Model's QuestionnaireList.
addQuestionnaire(Questionnaire, boolean) - Method in class uk.co.agena.minerva.model.Model
Adds the supplied Questionnaire to the Model's QuestionnaireList.
addQuestionnaires(List) - Method in class uk.co.agena.minerva.model.Model
Adds the supplied Questionnaires to the Model's QuestionnaireList.
addQuestionnaires(List, boolean) - Method in class uk.co.agena.minerva.model.Model
Adds the supplied Questionnaires to the Model's QuestionnaireList.
addRangeNotToBeSplit(Range) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
addRankedNode(String, String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Creates a new Ranked node with the specified name and with default states Very Low, Low, Medium, High and Very High.
addRealObservation(int, int, double) - Method in class uk.co.agena.minerva.model.scenario.Scenario
 
addScenario(String) - Method in class uk.co.agena.minerva.model.Model
 
addScenario(Scenario, Object) - Method in class uk.co.agena.minerva.model.Model
Adds the supplied Scenario to the Model's ScenarioList.
addScenario(Scenario, boolean, Object) - Method in class uk.co.agena.minerva.model.Model
Adds a scenario to the model
addScenario(Scenario) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
Adds the supplied Scenario to this ScenarioList.
addScenarioListenerPrimary(ScenarioListener) - Method in class uk.co.agena.minerva.model.scenario.Scenario
Adds an object interested in ScenarioEvents to the List of ScenarioListeners (actually held by an internal ScenarioEventGenerator).
addScenarioListenerSecondary(ScenarioListener) - Method in class uk.co.agena.minerva.model.scenario.Scenario
Adds an object interested in ScenarioEvents to the List of ScenarioListeners (actually held by an internal ScenarioEventGenerator).
addScenarios(List) - Method in class uk.co.agena.minerva.model.Model
Adds the supplied Scenarios to the Model's ScenarioList.
addScenarios(List, boolean) - Method in class uk.co.agena.minerva.model.Model
 
addSoftEvidenceObservation(int, int, int[], double[]) - Method in class uk.co.agena.minerva.model.scenario.Scenario
 
addStringVars(List) - Method in class uk.co.agena.minerva.util.nptgenerator.ExpressionParser
Adds list of strings as variables to parser with value of 0.0.
addUserDefinedRevantExtendedBNIds(int[]) - Method in class uk.co.agena.minerva.model.scenario.Scenario
 
addVariable(String) - Method in class uk.co.agena.minerva.util.model.VariableList
Creates a new Variable with the supplied name and adds it to the List of Variables.
addVariable(String, double) - Method in class uk.co.agena.minerva.util.model.VariableList
Creates a new Variable with the supplied name and default value and adds it to the List of Variables.
addVariable(String, double, double) - Method in class uk.co.agena.minerva.util.model.VariableList
Creates a new Variable with the supplied name, actual value and default value and adds it to the List of Variables.
addVariable(Variable) - Method in class uk.co.agena.minerva.util.model.VariableList
Adds the supplied Variable to the list of variables.
addVariableVars(List) - Method in class uk.co.agena.minerva.util.nptgenerator.ExpressionParser
Adds list of strings as variables to parser with value set.
ALL_NPTS_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
ALLOWED_CHARACTERS - Static variable in class uk.co.agena.minerva.util.nptgenerator.Function
 
allParentsPresent(ExtendedNode, ExtendedBN, Collection) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns true if all the parents of the specified node in the specified ExtendedBN are present in the Collection or in this ExtendedBN.
allParentsPresent(String, ExtendedBN, Collection) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns true if all the parents of the node with the connected CoreBNNode AltID in the specified ExtendedBN are present in the Collection or in this ExtendedBN.
answerable - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Whether the ExtendedNode should have a connected Question.
appendToAllNotes(String, String) - Method in class uk.co.agena.minerva.util.model.Notes
Appends the specified Strings to the short/long description field of the NameDescription attatched to each Note.
APPLY_SCENARIO_EXCLUDE_NODES - Static variable in class uk.co.agena.minerva.model.Model
Indicates that a Scenario should be applied to all specified ExtendedNodes in a given ExtendedBN except those specified.
APPLY_SCENARIO_EXCLUSIVELY - Static variable in class uk.co.agena.minerva.model.Model
Indicates that before a Scenario is applied to any ExtendedBN which this Scenario affects, all other evidence is removed.
APPLY_SCENARIO_INCLUDE_ONLY_NODES - Static variable in class uk.co.agena.minerva.model.Model
Indicates that a Scenario should only be applied to the specified ExtendedNodes in a given ExtendedBN.
APPLY_SCENARIO_INEXCLUSIVELY - Static variable in class uk.co.agena.minerva.model.Model
Indicates that before a Scenario is applied to any ExtendedBN in this model, all other evidence is left in the ExtendedBN; the new Scenario is applied "on top of" any existing evidence.
APPLY_SCENARIO_MODEL_EXCLUSIVELY - Static variable in class uk.co.agena.minerva.model.Model
Indicates that before a Scenario is applied to any ExtendedBN in this model, all other evidence is removed.
APPLY_SCENARIO_NO_SPECIFIC_NODES - Static variable in class uk.co.agena.minerva.model.Model
Indicates that a Scenario should be applied to all ExtendedNodes in a given ExtendedBN.
applyObservationResults(MarginalDataItem) - Method in class uk.co.agena.minerva.model.querymodel.UpdateInstance
 
applyScenario(Scenario, boolean, int, boolean) - Method in class uk.co.agena.minerva.model.Model
Applies the Scenario to all the relevant ExtendedBNs in this Model.
applyScenario(Scenario, boolean, int, List, boolean) - Method in class uk.co.agena.minerva.model.Model
Applies the Scenarios only to the ExtendedBNs contained in the supplied List.
applyScenario(Scenario, boolean, int, List, boolean, String[], boolean) - Method in class uk.co.agena.minerva.model.Model
Applies the Scenarios only to the ExtendedBNs contained in the supplied List using the supplied call sign information.
applyScenario(Scenario, boolean, int, List, int, String[], boolean, String[], boolean) - Method in class uk.co.agena.minerva.model.Model
Applies the Scenarios only to the ExtendedBNs contained in the supplied list using the supplied call sign information and information about which nodes to include and exclude.
APPNAME - Static variable in class uk.co.agena.minerva.util.BuildInformation
 
area() - Method in class uk.co.agena.minerva.util.model.IntervalDataPoint
This returns the "area" of the DataPoint i.e.
areNeighboringStatesDisceteValues(int) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
For any given stateIndex, this method checks if the adjacent/neighbouring states are discreteValue states.
Arithmetic - Class in uk.co.agena.minerva.util.nptgenerator
 
Arithmetic(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Arithmetic
Will Generate a Arithmetic NPT using the node and its parent nodes.
Arithmetic(List, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.Arithmetic
calculates the arithmetic variable.
ATTRIBUTECHANGED_DISPLAY_ON_GRAPH - Static variable in class uk.co.agena.minerva.model.scenario.ScenarioEvent
 
ATTRIBUTECHANGED_ENTROPYCONVERGENCE - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
ATTRIBUTECHANGED_INPUTNODE - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
ATTRIBUTECHANGED_NAME - Static variable in class uk.co.agena.minerva.model.scenario.ScenarioEvent
 
ATTRIBUTECHANGED_OUTPUTNODE - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
ATTRIBUTECHANGED_RECALC_REQUIRED - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
ATTRIBUTECHANGED_REPORTABLE - Static variable in class uk.co.agena.minerva.model.scenario.ScenarioEvent
 
ATTRIBUTECHANGED_SIMULATIONNODE - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
ATTRIBUTECHANGED_THRESHOLDVALUE_DEFINED - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
autoGenerateMessagePassingLinks(ExtendedBN, ExtendedBN) - Method in class uk.co.agena.minerva.model.Model
Automatically generates MessagePassingLinks objects between the supplied ExtendedBNs depending on their input and output nodes.
autoLinkBNOs() - Method in class uk.co.agena.minerva.model.Model
This method uses the generic link generator and the link generator property uk.co.agena.minervaapps.basicminerva.linkgenerator in the minerva.properties file to generate the message passing8 links on this model between the BNO's.

B

BASIC_PROPAGATION - Static variable in class uk.co.agena.minerva.model.Propagation
 
Beta - Class in uk.co.agena.minerva.util.nptgenerator
 
Beta(List, double, double, double, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.Beta
calculates the Beta over a defined set of ranges given a mean and a variance.
Beta(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Beta
 
Binomial - Class in uk.co.agena.minerva.util.nptgenerator
 
Binomial(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Binomial
 
Binomial(List, int, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.Binomial
calculates the Binomial over a defined set of ranges given a mean and a variance.
BooleanEN - Class in uk.co.agena.minerva.model.extendedbn
This class is used to represent nodes with just two states that correspond to {true, false} or {yes, no}.
BooleanEN() - Constructor for class uk.co.agena.minerva.model.extendedbn.BooleanEN
Creates a default BooleanEN.
BooleanEN(NameDescription, String, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.BooleanEN
 
BooleanEN(NameDescription, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.BooleanEN
 
BuildInformation - Class in uk.co.agena.minerva.util
Contains version information for the software.
BuildInformation() - Constructor for class uk.co.agena.minerva.util.BuildInformation
 

C

calculate() - Method in class uk.co.agena.minerva.model.Model
 
calculate(List) - Method in class uk.co.agena.minerva.model.Model
 
calculate(List, List) - Method in class uk.co.agena.minerva.model.Model
 
calculateFunction(String, List, String[], ExtendedNode) - Static method in class uk.co.agena.minerva.util.nptgenerator.Function
 
calculateLengthOfProgressableTask(List) - Method in class uk.co.agena.minerva.model.DynDiscPropagation
Calculates the length of a propagation task based upon the Scenario's and ExtendedBN's being propagated and the types of ExtendedNode contained in the ExtnededBN's (Normal or Simulation).
calculateLengthOfProgressableTask(List) - Method in class uk.co.agena.minerva.model.Propagation
Calculates the length of a propagation task based upon the Scenario's and ExtendedBN's being propagated.
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Arithmetic
This will calculate the arithmetic function and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex.
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Beta
This will calculate the betaDistribution and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Binomial
This will calculate the normal and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.ChiSquared
This will calculate the betaDistribution and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Comparative
This will calculate the SimpleComparative function and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex.
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Exponential
This will calculate the distribution and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.ExtremeValue
This will calculate the distribution and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Function
Override this method to do what the function requires.
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Gamma
This will calculate the betaDistribution and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Geometric
This will calculate the distribution and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Hypergeometric
This will calculate the distribution and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Logistic
This will calculate the distribution and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.LogNormal
This will calculate the betaDistribution and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.NegativeBinomial
This will calculate the normal and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Normal
This will calculate the normal and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Poisson
This will calculate the normal and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Student
This will calculate the distribution and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.TNormal
This will calculate the normal and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Triangle
This will calculate the distribution and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Uniform
This will calculate the normal and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
calculateProbability(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.Weibull
This will calculate the betaDistribution and add it to the relevant cell of the npt using the rowMajorParentStateCombIndex
changeExtendedBNId(int, int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Changes all occurences of the specified old ExtendedBN ID to the specified new ExtendedBN ID, wherever it occurs in any of the links.
changeNodeStates(ExtendedNode, DataSet) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Takes the supplied node and removes its current States replacing them with the ones represented in the specified DataSet.
changeNodeType(ExtendedNode, Class, DataSet) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Takes the supplied node, creates a new instance of the supplied type and then copies the data from the old node into the new one.
changeNodeType(ExtendedNode, Class) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Takes the supplied node, creates a new instance of the supplied type and then copies the data from the old node into the new one.
checkBasicPropagationRequirements(String) - Method in class uk.co.agena.minerva.model.Model
This method will call the propagation algorithm to do some basic checks.
checkCreationTimestamps(String) - Method in class uk.co.agena.minerva.model.Model
Check the difference between the creation timestamp, stored in the CoreBN's associated with this model, and the current time does not exceed a certain limit.
checkForErrors(String) - Method in class uk.co.agena.minerva.util.nptgenerator.ExpressionParser
 
checkUpdateParameters(QueryInstance) - Method in class uk.co.agena.minerva.model.querymodel.UpdateInstance
 
checkVariableName(String) - Method in class uk.co.agena.minerva.util.model.VariableList
Throws a MinervaVariableException if the variableName is not valid e.g.
CHILD_ADDED - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
ChiSquared - Class in uk.co.agena.minerva.util.nptgenerator
 
ChiSquared(List, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.ChiSquared
calculates the ChiSquared over a defined set of ranges given a mean and a variance.
ChiSquared(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.ChiSquared
 
ClassQueryModel - Class in uk.co.agena.minerva.model.querymodel
The root class of the Class/query model.
ClassQueryModel(MinervaMainFrame) - Constructor for class uk.co.agena.minerva.model.querymodel.ClassQueryModel
Constructor.
classQueryModel - Static variable in class uk.co.agena.minerva.model.querymodel.ClassQueryModel
 
clearAllObservations(ExtendedBN) - Method in class uk.co.agena.minerva.model.Model
Clears all the observations for a given ExtendedBN.
clearAllObservations() - Method in class uk.co.agena.minerva.model.Model
Clears all observations in this model.
clearAllObservations() - Method in class uk.co.agena.minerva.model.scenario.Scenario
Removes all Observations from the Scenario.
clearDataPoints() - Method in class uk.co.agena.minerva.util.model.DataSet
Clears all DataPoints out of the DataSet and reinitialises the DataSet with an empty List.
clearDataSets() - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Clears all the DataSets in this DataSetGrouping.
clearLog() - Method in class uk.co.agena.minerva.util.model.ModificationLog
Removes all items from the log
clearObservations(ExtendedBN, boolean) - Method in class uk.co.agena.minerva.model.Model
Removes all the observations for a given ExtendedBN.
clearObservations(boolean) - Method in class uk.co.agena.minerva.model.Model
Removes all the Observations for all the ExtendedBNs in this Model.
clearObservationsForNode(int, int) - Method in class uk.co.agena.minerva.model.scenario.Scenario
Removes all observations for the supplied BN and Node.
clearProblemNodes() - Method in class uk.co.agena.minerva.model.Model
Empties out the list of problem nodes.
clearUnpropagatedEvidence() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
This method should be called if anything fails after some evidence has been entered.
clearUnpropagatedEvidence() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Clears all unpropagated evidence from the extendedbns in the list
clone() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Makes a copy of this ExtendedNodeFunction.
clone() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
 
clone() - Method in class uk.co.agena.minerva.model.scenario.Observation
This method will clone the observation, and return the new;y cloned object
clone() - Method in class uk.co.agena.minerva.model.scenario.Scenario
This method will clone the scenario, and return the copy
clone() - Method in class uk.co.agena.minerva.util.model.AbsoluteDataPoint
Makes a copy of this AbsoluteDataPoint
clone() - Method in class uk.co.agena.minerva.util.model.DataPoint
Creates a copy of this DataPoint.
clone() - Method in class uk.co.agena.minerva.util.model.DataSet
Creates a copy of this DataSet.
clone() - Method in class uk.co.agena.minerva.util.model.IntervalDataPoint
Makes a copy of the IntervalDataPoint.
clone() - Method in class uk.co.agena.minerva.util.model.NameDescription
Makes a copy of this NameDescription object.
clone() - Method in class uk.co.agena.minerva.util.model.Note
Clones the note
clone() - Method in class uk.co.agena.minerva.util.model.Notes
Clones the notes set
clone() - Method in class uk.co.agena.minerva.util.model.StringDataPoint
Creates a copy of this DataPoint.
clone() - Method in class uk.co.agena.minerva.util.model.Variable
Makes a copy of this Variable object.
clone() - Method in class uk.co.agena.minerva.util.model.VariableList
Clones the VariableList.
cloneNodeFunctions(Map, ExtendedBN) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Given a Map of the Original ExtendedNodes to their Cloned versions this method clones all the Function information from the original ExtendedNode to the Clone.
cloneNodeNPTs(Map, ExtendedBN) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Given a Map of the Original ExtendedNodes to their Cloned versions this method clones all the CoreNPT data from the original Node to its Clone.
cloneTypeSpecific(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Data specific to the ContinuousEN node type is cloned from the specified old node into this one.
cloneTypeSpecific(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Empty method which can be overridden by subclass ExtendedNodes so data specific to that type can be cloned.
closeConnection() - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
closeDatabaseConnections() - Method in class uk.co.agena.minerva.model.querymodel.ClassQueryModel
Closes all database connections.
columnNameToNumber(String) - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
Comparative - Class in uk.co.agena.minerva.util.nptgenerator
Comparative allows comparison operations using if-then.
Comparative(ExtendedNode, List, String[]) - Constructor for class uk.co.agena.minerva.util.nptgenerator.Comparative
 
Comparative(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Comparative
Will Generate a SimpleComparative NPT using the node and its parent nodes.
Comparative(List, Object) - Static method in class uk.co.agena.minerva.util.nptgenerator.Comparative
 
compareTo(Object) - Method in class uk.co.agena.minerva.model.DDEntropyErrorHeap
Comparison method to sort the cliques during building of the junction tree.
compareTo(Object) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Compares this object with the specified object for order.
compareUsingValue - Static variable in class uk.co.agena.minerva.model.DDEntropyErrorHeap
Leave this as true when sorting using the value field.
compile() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Compiles the underlying BN.
compileAllExtendedBNs(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Compiles all the ExtendedBNs in the list.
compileAllExtendedBNs() - Method in class uk.co.agena.minerva.model.Model
Compiles all ExtendedBNs in the Model.
configureDefaultExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.BooleanEN
Sets up a default list of ExtendedStates for this node based on the default state names for this class.
configureDefaultExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousIntervalEN
Sets up a default list of ExtendedStates for this node based on the default state names for this class.
configureDefaultExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
Sets up a default list of ExtendedStates for this node based on the default state names for this class.
configureDefaultExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Configures a default set of ExtendedStates for a node.
configureDefaultExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
Sets up a default list of ExtendedStates for this node based on the default state names for this class.
configureDefaultExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.LabelledEN
Sets up a default list of ExtendedStates for this node based on the default state names for this class.
configureDefaultExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.RankedEN
Sets up a default list of ExtendedStates for this node based on the default state names for this class.
connBn - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
A reference to an underlying CoreBN.
Connectable - Interface in uk.co.agena.minerva.util.model
 
connectableInputNode - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Defines whether the node is a possible input node for an ExtendedBN.
connectableOutputNode - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Defines whether the node is a possible output node for an ExtendedBN.
Connection - Class in uk.co.agena.minerva.util.model
 
Connection() - Constructor for class uk.co.agena.minerva.util.model.Connection
Basic constructor
Connection(int) - Constructor for class uk.co.agena.minerva.util.model.Connection
Constructor sets up some basic attributes, calls the basic constructor
CONNECTION_TYPE_CHILD - Static variable in class uk.co.agena.minerva.util.model.Connection
 
CONNECTION_TYPE_GRAPH - Static variable in class uk.co.agena.minerva.util.model.Connection
 
ConnectionProcessor - Class in uk.co.agena.minerva.util.model
 
ConnectionProcessor() - Constructor for class uk.co.agena.minerva.util.model.ConnectionProcessor
 
connNodeId - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
The ID of the connected node in the underlying BN (which will a String rather than an Integer).
connObjectId - Variable in class uk.co.agena.minerva.util.model.DataPoint
The unique identifier of the object (e.g.
constructExtraFieldString() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
constructExtraFieldString() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This should be overridden by any subclass of ExtendedNode that has additional fields that need to be written out.
contains(ExtendedBN) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Checks if the argument ExtendedBN is contained in this list of ExtendedBNs
contains(double) - Method in class uk.co.agena.minerva.util.model.Range
Determines whether the supplied value lies in this range or not.
contains(double, boolean, boolean) - Method in class uk.co.agena.minerva.util.model.Range
Determines whether the supplied value lies in this range or not.
contains(Range) - Method in class uk.co.agena.minerva.util.model.Range
This method returns true if this range contains the argument range r.
containsDDNodes() - Method in class uk.co.agena.minerva.model.Model
 
containsFunctionOfType(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
containsOnlyStatisticalFunctions() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Looks at the node's function or functions and returns true if there are only statistical (i.e.
containsXNoZeroDataPoints(int) - Method in class uk.co.agena.minerva.util.model.DataSet
This method returns a boolean that is true if the data set contains a number of non-0 data points equal to the specified argurment.
continueToDynamicallyDiscretise - Variable in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
This flag is set/unset during the DD propagation.
CONTINUOUS_INTERVAL_E_N - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Constant corresponding to the ContinuousIntervalEN type.
ContinuousEN - Class in uk.co.agena.minerva.model.extendedbn
 
ContinuousEN() - Constructor for class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Default constructor.
ContinuousEN(NameDescription, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Creates a new ContinuousEN with the supplied name and connected Core BN.
ContinuousEN(NameDescription, String, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Constructs a ContinuousEN with the specified name, connected node ID and connected BN.
ContinuousIntervalEN - Class in uk.co.agena.minerva.model.extendedbn
This class represents NumericalExtendedNodes whose ExtendedStates contain ranges (e.g.
ContinuousIntervalEN() - Constructor for class uk.co.agena.minerva.model.extendedbn.ContinuousIntervalEN
Default constructor.
ContinuousIntervalEN(NameDescription, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.ContinuousIntervalEN
Creates a new ContinuousIntervalEN with the supplied name and connected Core BN.
ContinuousIntervalEN(NameDescription, String, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.ContinuousIntervalEN
Constructs an ContinuousIntervalEN with the specified name, connected node ID and connected BN.
CONVERGENCE_THRESHOLD_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
convertLabelsToIntegerFormat() - Method in class uk.co.agena.minerva.util.model.DataSet
This method will iterate over the data points in the data set.
convertLabelsToScientificFormat(String) - Method in class uk.co.agena.minerva.util.model.DataSet
This method will itterate over the data points in the data set, If they are interval data points it will construct new labels for the data points using their range values the number mask will be appiled to the numbers before they are used in the string If the number formatted mask provided is null "", then "0.00E0" is used.
convertSpecialChars(String) - Static method in class uk.co.agena.minerva.model.querymodel.XmlHelper
 
copy(Class) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Creates a shallow copy of this ExtendedNode by copying references to all of its data into a new instance of the supplied node type.
copy(Class) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Creates a shallow copy of this ExtendedNode by copying references to all of its data into a new instance of the supplied node type.
copyQuestions(List, List, String, int, int) - Method in class uk.co.agena.minerva.model.Model
Copy the properties of the source Questions to those of the target Questions.
coreBNPropagationStageComplete(CoreBNEvent) - Method in class uk.co.agena.minerva.model.Propagation
A stage of the Propagation has completed for the CoreBN in the specified event.
createClonedNodes(List, ExtendedBN, Map) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Creates a clone of each of the ExtendedNodes if the specified List.
createContinuousIntervalState(double, double) - Static method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Creates a new continuous interval state with the supplied lower and upper bounds.
createDataPointFromExtendedState(ExtendedState, double) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Creates a DataPoint from the supplied ExtendedState and probability value.
createDataPointFromExtendedState(ExtendedState, double) - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
Creates a DataPoint for the supplied ExtendedState that represents the marginal probability associated with the ExtendedState.
createDataPointFromExtendedState(ExtendedState, double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Creates a DataPoint using information in the supplied ExtendedState.
createDataPointFromExtendedState(ExtendedState, double) - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
Creates a DataPoint from the supplied ExtendedState and probability value.
createDataSet(String[]) - Static method in class uk.co.agena.minerva.util.model.DataSet
This method creates a dataset, with a set of data points, with names equal to the strings passed as an arguement.
createDataSetForExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.BooleanEN
Create a DatsSet from the Extended States of this node.
createDataSetForExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Create a DatsSet from the Extended States of this node.
createDataSetForExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
Create a DatsSet from the Extended States of this node.
createDataSetForExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Create a DatsSet from the Extended States of this node.
createDataSetForExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
Create a DatsSet from the Extended States of this node.
createDataSetForExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.LabelledEN
Create a DatsSet from the Extended States of this node.
createDataSetFromNumericValue(double, NameDescription) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Takes the supplied value and creates a DataSet (the first) of likelihood evidence based upon where the value falls with respect to the ExtendedNode's ExtendedStates.
createDataSetFromNumericValue(double, NameDescription) - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
Takes the supplied value and creates a DataSet of evidence.
createDataSetFromNumericValue(double, NameDescription) - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
 
createDataSetFromNumericValue(double, NameDescription) - Method in class uk.co.agena.minerva.model.extendedbn.NumericalEN
Takes the supplied value and creates a DataSet of hard evidence i.e.
createDiscreteRealState(double) - Static method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Creates a new discrete real state with the supplied name and description.
createEmptyDataSet() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Creates a DataSet containing Ranges that correspond to the ExtendedStates in this ContinuousIntervalEN.
createEmptyExtendedBN() - Static method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
createEmptyModel() - Static method in class uk.co.agena.minerva.model.Model
 
createExtendedBN() - Static method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Creates and returns a new extended BN, a new core is also created and connected to the newly created BN
createExtendedBNFromCoreBN(CoreBN) - Static method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Creates an ExtendedBN from the supplied CoreBN.
createExtendedBNFromNetFile(String, List) - Static method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Creates an ExtendedBN from the supplied .net file.
createExtendedStates(DataSet) - Method in class uk.co.agena.minerva.model.extendedbn.BooleanEN
 
createExtendedStates(DataSet) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousIntervalEN
 
createExtendedStates(DataSet) - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
 
createExtendedStates(DataSet) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Takes the supplied DataSet and uses it to generate a List of ExtendedStates which are then returned.
createExtendedStates(DataSet) - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
 
createExtendedStates(DataSet) - Method in class uk.co.agena.minerva.model.extendedbn.LabelledEN
 
createExtendedStates(DataSet) - Method in class uk.co.agena.minerva.model.extendedbn.RankedEN
 
createFunction(String, ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Function
 
createFunctionListForModelNodes(List, List) - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
This method creates a full list of Functions (function array) whoses length is equal to the noOfParentsStateCombinations.
createIntegerIntervalState(int, int) - Static method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Creates a new integer interval state with the supplied lower and upper bounds.
createLabelledState(String, String) - Static method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Creates a new labelled state with the supplied name and description.
createLogStates(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Creates all the log states for this node.
createLogStates(double, double, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Creates the log states for this node between the argument doubles.
createModelFromNetFile(String) - Static method in class uk.co.agena.minerva.model.Model
Creates a new model adding the net file in the string
createModificationLogsInreleventBNs(List, ModelEvent, NameDescription) - Method in class uk.co.agena.minerva.model.Model
Locates the extended Bns that require a modifcation log, and creates them.
createMPLinksFromFile(String) - Method in class uk.co.agena.minerva.model.Model
Message passing links are created using a configuration file.
createNewExtendedNode(String, NameDescription) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Creates a new ExtendedNode of the supplied type, adds it to this ExtendedBN and returns it.
createNewExtendedState(int) - Method in class uk.co.agena.minerva.model.extendedbn.BooleanEN
 
createNewExtendedState(int) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
createNewExtendedState(int, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
createNewExtendedState(int) - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
 
createNewExtendedState(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Creates a new ExtendedState, all the way to the core.
createNewExtendedState(int) - Method in class uk.co.agena.minerva.model.extendedbn.LabelledEN
 
createQuestionnaireFromExtendedBN(ExtendedBN) - Static method in class uk.co.agena.minerva.model.Model
Creates a default Questionnaire from the supplied ExtendedBN.
cropFunctions() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
In the case where there are partitioned expressions, this method makes sure that the number of current and default functions is the same size as the number expected based up on the number of state combinations of the model parent nodes.
CURRENT_FUNCTION_STRING - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Used to indicate function data members that are "current".
CURRENT_TYPE - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Constant indicating that a function is the current one for an ExtendedNode.
currentNodeFunction - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
The current function specified across the entire NPT for this node.
currentParentModelNodeAltId - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Only used during loading and saving, so that current model node information can be stored.
currentPartitionedModelNodeFunctions - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
The current functions specified for each state combination of the node's parents.
currentPartitionedParentModelNodeAltIds - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Only used during loading and saving, so that current model node information can be stored.
currentPartitionedParentModelNodes - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
The current model (parent) nodes for the node functions.

D

DatabaseQuery - Class in uk.co.agena.minerva.model.querymodel
Holds the query string needed to perform a database query.
DatabaseQuery(DataSource, String, String, String) - Constructor for class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
DataPoint - Class in uk.co.agena.minerva.util.model
A DataPoint represents a single numerical value.
DataPoint() - Constructor for class uk.co.agena.minerva.util.model.DataPoint
Default constructor.
DataPoint(String, double, int) - Constructor for class uk.co.agena.minerva.util.model.DataPoint
Creates a DataPoint with the specified label, connected object ID (e.g.
DataPoint(String) - Constructor for class uk.co.agena.minerva.util.model.DataPoint
 
DataPoint(double) - Constructor for class uk.co.agena.minerva.util.model.DataPoint
 
DataSet - Class in uk.co.agena.minerva.util.model
A DataSet contains a set of DataPoints (i.e.
DataSet() - Constructor for class uk.co.agena.minerva.util.model.DataSet
Default constructor.
DataSet(NameDescription, int) - Constructor for class uk.co.agena.minerva.util.model.DataSet
Creates a DataSet with the specified name and connected object ID.
DataSet(NameDescription, int, List) - Constructor for class uk.co.agena.minerva.util.model.DataSet
Creates a DataSet with the specified name, connected object ID and DataPoints.
DataSetGrouping - Class in uk.co.agena.minerva.util.model
The DataSetGrouping class encapsulates a set of DataSet objects.
DataSetGrouping() - Constructor for class uk.co.agena.minerva.util.model.DataSetGrouping
Default constructor.
DataSetGrouping(NameDescription, int) - Constructor for class uk.co.agena.minerva.util.model.DataSetGrouping
Constructs a DataSetGrouping with the specified name and connected object ID.
DataSource - Class in uk.co.agena.minerva.model.querymodel
Data packet for Data Sources and their DatabaseQuery objects.
DataSource(ClassQueryModel, String, String, String, String, String) - Constructor for class uk.co.agena.minerva.model.querymodel.DataSource
 
DD_PROPAGATION - Static variable in class uk.co.agena.minerva.model.Propagation
 
DDEntropyErrorHeap - Class in uk.co.agena.minerva.model
This is an entropy object used to sort the entropy values according to their position.
ddPropagate(ExtendedBN, Scenario) - Method in class uk.co.agena.minerva.model.DynDiscPropagation
 
ddRelativeSumWidthEntropyErrors - Variable in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
This is the relative sum entropy errors for this node.
decreasePriorityLevel() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Decrements the current priority level by one (unless the priority level is already PRIORITY_VERY_LOW i.e.
DEFAULT_CERTAINTY - Static variable in class uk.co.agena.minerva.model.scenario.Observation
The value representing certainty an ExtendedState that has been observed with certainty.
DEFAULT_FUNCTION_STRING - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Used to indicate function data members that are "default".
DEFAULT_TYPE - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Constant indicating that a function is a default one.
defaultNodeFunction - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
The original function specified across the entire NPT for this node.
defaultParentModelNodeAltId - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Only used during loading and saving, so that default model node information can be stored.
defaultPartitionedModelNodeFunctions - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
The current functions specified for each state combination of the node's parents.
defaultPartitionedParentModelNodeAltIds - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Only used during loading and saving, so that default model node information can be stored.
defaultPartitionedParentModelNodes - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
The original model (parent) nodes for the node functions.
defaultStateNames - Static variable in class uk.co.agena.minerva.model.extendedbn.BooleanEN
 
defaultStateNames - Static variable in class uk.co.agena.minerva.model.extendedbn.ContinuousIntervalEN
 
defaultStateNames - Static variable in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
 
defaultStateNames - Static variable in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
 
defaultStateNames - Static variable in class uk.co.agena.minerva.model.extendedbn.LabelledEN
 
defaultStateNames - Static variable in class uk.co.agena.minerva.model.extendedbn.RankedEN
 
deleteExtendedBN(ExtendedBN) - Method in class uk.co.agena.minerva.model.Model
Deletes the supplied BN from the model.
deleteExtendedBNs(List) - Method in class uk.co.agena.minerva.model.Model
Removes the BNs in the supplied list from the model.
deleteExtendedNode(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Deletes the supplied ExtendedNode from this BN.
deleteScenario(Scenario) - Method in class uk.co.agena.minerva.model.Model
Deletes the supplied Scenario from the model.
deleteScenarios(List) - Method in class uk.co.agena.minerva.model.Model
Removes the Scenarios in the supplied list from the model.
DELTA - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This is the delta value we use when comparing equality between probabilities.
DELTA - Static variable in class uk.co.agena.minerva.util.nptgenerator.Arithmetic
 
destroy() - Method in class uk.co.agena.minerva.model.DynDiscPropagation
Removes DDP as a Listener from the Model and does any other necessary cleaning up.
destroy() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Removes itself as a listener from all of its ExtendedNodes.
destroy() - Method in class uk.co.agena.minerva.model.MarginalDataItemList
Cleans up objects.
destroy() - Method in class uk.co.agena.minerva.model.MarginalDataStore
 
destroy() - Method in class uk.co.agena.minerva.model.Model
Removes this Model as a listener from all Scenarios, Questionnaires and ExtendedBNs.
destroy() - Method in class uk.co.agena.minerva.model.Propagation
 
DISCRETE_REAL_E_N - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Constant corresponding to the DiscreteRealEN type.
DiscreteRealEN - Class in uk.co.agena.minerva.model.extendedbn
A DiscreteRealEN is a node whose states represent real numbers that are in no particular order e.g.
DiscreteRealEN() - Constructor for class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
Default constructor.
DiscreteRealEN(NameDescription, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
Constructs a DiscreteRealEN with the specified name and connected Core BN.
DiscreteRealEN(NameDescription, String, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
Constructs a DiscreteRealEN with the specified name, connected node ID and connected BN.
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Arithmetic
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Beta
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Binomial
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.ChiSquared
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Comparative
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Exponential
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.ExtremeValue
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Function
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Gamma
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Geometric
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Hypergeometric
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Logistic
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.LogNormal
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.NegativeBinomial
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Normal
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Poisson
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Student
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.TNormal
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Triangle
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Uniform
 
displayName - Static variable in class uk.co.agena.minerva.util.nptgenerator.Weibull
 
doDataPointsHaveIntervalLabels() - Method in class uk.co.agena.minerva.util.model.DataSet
This checks the first DataPoint to see if its label contains an interval.
doesBasicChecksPass() - Method in class uk.co.agena.minerva.model.DynDiscPropagation
This method should run some basic check that need to pass before the DD propagation can continue.
doesBasicChecksPass() - Method in class uk.co.agena.minerva.model.Propagation
This method should run some basic check that need to pass before the propagation can continue.
doInserts(Model, QueryObjectNode) - Method in class uk.co.agena.minerva.model.querymodel.StructureElement
 
dynamicallyDiscretisable - Variable in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
This indicates whether the node is dynamically discretisable.
DynDiscPropagation - Class in uk.co.agena.minerva.model
 
DynDiscPropagation(Model) - Constructor for class uk.co.agena.minerva.model.DynDiscPropagation
 

E

EDITABLE_NODE_FUNCTION - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
If the ExtendedNode's functionMode has this value, it will have null values for parentState function objects.
EDITABLE_NPT - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
If the ExtendedNode's functionMode has this value, it will have null values for all function objects.
EDITABLE_PARENT_STATE_FUNCTIONS - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
If the ExtendedNode's functionMode has this value, it will have null values for node function objects.
enterDistributionOfEvidence(DataSet, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Enters evidence on this ExtendedNode in the form of a distribution of likelihoods across all ExtendedStates.
enterDistributionOfEvidence(DataSet, boolean, DataSet) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Enters evidence on this ExtendedNode in the form of a distribution of likelihoods across all ExtendedStates.
enterHardEvidence(int, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Enters evidence on this node to indicate that the ExtendedState specified has been selected.
enterHardEvidence(int, boolean, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Enters evidence on this node to indicate that the ExtendedState specified has been selected.
entropyConvergenceThreshold - Variable in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
evaluateExpressionAsDouble(DataSet, int) - Method in class uk.co.agena.minerva.util.nptgenerator.Function
Evaluates the expression at the supplied index.
evaluateExpressionAsObject(DataSet, int) - Method in class uk.co.agena.minerva.util.nptgenerator.Function
Evaluates the expression at the supplied index.
EVIDENCE_TOLERANCE_PERCENTAGE_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
execute() - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
Executes the query string and stores the results in "result".
execute() - Method in class uk.co.agena.minerva.model.querymodel.UpdateInstance
Executes the query string and stores the results in "result".
executeOwnQuery(String) - Method in class uk.co.agena.minerva.model.querymodel.DataSource
Used by the AgenaRisk datasource to execute queries internally without reference to a database.
executeQuery(String, int) - Method in class uk.co.agena.minerva.model.querymodel.DataSource
Used to perform dynamic queries for data browsing.
executeUpdate(String) - Method in class uk.co.agena.minerva.model.querymodel.DataSource
Used to perform updates.
Exponential - Class in uk.co.agena.minerva.util.nptgenerator
 
Exponential(List, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.Exponential
calculates the Exponential over a defined set of ranges given a mean and a variance.
Exponential(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Exponential
 
EXPRESSION_VARIABLE_CHANGED - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
ExpressionParser - Class in uk.co.agena.minerva.util.nptgenerator
This is a Minerva-specific parser that encapsulates various data and behaviour common throughout the NPT generation process.
ExpressionParser() - Constructor for class uk.co.agena.minerva.util.nptgenerator.ExpressionParser
Creates a basic Expression parser.
EXTENDED_NODE_ADDED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
EXTENDED_NODE_REPLACED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
EXTENDED_NODES_DELETED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
EXTENDED_STATE_ADDED - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
EXTENDED_STATE_REMOVED - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
ExtendedBN - Class in uk.co.agena.minerva.model.extendedbn
An ExtendedBN is an encapsulation of a Bayesian Network.
ExtendedBN() - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Default constructor.
EXTENDEDBN_NAME_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
extendedBNAboutToBePropagated(ExtendedBNEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedBNListener
Invoked whenever an ExtendedBN has received a request to propagate itself
extendedBNAboutToBePropagated(ExtendedNode, String[]) - Method in class uk.co.agena.minerva.model.MarginalDataItem
Event invoked by the connected extended Bn if it is about to propagate.
extendedBNAboutToBePropagated(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
Event invoked by the connected extended Bn if it is about to propagate.
extendedBNAboutToBePropagated(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.Model
Not currently implemented
extendedBNAllEvidenceRetracted(ExtendedBNEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedBNListener
Invoked whenever all evidence has been removed from an ExtendedBN.
extendedBNAllEvidenceRetracted(ExtendedNode, String[]) - Method in class uk.co.agena.minerva.model.MarginalDataItem
Invoked by any extended BN's that this class is listening to, event prompts the listener that the extended BN has had all its eveidence retracted
extendedBNAllEvidenceRetracted(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
Invoked by any extended BN's that this class is listening to, event prompts the listener that the extended BN has had all its eveidence retracted
extendedBNAllEvidenceRetracted(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.Model
Not currently implemented.
extendedBNConnBNNotFound(ExtendedBNEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedBNListener
Invoked whenever an ExtendedBN's connected CoreBN is needed but is not initialised.
extendedBNConnBNNotFound(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
Currently empty.
extendedBNConnBNNotFound(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.Model
Loads up the relevant CoreBN when it is required and when its ExtendedBN has informed listeners that it is not present.
ExtendedBNEvent - Class in uk.co.agena.minerva.model.extendedbn
ExtendedBNEvent is used to notify interested parties that an ExtendedBN has changed in some way.
ExtendedBNEvent(ExtendedBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedBNEvent
Constructs a new ExtendedBNEvent.
ExtendedBNEvent(ExtendedBN, String) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedBNEvent
Constructs a new ExtendedBNEvent.
ExtendedBNEvent(ExtendedBN, int) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedBNEvent
Constructs a new ExtendedBNEvent.
ExtendedBNEvent(ExtendedBN, boolean) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedBNEvent
Constructs a new ExtendedBNEvent.
ExtendedBNEvent(ExtendedBN, String, String[]) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedBNEvent
Constructs a new ExtendedBNEvent.
ExtendedBNException - Exception in uk.co.agena.minerva.model.extendedbn
Thrown whenever there is a general problem with ExtendedBNs.
ExtendedBNException() - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedBNException
Constructs an empty ExtendedBNException.
ExtendedBNException(String) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedBNException
Constructs an ExtendedBNException with the specified message.
ExtendedBNException(Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedBNException
Constructs an ExtendedBNException with the specified cause.
ExtendedBNException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedBNException
Constructs an ExtendedBNException with the specified cause and message.
extendedBNIDChanged(ExtendedBNEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedBNListener
Invoked whenever the ID for the ExtendedBN is changed.
extendedBNIDChanged(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
extendedBNIDChanged(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.Model
Changes the connected IDs on Questions, Observations and MessagePassingLinks objects in response to the ID on an ExtendedBN changing.
extendedBNInconsistentEvidencePropagated(ExtendedBNEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedBNListener
Invoked whenever inconsistent evidence is propagated.
extendedBNInconsistentEvidencePropagated() - Method in class uk.co.agena.minerva.model.MarginalDataItem
Event fired by the extended BN if the last propagation caused inconsistant evidence to be propagated.
extendedBNInconsistentEvidencePropagated(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
Event fired by the extended BN if the last propagation caused inconsistant evidence to be propagated.
extendedBNInconsistentEvidencePropagated(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.Model
Responds to inconsistent evidence being propagated on one of this Model's ExtendedBNs.
ExtendedBNList - Class in uk.co.agena.minerva.model.extendedbn
This class encapsulates a List of ExtendedBNs and provides extra utility methods for accessing the ExtendedBNs in the underlying List.
ExtendedBNList() - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Creates an empty ExtendedBNList.
ExtendedBNList(List) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Creates an ExtendedBNList containing the supplied List of ExtendedBNs.
ExtendedBNListener - Interface in uk.co.agena.minerva.model.extendedbn
Defines a listener for ExtendedBNEvents.
extendedBNNameDescriptionChanged(ExtendedBNEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedBNListener
Invoked whenever the name of an ExtendedBN has changed.
extendedBNNameDescriptionChanged(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
Currently empty.
extendedBNNameDescriptionChanged(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.Model
Tells all registered listeners that this Model has changed (in response to the name of one of its ExtendedBNs having changed).
ExtendedBNNotCompiledException - Exception in uk.co.agena.minerva.model.extendedbn
Thrown whenever an operation is performed on an ExtendedBN before it is compiled and when compilation is necessary.
ExtendedBNNotCompiledException() - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedBNNotCompiledException
Constructs an empty ExtendedBNNotCompiledException.
ExtendedBNNotCompiledException(String) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedBNNotCompiledException
Constructs an ExtendedBNNotCompiledException with the specified message.
ExtendedBNNotCompiledException(Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedBNNotCompiledException
Constructs an ExtendedBNNotCompiledException with the specified cause.
ExtendedBNNotCompiledException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedBNNotCompiledException
Constructs an ExtendedBNNotCompiledException with the specified cause and message.
ExtendedBNNotFoundException - Exception in uk.co.agena.minerva.model.extendedbn
Thrown whenever an ExtendedBN is not found.
ExtendedBNNotFoundException() - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedBNNotFoundException
Constructs an empty ExtendedBNNotFoundException.
ExtendedBNNotFoundException(String) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedBNNotFoundException
Constructs an ExtendedBNNotFoundException with the specified message.
ExtendedBNNotFoundException(Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedBNNotFoundException
Constructs an ExtendedBNNotFoundException with the specified cause.
ExtendedBNNotFoundException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedBNNotFoundException
Constructs an ExtendedBNNotFoundException with the specified cause and message.
extendedBNPropagated(ExtendedBNEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedBNListener
Invoked whenever an ExtendedBN has been propagated.
extendedBNPropagated(ExtendedNode, String[]) - Method in class uk.co.agena.minerva.model.MarginalDataItem
Invoked by any extended BN's that this class is listening to, event prompts the listener that the extended BN has been propagated
extendedBNPropagated(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
Invoked by any extended BN's that this class is listening to, event prompts the listener that the extended BN has been propagated
extendedBNPropagated(ExtendedBNEvent) - Method in class uk.co.agena.minerva.model.Model
Not currently implemented.
EXTENDEDBNS_ADDED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
EXTENDEDBNS_REMOVED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
EXTENDEDBNS_REPLACED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
ExtendedNode - Class in uk.co.agena.minerva.model.extendedbn
An ExtendedNode corresponds to a node in an underlying BN.
ExtendedNode() - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Default constructor.
ExtendedNode(NameDescription, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Constructs an ExtendedNode with the specified name and connected BN.
ExtendedNode(NameDescription, String, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Constructs an ExtendedNode with the specified name, connected node ID and connected BN.
EXTENDEDNODE_ATTRIBUTE_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
EXTENDEDNODE_CLONED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
EXTENDEDNODE_REMOVED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
extendedNodeAboutToBeCut(ExtendedBNEvent, ExtendedBN, int, int, String) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedBNListener
This event is fired when an ExtendedNode has been pasted to the destination ExtendedBN and is about to be cut from the specified source ExtendedBN.
extendedNodeAboutToBeCut(ExtendedBNEvent, ExtendedBN, int, int, String) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
This event is fired when an ExtendedNode has been pasted to the destination ExtendedBN and is about to be cut from the specified source ExtendedBN.
extendedNodeAboutToBeCut(ExtendedBNEvent, ExtendedBN, int, int, String) - Method in class uk.co.agena.minerva.model.Model
This event is fired when an ExtendedNode has been pasted to the destination ExtendedBN and is about to be cut from the specified source ExtendedBN.
ExtendedNodeAdapter - Class in uk.co.agena.minerva.model.extendedbn
Defines an adapter for ExtendedNodes.
ExtendedNodeAdapter() - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
extendedNodeAdded(ExtendedBNEvent, ExtendedNode) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedBNListener
This event is fired when ever a new node has been added to the extendedBN
extendedNodeAdded(ExtendedBNEvent, ExtendedNode) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
This event is fired when ever a new node has been added to the extendedBN
extendedNodeAdded(ExtendedBNEvent, ExtendedNode) - Method in class uk.co.agena.minerva.model.Model
This event is fired when ever a new node has been added to the extendedBN.
extendedNodeAttributeChanged(ExtendedNodeEvent, int) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousIntervalEN
 
extendedNodeAttributeChanged(ExtendedNodeEvent, int) - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
 
extendedNodeAttributeChanged(ExtendedNodeEvent, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Event caught by the extend BN from a node it was listening to.
extendedNodeAttributeChanged(ExtendedNodeEvent, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Called when selected attributes of the node are changed.
extendedNodeAttributeChanged(ExtendedNodeEvent, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
extendedNodeAttributeChanged(ExtendedNodeEvent, int) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedNodeListener
Called when selected attributes of the node are changed.
extendedNodeAttributeChanged(ExtendedNodeEvent, int) - Method in class uk.co.agena.minerva.model.extendedbn.LabelledEN
 
extendedNodeConnBNNotFound(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Called by an ExtendedNode when it cannot find the connected CoreBN in memory.
extendedNodeConnBNNotFound(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This method is not implemented - it is an empty stub to ensure compliance with the ExtendedNodeListener interface.
extendedNodeConnBNNotFound(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
extendedNodeConnBNNotFound(ExtendedNodeEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedNodeListener
Invoked whenever the a CoreBN is needed but is not initialised.
extendedNodeConnNodeIdChanged(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
When the connNodeId of a node is changed then we need to ensure that all the children of this node are told that the name has changed to that they can change their functions (if they have any) to reflect this change.
extendedNodeConnNodeIdChanged(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
No action needed when the ConnNodeId of an ExtendedNode is changed.
extendedNodeConnNodeIdChanged(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
extendedNodeConnNodeIdChanged(ExtendedNodeEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedNodeListener
Invoked when the ConnNodeId of an ExtendedNode is changed.
ExtendedNodeCreationException - Exception in uk.co.agena.minerva.model.extendedbn
Thrown when there is a problem creating an ExtendedNode.
ExtendedNodeCreationException() - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeCreationException
Constructs an empty ExtendedNodeCreationException.
ExtendedNodeCreationException(String) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeCreationException
Constructs an ExtendedNodeCreationException with the specified message.
ExtendedNodeCreationException(Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeCreationException
Constructs a ExtendedNodeCreationException with the specified cause.
ExtendedNodeCreationException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeCreationException
Constructs a ExtendedNodeCreationException with the specified cause and message.
ExtendedNodeEvent - Class in uk.co.agena.minerva.model.extendedbn
ExtendedNodeEvent is used to notify interested parties that an ExtendedNode has changed in some way.
ExtendedNodeEvent(ExtendedNode) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
Constructs a new ExtendedNodeEvent.
ExtendedNodeEvent(ExtendedNode, int, List) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
Constructs a new ExtendedNodeEvent for the Node Changed specific event
ExtendedNodeEvent(ExtendedNode, DataSet) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
Constructs a new ExtendedNodeEvent.
ExtendedNodeEvent(ExtendedNode, String) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
Constructs a new ExtendedNodeEvent.
ExtendedNodeEvent(ExtendedNode, ExtendedState) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
An event that incapsulates an extendedState which is added/removed.
ExtendedNodeEvent(ExtendedNode, Variable) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
An event that incapsulates a Variable which is added/removed.
ExtendedNodeEvent(ExtendedNode, String, String) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
extendedNodeEventFired(ExtendedBNEvent, ExtendedNodeEvent, String) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedBNListener
Invoked whenever the extended BN recieves a BN Node event, this event throws the event up to any listeners on the extended BN.
extendedNodeEventFired(ExtendedBNEvent, ExtendedNodeEvent, String) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
Event received from the extended BN Invoked whenever the extended BN recieves a BN Node event, this event throws the event up to any listeners on the extended BN.
extendedNodeEventFired(ExtendedBNEvent, ExtendedNodeEvent, String) - Method in class uk.co.agena.minerva.model.Model
Event received from the extended BN Invoked whenever the extended BN recieves a BN Node event, this event throws the event up to any listeners on the extended BN.
ExtendedNodeEventGenerator - Class in uk.co.agena.minerva.model.extendedbn
This class encapsulates the generation and broadcasting of ExtendedNodeEvents to interested ExtendedNodeListeners.
ExtendedNodeFunction - Class in uk.co.agena.minerva.model.extendedbn
This class encapsulates a function used to define (in full or in part) the NPT for an ExtendedNode.
ExtendedNodeFunction() - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Default constructor.
ExtendedNodeFunction(String, List) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Creates a new ExtendedNodeFunction with the supplied name and parameters.
ExtendedNodeFunction(String, List, int) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Constructs an ExtendedNodeFunction with the supplied name, parameters and type.
ExtendedNodeFunctionException - Exception in uk.co.agena.minerva.model.extendedbn
Thrown when there is some kind of problem when handling ExtendedNodeFunctions.
ExtendedNodeFunctionException() - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunctionException
Constructs an empty ExtendedNodeFunctionException.
ExtendedNodeFunctionException(String) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunctionException
Constructs an ExtendedNodeFunctionException with the specified message.
ExtendedNodeFunctionException(Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunctionException
Constructs an ExtendedNodeFunctionException with the specified cause.
ExtendedNodeFunctionException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunctionException
Constructs an ExtendedNodeFunctionException with the specified cause and message.
extendedNodeInconsistentEvidenceEntered(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Called when an ExtendedNode has had inconsistent evidence entered on it.
extendedNodeInconsistentEvidenceEntered(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This method is not implemented - it is an empty stub to ensure compliance with the ExtendedNodeListener interface.
extendedNodeInconsistentEvidenceEntered(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
extendedNodeInconsistentEvidenceEntered(ExtendedNodeEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedNodeListener
Invoked whenever an inconsistent evidence exception is thrown when entering evidence.
ExtendedNodeListener - Interface in uk.co.agena.minerva.model.extendedbn
Defines a listener for ExtendedNodes.
extendedNodeMarginalsChanged(ExtendedNodeEvent, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Not implemented - the ExtendedBN is not interested when this happens.
extendedNodeMarginalsChanged(ExtendedNodeEvent, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Called whenever the marginals for a particular node have changed.
extendedNodeMarginalsChanged(ExtendedNodeEvent, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
extendedNodeMarginalsChanged(ExtendedNodeEvent, boolean) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedNodeListener
Invoked whenever the marginals of an ExtendedNode has changed.
ExtendedNodeMethodNotSupportedException - Exception in uk.co.agena.minerva.model.extendedbn
Thrown when an attempt is made to call an implementation of a method on a subclass of ExtendedNode when there is no implementation.
ExtendedNodeMethodNotSupportedException() - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeMethodNotSupportedException
Constructs an empty ExtendedNodeMethodNotSupportedException.
ExtendedNodeMethodNotSupportedException(String) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeMethodNotSupportedException
Constructs an ExtendedNodeMethodNotSupportedException with the specified message.
ExtendedNodeMethodNotSupportedException(Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeMethodNotSupportedException
Constructs an ExtendedNodeMethodNotSupportedException with the specified cause.
ExtendedNodeMethodNotSupportedException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeMethodNotSupportedException
Constructs an ExtendedNodeMethodNotSupportedException with the specified cause and message.
extendedNodeNameDescriptionChanged(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Not implemented - the ExtendedBN is not interested when this happens.
extendedNodeNameDescriptionChanged(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This method is not implemented - it is an empty stub to ensure compliance with the ExtendedNodeListener interface.
ExtendedNodeNotFoundException - Exception in uk.co.agena.minerva.model.extendedbn
Thrown when an attempt is made to access an ExtendedNode that does not exist.
ExtendedNodeNotFoundException() - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeNotFoundException
Constructs an empty ExtendedNodeNotFoundException.
ExtendedNodeNotFoundException(String) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeNotFoundException
Constructs an ExtendedNodeNotFoundException with the specified message.
ExtendedNodeNotFoundException(Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeNotFoundException
Constructs an ExtendedNodeNotFoundException with the specified cause.
ExtendedNodeNotFoundException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedNodeNotFoundException
Constructs an ExtendedNodeNotFoundException with the specified cause and message.
extendedNodePasted(ExtendedBNEvent, ExtendedBN, ExtendedNode, ExtendedNode) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedBNListener
This event is fired when an extended node is pasted into the extended BN
extendedNodePasted(ExtendedBNEvent, ExtendedBN, ExtendedNode, ExtendedNode) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
extendedNodePasted(ExtendedBNEvent, ExtendedBN, ExtendedNode, ExtendedNode) - Method in class uk.co.agena.minerva.model.Model
Extended Node pasted event, fired by the extended BN
extendedNodeRemoved(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Informs all listeners (via the event generator) that this ExtendedBN has had a NodeRemoved.
extendedNodeRemoved(ExtendedBNEvent, ExtendedNode) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedBNListener
This event is fired when an extended node is removed from the extended BN
extendedNodeRemoved(ExtendedBNEvent, ExtendedNode) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
extendedNodeRemoved(ExtendedBNEvent, ExtendedNode) - Method in class uk.co.agena.minerva.model.Model
Extended Node removed event, fired by the extended BN
extendedNodeReplaced(ExtendedBNEvent, ExtendedNode, ExtendedNode, ExtendedBN) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedBNListener
This event is fired whenever a node is replaced with another one.
extendedNodeReplaced(ExtendedBNEvent, ExtendedNode, ExtendedNode, ExtendedBN) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
extendedNodeReplaced(ExtendedBNEvent, ExtendedNode, ExtendedNode, ExtendedBN) - Method in class uk.co.agena.minerva.model.Model
 
extendedNodeStateNameChanged(ExtendedNodeEvent, ExtendedState) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
extendedNodeStateNameChanged(ExtendedNodeEvent, ExtendedState) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Dont need to do anything if one of its states have changed their names.
extendedNodeStateNameChanged(ExtendedNodeEvent, ExtendedState) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
extendedNodeStateNameChanged(ExtendedNodeEvent, ExtendedState) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedNodeListener
Invoked when an ExtendedState name is changed.
extendedNodeStatesReplaced(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
extendedNodeStatesReplaced(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
extendedNodeStatesReplaced(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
extendedNodeStatesReplaced(ExtendedNodeEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedNodeListener
Called when the node's states are replaced.
extendedNodeVariableAdded(ExtendedNodeEvent, Variable) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Invoked when a Variable is added to the ExtendedNodes VariableList.
extendedNodeVariableAdded(ExtendedNodeEvent, Variable) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Invoked when a Variable is added to the ExtendedNodes VariableList.
extendedNodeVariableAdded(ExtendedNodeEvent, Variable) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
extendedNodeVariableAdded(ExtendedNodeEvent, Variable) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedNodeListener
Invoked when a Variable is added to the ExtendedNodes VariableList.
extendedNodeVariableRemoved(ExtendedNodeEvent, Variable) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Invoked when a Variable is removed from the ExtendedNodes VariableList.
extendedNodeVariableRemoved(ExtendedNodeEvent, Variable) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Invoked when a Variable is removed from the ExtendedNodes VariableList.
extendedNodeVariableRemoved(ExtendedNodeEvent, Variable) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
extendedNodeVariableRemoved(ExtendedNodeEvent, Variable) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedNodeListener
Invoked when a Variable is removed from the ExtendedNodes VariableList.
extendedNodeVariableRemoved(ExtendedNodeEvent, Variable) - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
Invoked when a Variable is removed from the ExtendedNodes VariableList.
extendedNodeVisibleAttributeChanged(ExtendedNodeEvent, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
ExtendedNode visible attribute has been changed.
extendedNodeVisibleAttributeChanged(ExtendedNodeEvent, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
extendedNodeVisibleAttributeChanged(ExtendedNodeEvent, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
extendedNodeVisibleAttributeChanged(ExtendedNodeEvent, boolean) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedNodeListener
Invoked when an ExtendedNode visible attribute is changed.
ExtendedState - Class in uk.co.agena.minerva.model.extendedbn
An ExtendedState corresponds to a state on a node in an underlying BN.
ExtendedState() - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedState
Default constructor.
ExtendedState(int, NameDescription, double, Range, boolean) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedState
Creates an ExtendedState with the supplied connected state index, name, numerical value, Range and visibility.
ExtendedState(int, NameDescription, boolean) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedState
Creates an ExtendedState with the supplied connected state index, name, and visibility.
extendedStateAdded(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
New ExtendedState created and added to this node and added all the way to the core.
extendedStateAdded(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
New ExtendedState created and added to this node and added all the way to the core.
extendedStateAdded(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
extendedStateAdded(ExtendedNodeEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedNodeListener
Invoked when an ExtendedState is added to this ExtendedNode
ExtendedStateEvent - Class in uk.co.agena.minerva.model.extendedbn
ExtendedStateEvent is used to notify interested parties that an ExtendedState has changed in some way.
ExtendedStateEvent(ExtendedState) - Constructor for class uk.co.agena.minerva.model.extendedbn.ExtendedStateEvent
Constructs a new ExtendedStateEvent.
ExtendedStateException - Exception in uk.co.agena.minerva.model.extendedbn
Thrown when there is a problem with creating or adding an ExtendedState.
ExtendedStateException() - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedStateException
Constructs an empty ExtendedStateException.
ExtendedStateException(String) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedStateException
Constructs an ExtendedStateException with the specified message.
ExtendedStateException(Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedStateException
Constructs a ExtendedStateException with the specified cause.
ExtendedStateException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedStateException
Constructs a ExtendedStateException with the specified cause and message.
ExtendedStateListener - Interface in uk.co.agena.minerva.model.extendedbn
Defines a listener for s.
extendedStateNameDescriptionChanged(ExtendedStateEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Listens to the extendedstate to see if they fire an event that their name has changed.
extendedStateNameDescriptionChanged(ExtendedStateEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedStateListener
Invoked whenever the name of an ExtendedState has changed.
ExtendedStateNotFoundException - Exception in uk.co.agena.minerva.model.extendedbn
Thrown when an attempt is made to access an ExtendedState that does not exist.
ExtendedStateNotFoundException() - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedStateNotFoundException
Constructs an empty ExtendedStateNotFoundException.
ExtendedStateNotFoundException(String) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedStateNotFoundException
Constructs an ExtendedStateNotFoundException with the specified message.
ExtendedStateNotFoundException(Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedStateNotFoundException
Constructs an ExtendedStateNotFoundException with the specified cause.
ExtendedStateNotFoundException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedStateNotFoundException
Constructs an ExtendedStateNotFoundException with the specified cause and message.
ExtendedStateNumberingException - Exception in uk.co.agena.minerva.model.extendedbn
Thrown whenever there is a state-numbering problem in an ExtendedNode.
ExtendedStateNumberingException() - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedStateNumberingException
Constructs an empty ExtendedStateNumberingException.
ExtendedStateNumberingException(String) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedStateNumberingException
Constructs an ExtendedStateNumberingException with the specified message.
ExtendedStateNumberingException(Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedStateNumberingException
Constructs an ExtendedStateNumberingException with the specified cause.
ExtendedStateNumberingException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.ExtendedStateNumberingException
Constructs an ExtendedStateNumberingException with the specified cause and message.
extendedStateRangesForValue(double, int, boolean, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
This method should extended the state ranges of this node to allow the value supplied in the argument to be included.
extendedStateRemoved(ExtendedNodeEvent, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
ExtendedNode removed from this node and all the way to the core.
extendedStateRemoved(ExtendedNodeEvent, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
ExtendedNode removed from this node and all the way to the core.
extendedStateRemoved(ExtendedNodeEvent, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
extendedStateRemoved(ExtendedNodeEvent, int) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedNodeListener
Invoked when an ExtendedState is removed from this ExtendedNode
extendedStates - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
The ExtendedStates contained in the ExtendedNode.
ExtremeValue - Class in uk.co.agena.minerva.util.nptgenerator
 
ExtremeValue(List, int) - Static method in class uk.co.agena.minerva.util.nptgenerator.ExtremeValue
calculates the distribution over a defined set of ranges
ExtremeValue(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.ExtremeValue
 

F

FamilyMember - Interface in uk.co.agena.minerva.util.model
This interface is implemented by any object that is a member of a family tree.
FamilyMemberException - Exception in uk.co.agena.minerva.util.model
Throw when the requested FamilyMember is not found.
FamilyMemberException() - Constructor for exception uk.co.agena.minerva.util.model.FamilyMemberException
Constructs an empty FamilyMemberException.
FamilyMemberException(String) - Constructor for exception uk.co.agena.minerva.util.model.FamilyMemberException
Constructs a FamilyMemberException with the specified message.
FamilyMemberException(Throwable) - Constructor for exception uk.co.agena.minerva.util.model.FamilyMemberException
Constructs a FamilyMemberException with the specified cause.
FamilyMemberException(String, Throwable) - Constructor for exception uk.co.agena.minerva.util.model.FamilyMemberException
Constructs a FamilyMemberException with the specified cause and message.
FamilyProcessor - Class in uk.co.agena.minerva.util.model
This abstract class contains various static utility methods for handling trees of FamilyMember objects.
FamilyProcessor() - Constructor for class uk.co.agena.minerva.util.model.FamilyProcessor
 
FIELD_SEPARATOR - Static variable in interface uk.co.agena.minerva.util.model.Writable
Used for separating fields when objects are written out to Strings.
fillArraysUsingAbsolutes(double[], double[]) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousIntervalEN
 
fillArraysUsingAbsolutes(double[], double[]) - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
Fills the two specified arrays with numerical values and their associated probabilities using the node marginals.
fillArraysUsingAbsolutes(double[], double[]) - Method in class uk.co.agena.minerva.model.extendedbn.NumericalEN
Fills the two specified arrays with numerical values and their associated probabilities using the node marginals.
fillArraysUsingIntervals(Range[], double[]) - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
Fills the two specified arrays with Ranges and their associated probabilities using the node marginals.
fillArraysUsingIntervals(Range[], double[]) - Method in class uk.co.agena.minerva.model.extendedbn.NumericalEN
Fills the two specified arrays with Ranges and their associated probabilities using the node marginals.
findIdentifiables(String, String) - Method in class uk.co.agena.minerva.model.Model
Searches for all Identifiable objects of the supplied class using the supplied search term.
findMasterQuery(String) - Method in class uk.co.agena.minerva.model.querymodel.ClassQueryModel
Finds a named query instance in the master query list.
findMasterUpdate(String) - Method in class uk.co.agena.minerva.model.querymodel.ClassQueryModel
 
fireExtendedBNAboutToBePropagated(ExtendedBN) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Informs all listeners (via the event generator) that this ExtendedBN is about to be propagated.
fireExtendedBNConnBNNotFound(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Informs all listeners (via the event generator) that the CoreBN for this ExtendedBN is is not in memory.
fireMarginalsChangedEvent() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Called by an ExtendedBN when either propagation or retraction is called, because this node's marginals may have changed.
fireModelChangedEvent(Model, int, List) - Method in class uk.co.agena.minerva.model.Model
Fires a model changed event with the specified parameters
firePropagationIncremented(Propagation, int) - Method in class uk.co.agena.minerva.model.Propagation.PropagationEventGenerator
Fires a Propagation event to indicate that a cycle of a Propagation has finished.
fireSimulationFinished(Propagation, boolean, List) - Method in class uk.co.agena.minerva.model.Propagation.PropagationEventGenerator
Fires a Propagation event to indicate that a Propagation has finished.
fireSimulationStarted(Propagation) - Method in class uk.co.agena.minerva.model.Propagation.PropagationEventGenerator
Fires a Propagation event to indicate that a Propagation is about to start.
forceCoreNPTsSizeUpdates(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
This should be called if the states on nodes have been update, but the core NPT sizes havent been updated.
Function - Class in uk.co.agena.minerva.util.nptgenerator
 
Function() - Constructor for class uk.co.agena.minerva.util.nptgenerator.Function
 
Function(ExtendedNode, List, String[], String) - Constructor for class uk.co.agena.minerva.util.nptgenerator.Function
 
functionMode - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Indicates whether this node has any functions specified for it along with the basic NPT.
functionParametersMap - Static variable in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
Map of functions along with their parameter names.

G

Gamma - Class in uk.co.agena.minerva.util.nptgenerator
 
Gamma(List, double, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.Gamma
calculates the Beta over a defined set of ranges given a mean and a variance.
Gamma(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Gamma
 
generateNPT(boolean, boolean, boolean, boolean) - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
This will actually create the NPT for the Node which has a Funtions Defined on it.
generateNPTForNodeWithoutSampling() - Method in class uk.co.agena.minerva.util.nptgenerator.Function
This is used to create a single column NPT for a node which is asked to generate an NPT but doesn't have any parents.
generateParentIds(List) - Static method in class uk.co.agena.minerva.util.model.FamilyProcessor
Assigns parent IDs to all children in a hierarchy.
generateParentIds(FamilyMember) - Static method in class uk.co.agena.minerva.util.model.FamilyProcessor
Takes the supplied FamilyMember (that exists as the root of a family subtree) and goes through recursively setting the parent ID attributes of children using the ID of the parent.
generateQuestionFromNode(ExtendedBN, ExtendedNode) - Static method in class uk.co.agena.minerva.model.Model
 
Geometric - Class in uk.co.agena.minerva.util.nptgenerator
 
Geometric(List, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.Geometric
calculates the distribution over a defined set of ranges
Geometric(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Geometric
 
getAbsoluteValue() - Method in class uk.co.agena.minerva.util.model.AbsoluteDataPoint
Returns the absolute "x" value.
getActOnMarginalsChangedEvent() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getAdjustedValue() - Method in class uk.co.agena.minerva.util.model.DataPoint
Returns a double value that is equal to the value encapsulated by the DataPoint.
getAdjustedValue() - Method in class uk.co.agena.minerva.util.model.IntervalDataPoint
This method will return the value adjusted for its probability mass.
getAllExtendedBNIds() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Returns an array of IDs for all the extenededBNs in this list.
getAllExtendedNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Returns a List of all ExtendedNodes in all stored ExtendedBNs.
getAllObservations() - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
Returns a List of all Observations in all stored Scenarios.
getAllVariableNames() - Method in class uk.co.agena.minerva.util.model.VariableList
Gets the String Names of all the Variables in this VariableList and adds them to a List which can be returned.
getAncestorExtendedBNs(ExtendedBN) - Method in class uk.co.agena.minerva.model.Model
This method will use the MessagePassingLinks to get all the Ancestors of the argument ExtendedBN This is done recursively using the getParentExtendedBNs method.
getAnswerable() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns whether the ExtendedNode is answerable.
getAsDoubles() - Method in class uk.co.agena.minerva.util.model.DataSet
Returns the DataSet's DataPoints as simple array of doubles.
getAttributeChanaged() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
Stores the integer value if the attribute changed event was triggered
getBnToEvidenceMapping() - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
getBooleanValue(String) - Method in class uk.co.agena.minerva.model.querymodel.XmlHelper
 
getCallSigns() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNEvent
Return the callSigns message.
getCallSignToUpdateOn() - Method in class uk.co.agena.minerva.model.MarginalDataItem
This attribute is matched against the call sign passed during a propagation event invoked by the connected extended BN.
getChangedMarginals() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
Returns the DataSet representing the changed marginals for the event.
getChildNodes(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns the child ExtendedNodes of the supplied ExtendedNode.
getChildQueries() - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
getChildren() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
getChildren() - Method in class uk.co.agena.minerva.model.Model
Returns the children of this Model.
getChildren() - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
getChildren() - Method in interface uk.co.agena.minerva.util.model.FamilyMember
Returns the children of this FamilyMember.
getChildrenExtendedBNIds(int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Returns all child ExtendedBN IDs that are connected to the supplied parent ExtendedBN ID in the links contained in this MessagePassingLinks object.
getChildrenExtendedBNs(ExtendedBN) - Method in class uk.co.agena.minerva.model.Model
This method uses the message passing links to return a list of the children ExtendedBNs of the argument BN.
getChildResult(int, int, int) - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
getClosestMedianStateIndex(int, DataSet) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
getColumnNames(String) - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
getColumnNames() - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
getColumnNumber() - Method in class uk.co.agena.minerva.model.querymodel.NodeQueryMapping
 
getCon() - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
getConcreteNodeName(Class) - Static method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Given the class of a node type, the user-friendly name of the node type is returned.
getConcreteNodeType(String) - Static method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Given the user-friendly name of a node type, the actual class of the node type is returned.
getConcreteNodeTypeNames() - Static method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the user-friendly names of all node types that are concrete i.e.
getConfidenceInterval() - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
getConnBN() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns the BN to which the ExtendedBN is connected.
getConnBn() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Gets the underlying BN to which this ExtendedNode is connected.
getConnCoreFileName() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns the name of the file in which the connected CoreBN is stored.
getConnections() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns a list of the connections that this BN has with other connectable objects (which) will be other exBNs
getConnections() - Method in interface uk.co.agena.minerva.util.model.Connectable
 
getConnectionType() - Method in class uk.co.agena.minerva.util.model.Connection
Defines the nature of the connection, which must take one of the constant values defined on this class
getConnExtendedBNId() - Method in class uk.co.agena.minerva.model.scenario.Observation
Returns the ID of the ExtendedBN to which the Observation is connected.
getConnExtendedNodeId() - Method in class uk.co.agena.minerva.model.scenario.Observation
Returns the ID of the ExtendedNode to which the Observation is connected.
getConnNodeId() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the ID of the underlying connected node.
getConnNodeIds(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
getConnObjectId() - Method in class uk.co.agena.minerva.util.model.DataPoint
Returns the connected object ID of the DataPoint.
getConnObjectId() - Method in class uk.co.agena.minerva.util.model.DataSet
Returns the connected object ID of the DataSet.
getConnObjectId() - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Returns the connected object ID of the DataSetGrouping.
getConnQuestionnaireId() - Method in class uk.co.agena.minerva.model.scenario.Observation
Returns the ID of the Questionnaire to which the Observation is connected.
getConnStateIndex() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Returns the index of the underlying state to which this ExtendedState is connected.
getConstantName() - Method in class uk.co.agena.minerva.model.querymodel.NodeQueryMapping
 
getCoreBNNodeEquivalents(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getCoreFilenamesToCoreBNs() - Method in class uk.co.agena.minerva.model.Model
 
getCurrentNodeFunction() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Gets the current node function for this ExtendedNode.
getCurrentParentModelNodeAltId() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getCurrentPartitionedModelNodeFunctions() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getCurrentPartitionedParentModelNodeAltIds() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getCurrentPartitionedParentModelNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getCurrentProgress() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
getCurrentProgress() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
 
getCurrentProgress() - Method in class uk.co.agena.minerva.model.Propagation
Represents the current progress of any operation which is currently being monitored in this class.
getCurrentProgress() - Method in interface uk.co.agena.minerva.util.model.Progressable
 
getCurrentProgress() - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
Represents the current progress of any operation which is currently being monitored in this class.
getDataPointAtOrderPosition(int) - Method in class uk.co.agena.minerva.util.model.DataSet
Returns the DataPoint at the specified order position in the DataSet.
getDataPointLabels() - Method in class uk.co.agena.minerva.util.model.DataSet
Returns an array of the labels of all DataPoints.
getDataPoints() - Method in class uk.co.agena.minerva.util.model.DataSet
Returns the DataPoints associated with the DataSet.
getDataPointWithConnObjectID(int) - Method in class uk.co.agena.minerva.util.model.DataSet
Returns the first data point that has the connObjectID attribute value equal to the one specified.
getDataQuery() - Method in class uk.co.agena.minerva.model.querymodel.NodeQueryMapping
 
getDataset() - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
getDataSet() - Method in class uk.co.agena.minerva.model.scenario.Observation
Returns the DataSet containing the actual observation data.
getDataSets() - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Returns all of the DataSets in this DataSetGrouping.
getDataSetsForConnObject(int) - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Returns the DataSets associated with the specified connected object ID from this DataSetGrouping.
getDataSetWithId(int) - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Returns the DataSet with the specified ID from this DataSetGrouping.
getDataSource() - Method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
getDataSources() - Method in class uk.co.agena.minerva.model.querymodel.ClassQueryModel
 
getDdRelativeSumWidthEntropyErrors() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
getDecendentExtendedBNs(ExtendedBN) - Method in class uk.co.agena.minerva.model.Model
This method will use the MessagePassingLinks to get all the decendents of the argument ExtendedBN This is done recursively using the getChildrenExtendedBNs method.
getDefaultNodeFunction() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Gets the default node function for this ExtendedNode.
getDefaultParentModelNodeAltId() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getDefaultPartitionedModelNodeFunctions() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getDefaultPartitionedParentModelNodeAltIds() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getDefaultPartitionedParentModelNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getDefaultStateNames() - Static method in class uk.co.agena.minerva.model.extendedbn.BooleanEN
 
getDefaultStateNames() - Static method in class uk.co.agena.minerva.model.extendedbn.ContinuousIntervalEN
 
getDefaultStateNames() - Static method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
 
getDefaultStateNames() - Static method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
 
getDefaultStateNames() - Static method in class uk.co.agena.minerva.model.extendedbn.LabelledEN
 
getDefaultStateNames() - Static method in class uk.co.agena.minerva.model.extendedbn.RankedEN
 
getDefaultValue() - Method in class uk.co.agena.minerva.util.model.Variable
 
getDescription() - Method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
getDescription() - Method in class uk.co.agena.minerva.util.model.ModificationLog.ModificationLogItem
A description of the change that caused this log to be created
getDirectObservation() - Method in class uk.co.agena.minerva.model.scenario.Observation
Returns the ID of the selected ExtendedState state associated with this Observation.
getDirectObservation(int, int) - Method in class uk.co.agena.minerva.model.scenario.Scenario
Returns the ID of the selected ExtendedState in the ExtendedNode.
getDisceteValues() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Returns a double[] of all the discrete values in this node - that is the states which have an range of 0.
getDisceteValues() - Method in class uk.co.agena.minerva.model.extendedbn.NumericalEN
Returns a double[] of all the discrete values in this node.
getDisceteValuesStateIndexes() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Returns a int[] of all the discrete values state indexes in this node - that is the states which have an range of 0.
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Arithmetic
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Beta
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Binomial
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.ChiSquared
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Comparative
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Exponential
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.ExtremeValue
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Function
Shows the name of the Function subclass as it should be displayed in a GUI etc.
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Gamma
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Geometric
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Hypergeometric
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Logistic
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.LogNormal
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.NegativeBinomial
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Normal
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Poisson
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Student
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.TNormal
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Triangle
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Uniform
 
getDisplayName() - Method in class uk.co.agena.minerva.util.nptgenerator.Weibull
 
getDisplayNode() - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
getDriver() - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
getDummyWeightedFunctionFromTrueName(String) - Static method in class uk.co.agena.minerva.util.nptgenerator.Function
 
getEntropyConvergenceThreshold() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
getErrorText() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNEvent
Returns the message associate with this error
getErrorText() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
Returns the explanatory text that accompanies any error.
getErrorText() - Method in class uk.co.agena.minerva.model.ModelEvent
Returns the message associated with this error encapsulated by this ModelEvent.
getEstimatedNumberOfCalculations() - Method in class uk.co.agena.minerva.model.Propagation
This method is used to intomathe user of the number
getEventAttributes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
getEventAttributes() - Method in class uk.co.agena.minerva.model.ModelEvent
 
getEventType() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
getEventType() - Method in class uk.co.agena.minerva.model.ModelEvent
 
getExBN() - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
getExNode() - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
getExpression() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Gets the name of the expression for this node.
getExpressionVariableName() - Method in class uk.co.agena.minerva.model.scenario.Observation
 
getExpressionVariables() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getExtendedBN(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Retrieves the ExtendedBN with the supplied ID.
getExtendedBN(int[], boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
This methos will return a list of extended BNs which have the Id's in the provided list.
getExtendedBNAtIndex(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
 
getExtendedBNAtIndex(int) - Method in class uk.co.agena.minerva.model.Model
Returns the BN at the supplied index in the model's list of BNs.
getExtendedBNForNode(ExtendedNode) - Method in class uk.co.agena.minerva.model.Model
 
getExtendedBNID() - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
getExtendedBNList() - Method in class uk.co.agena.minerva.model.Model
Returns this Model's ExtendedBNList.
getExtendedBNs() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Returns the List of all ExtendedBNs in this ExtendedBNList.
getExtendedBNs(int[]) - Method in class uk.co.agena.minerva.model.Model
Returns all ExtendedBNs corresponding to the supplied IDs.
getExtendedBNsThatShareThisCore(CoreBN) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
This method id responsible for returning all the ExtendedBns that share the same CoreBN, as that specified in the argument list.
getExtendedBnsWithDDNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Returns a list of exBns that contain 1 or more DD nodes
getExtendedBnsWithRankedNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Returns a list of exBns that contain 1 or more Ranked nodes
getExtendedBnsWithStatisticalNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Returns a list of exBns that contain 1 or more statistical function nodes
getExtendedBNThatContainsNode(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
This method will return the extended BN that contains the specified node
getExtendedBNWithName(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
 
getExtendedBNWithName(String) - Method in class uk.co.agena.minerva.model.Model
Returns the BN with the supplied name.
getExtendedNode(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns an ExtendedNode with the specified ID.
getExtendedNode(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
getExtendedNodeFromExtendedBN(int, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Returns the ExtendedNode with the given id from the ExtendedBN with the specified id.
getExtendedNodeID() - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
getExtendedNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns a List of all the ExtendedNodes contained in the ExtendedBN.
getExtendedNodes(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Retruns a list of ExtendedNodes that have a short name equal to that specified.
getExtendedNodeWithName(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns the first ExtendedNode that has a short name equal to that specified.
getExtendedNodeWithName(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Returns the ExtendedNode with the given short name if the node exists
getExtendedNodeWithName(String) - Method in class uk.co.agena.minerva.model.Model
 
getExtendedNodeWithUniqueIdentifier(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns the ExtendedNode that has a unique string identifier the same as that specified.
getExtendedState(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the ExtendedState with the specified ID.
getExtendedState() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
This is the extendedState that is added or removed.
getExtendedStateAtIndex(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the state at the supplied index in the list.
getExtendedStates() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns a list of all the ExtendedStates contained in this ExtendedNode.
getExtendedStateShortNames() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns an array of the short names of all ExtendedStates.
getExtendedStateWithName(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the state with the supplied name.
getExtendedStateWithShortDesc(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the ExtendedState with the specified Short NameDescription.
getFamilyMembersWithParentID(List, int) - Static method in class uk.co.agena.minerva.util.model.FamilyProcessor
Takes a list of family members and returns a list of all the family members with the specified parent ID
getFirstBound() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
getFullyQualifiedPathForNode(ExtendedNode) - Method in class uk.co.agena.minerva.model.Model
Returns a string that contains the full path of the selected node: mdiPath.exbnName
getFunctionFromArray(int[], int[][], List) - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
Similar to putFunctionInArray but instead when we find the first occurance of the pattern in the state combination array we return the ExtendedNodeFunction at the appropiate position in the allFunctions List.
getFunctionMode() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the function mode for this ExtendedNode.
getFunctionParametersMap() - Static method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
 
getHardEvidence() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This method will return an ExtendedState in which there is hard evidence.
getHelper(int) - Method in class uk.co.agena.minerva.model.querymodel.XmlHelper
 
getHelper(String) - Method in class uk.co.agena.minerva.model.querymodel.XmlHelper
 
getHighestAllocatedExtendedBNID() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Returns the highest ID currently allocated to the ExtendedBNs in this List..
getHighestDataPoint() - Method in class uk.co.agena.minerva.util.model.DataSet
This method will return the highest data point in the dataset.
getHighestDataPointAdjustedForProbailityMass() - Method in class uk.co.agena.minerva.util.model.DataSet
This method will return the highest data point adjusted for probaility mass.
getId() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns the unique ID of the ExtendedBN.
getId() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the unique ID of the ExtendedNode.
getId() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Returns the unique ID of the ExtendedState.
getId() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
 
getId() - Method in class uk.co.agena.minerva.model.Model
Returns the ID of this Model.
getId() - Method in class uk.co.agena.minerva.model.scenario.Observation
Returns the unique ID of the Observation.
getId() - Method in class uk.co.agena.minerva.model.scenario.Scenario
Returns the unique ID of the Scenario.
getId() - Method in class uk.co.agena.minerva.util.model.DataSet
Returns the unique ID of the DataSet.
getId() - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Returns the unique ID of the DataSetGrouping.
getId() - Method in interface uk.co.agena.minerva.util.model.Identifiable
Returns the unique integer ID of the object.
getIdentifiableWithId(List, int) - Static method in class uk.co.agena.minerva.util.model.Identifier
 
getInconsistentNode() - Method in exception uk.co.agena.minerva.model.extendedbn.InconsistentEvidenceException
 
getIndexOfStateThatContains(double, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Returns the index of the state that contains the specified value.
getIndexOfStateThatContains(double, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
This method will always treat the upperbound as exclusive.
getInformationMessage() - Method in exception uk.co.agena.minerva.model.extendedbn.InconsistentEvidenceException
 
getInputNodeRecivedMarginalsAsEvidenceDS() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getInputNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns a List of all ExtendedNodes that can be input nodes for message passing.
getInstance() - Static method in class uk.co.agena.minerva.util.nptgenerator.ExpressionParser
 
getIntervalDataPointWithHighestMidPoint() - Method in class uk.co.agena.minerva.util.model.DataSet
Return the Interval data point with the highest mid point (dirived from the bounding values) if there are no Interval data points connected to the data set then a null is returned.
getIntervalDataPointWithHighestRangeValue() - Method in class uk.co.agena.minerva.util.model.DataSet
Return the Interval data point with the lowest range value (lowest lower bound) if there are no Interval data points connected to the data set then a null is returned.
getIntervalDataPointWithLowestMidPoint() - Method in class uk.co.agena.minerva.util.model.DataSet
Return the Interval data point with the lowest mid point (dirived from the bounding values) if there are no Interval data points connected to the data set then a null is returned.
getIntervalDataPointWithLowestRangeValue() - Method in class uk.co.agena.minerva.util.model.DataSet
Return the Interval data point with the lowest range value (lowest lower bound) if there are no Interval data points connected to the data set then a null is returned.
getIntervalLowerBound() - Method in class uk.co.agena.minerva.util.model.IntervalDataPoint
Returns the lower bound of the "x" interval.
getIntervalUpperBound() - Method in class uk.co.agena.minerva.util.model.IntervalDataPoint
Returns the upper bound of the "x" interval.
getIterationChildExtendedBNId() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Gets the child ExtendedBN ID at the index specified by the current value of the iterator counter.
getIterationChildExtendedNodeId() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Gets the child ExtendedNode ID at the index specified by the current value of the iterator counter.
getIterationParentExtendedBNId() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Gets the parent ExtendedBN ID at the index specified by the current value of the iterator counter.
getIterationParentExtendedNodeId() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Gets the parent ExtendedNode ID at the index specified by the current value of the iterator counter.
getLabel() - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
getLabel() - Method in class uk.co.agena.minerva.util.model.DataPoint
Returns the label of the DataPoint.
getLastBound() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
getLastBound() - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
Differs from the superclass method because the Range doesn't actually contain the last value.
getLastQueryColumnNames() - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
getLastSavedPriorIndex() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the index of the last saved priors
getLengthOfProgressableTask() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
getLengthOfProgressableTask() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
 
getLengthOfProgressableTask() - Method in class uk.co.agena.minerva.model.Propagation
The length of the propagation task.
getLengthOfProgressableTask() - Method in interface uk.co.agena.minerva.util.model.Progressable
 
getLengthOfProgressableTask() - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
The length of the current task being monitored.
getListOfOrderedMessagePassingLinksLists() - Method in class uk.co.agena.minerva.model.Model
Returns the MessagePassingLinks objects associated with this Model as a set of Lists, such that each List contains MessagePassingLinks objects that have the same priority level.
getLongDescription() - Method in class uk.co.agena.minerva.util.model.NameDescription
Returns the long description of the NameDescription object.
getLowerBound() - Method in class uk.co.agena.minerva.util.model.Range
Returns the lower bound.
getLowerPercentile() - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
getLowestDataPoint() - Method in class uk.co.agena.minerva.util.model.DataSet
Returns the DataPoint in the DataSet that has the lowest value.
getLowestDataPointAdjustedForProbailityMass() - Method in class uk.co.agena.minerva.util.model.DataSet
This method will return the lowest data point adjusted for probaility mass.
getMarginalDataItemAtIndex(int) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
Returns the MarginalDataItem at the specified index in the list.
getMarginalDataItemListForNode(ExtendedBN, ExtendedNode) - Method in class uk.co.agena.minerva.model.MarginalDataStore
This method will return the first MarginaldataItemList that references the specified node in the specified BN.
getMarginalDataItems() - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
getMarginalDataStore() - Method in class uk.co.agena.minerva.model.Model
 
getMarginals() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the marginal probabilities for the node in the form of a DataSet.
getMasterQueries() - Method in class uk.co.agena.minerva.model.querymodel.ClassQueryModel
 
getMasterUpdates() - Method in class uk.co.agena.minerva.model.querymodel.ClassQueryModel
 
getMaximumValueReached() - Method in class uk.co.agena.minerva.util.nptgenerator.Function
 
getMaxNumParameters() - Static method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
 
getMdi() - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
getMeanValue() - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
getMedianValue() - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
getMessageParseLinkWithID(int) - Method in class uk.co.agena.minerva.model.Model
Returns the message parse link with the specified ID
getMessagePassingLinks() - Method in class uk.co.agena.minerva.model.Model
Return's this Model's List of MessagePassingLinks objects.
getMessagePassingLinksForChild(int) - Method in class uk.co.agena.minerva.model.Model
Returns the MessagePassingLinks objects that have the ExtendedBN with the supplied ID as a child.
getMessagePassingLinksForParent(int) - Method in class uk.co.agena.minerva.model.Model
Returns the MessagePassingLinks objects that have the ExtendedBN with the supplied ID as a parent.
getMetaData() - Method in class uk.co.agena.minerva.model.Model
 
getMidPoint() - Method in class uk.co.agena.minerva.util.model.IntervalDataPoint
Returns the mid point of the interval
getMinimumValueReached() - Method in class uk.co.agena.minerva.util.nptgenerator.Function
 
getModel() - Method in class uk.co.agena.minerva.model.MarginalDataStore
 
getModel() - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
getModificationItems() - Method in class uk.co.agena.minerva.util.model.ModificationLog
A list of the modifications for the log
getModificationLog() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
The modification log holds information about what has made this exBN inconsistent with the last known good propagation.
getName() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns the name of the ExtendedBN.
getName() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the name of the ExtendedNode.
getName() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Returns the name of this ExtendedNodeFunction.
getName() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Returns the name of the ExtendedState.
getName() - Method in class uk.co.agena.minerva.model.Model
Returns the name of this Model.
getName() - Method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
getName() - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
getName() - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
getName() - Method in class uk.co.agena.minerva.model.querymodel.Substitution
 
getName() - Method in class uk.co.agena.minerva.model.scenario.Scenario
Returns the name of the Scenario.
getName() - Method in class uk.co.agena.minerva.util.model.DataSet
Returns the name of the DataSet.
getName() - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Returns the name of the DataSetGrouping.
getName() - Method in interface uk.co.agena.minerva.util.model.Nameable
 
getName() - Method in class uk.co.agena.minerva.util.model.Variable
 
getNd() - Method in class uk.co.agena.minerva.util.model.Note
The name description that holds the contents of the note
getNetFileAestheticData() - Method in class uk.co.agena.minerva.model.Model
Returns a List holding the aesthetic data relating to nodes of a .net file such as x and y co-ordinates.
getNewConnNodeId() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
getNextAvailableId(List) - Static method in class uk.co.agena.minerva.util.model.Identifier
Takes a List of Identifiable objects, examines each object and determines the next free ID.
getNextDataSetId() - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Finds the next available ID to assign to a DataSet based on the IDs of DataSets currently in the DataSetGrouping.
getNextExtendedStateId() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Finds the next available ID to assign to an ExtendeNode based on the IDs of those currently in the ExtendedBN's List.
getNodeMarginalListMap() - Method in class uk.co.agena.minerva.model.MarginalDataStore
 
getNodeName() - Method in class uk.co.agena.minerva.model.querymodel.NodeEvidence
 
getNodeName() - Method in class uk.co.agena.minerva.model.querymodel.NodeQueryMapping
 
getNodeQueryMapping() - Method in class uk.co.agena.minerva.model.querymodel.NodeEvidence
 
getNodeType() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the type of this ExtendedNode.
getNodeWithInsufficientRange() - Method in exception uk.co.agena.minerva.util.nptgenerator.NPTGeneratorInsufficientStateRangeException
 
getNotes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the note object for the node
getNotes() - Method in class uk.co.agena.minerva.model.Model
Tne notes set connected to the model
getNotes() - Method in class uk.co.agena.minerva.util.model.Notes
Returns a list of all the notes
getNPT() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the NPT of this node as a 2D array of floats.
getNPTPopulationMethodAsString() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
returns a list of strings that represent the NPT editing mode (and function list if suitable)
getNPTSize(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This method calculates the expected size of its NPT using its parents' state sizes.
getNumberChildren() - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
getNumberOfCellsForNPT(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Used to know how many calculations it will take to fill the NPT from this node.
getNumberOfStateCombsForModelNodes(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the number of state combinations for the parent model nodes of this node.
getNumericalValue() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Returns the point value with which this ExtendedState is associated.
getNumExNodeStatesWhenCreated() - Method in class uk.co.agena.minerva.model.scenario.Observation
 
getNumParameters(String) - Static method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
 
getObjectName() - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
getObservation(int, int) - Method in class uk.co.agena.minerva.model.scenario.Scenario
Returns the Observation associated with the supplied ExtendedBN and ExtendedNode IDs.
getObservations() - Method in class uk.co.agena.minerva.model.scenario.Scenario
Returns a List of all the Observations contained in this Scenario.
getObservations(int, int) - Method in class uk.co.agena.minerva.model.scenario.Scenario
This method will return all observations connected to the specified node in the connected extended BN
getObservations() - Method in class uk.co.agena.minerva.model.scenario.ScenarioEvent
Returns the Observations that have been added to or removed from the Scenario.
getObservationsConnectedToExtendedNode(int) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
Returns a List of all Obsevations that are connected to the ExtendedNode with the given ID.
getOldConnNodeId() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
getOldExtendedBNId() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNEvent
 
getOutputNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns a List of all ExtendedNodes that can be output nodes for message passing.
getParameterCount() - Method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Arithmetic
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Beta
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Binomial
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.ChiSquared
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Comparative
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Exponential
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.ExtremeValue
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Function
Shows the name of the parameters of the Function subclass as they should be displayed in a GUI etc.
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Gamma
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Geometric
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Hypergeometric
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Logistic
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.LogNormal
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.NegativeBinomial
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Normal
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Poisson
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Student
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.TNormal
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Triangle
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Uniform
 
getParameterDisplayNames() - Method in class uk.co.agena.minerva.util.nptgenerator.Weibull
 
getParameters() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Returns the parameters for this ExtendedNodeFunction without any user entered Tabs or New Lines.
getParameters() - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
getParametersWithFormatting() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Returns the parameters for this ExtendedNodeFunction with all user entered Tabs and New Lines.
getParent() - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
getParentConnectedNodeIds(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns a List of the connected IDs for the supplied child node.
getParentExtendedBNIds(int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Returns all parent ExtendedBN IDs that are connected to the supplied child ExtendedBN ID in the links contained in this MessagePassingLinks object.
getParentExtendedBNs(ExtendedBN) - Method in class uk.co.agena.minerva.model.Model
This method uses the message passing links to return a list of the parent ExtendedBNs of the argument BN.
getParentId() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
getParentId() - Method in class uk.co.agena.minerva.model.Model
Returns the parent ID of this Model
getParentId() - Method in interface uk.co.agena.minerva.util.model.FamilyMember
Returns the ID of this FamilyMember's parent.
getParentNodes(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns the parent ExtendedNodes of the supplied ExtendedNode.
getParentNodes(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns the parent ExtendedNodes of the ExtendedNode with the supplied connected CoreBNNode AltID.
getPartitionedExpressionModelNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the partitioned expression model nodes currently defined on this node.
getPartitionedExpressions() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the partitioned expressions currently defined on this node.
getPasteErrorLog() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
When a paste operation is performed if any errors occur they will be stored as Strings in this List.
getPercentileValue() - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
getPossibleProblemNodes() - Method in exception uk.co.agena.minerva.model.extendedbn.InconsistentEvidenceException
 
getPriorityLevel() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Returns the current priority level of this MessagePassingLinks object with respect to any other MessagePassingLinks objects that are being navigated.
getProblemNodes() - Method in class uk.co.agena.minerva.model.Model
 
getPropagationAlgorithm() - Method in class uk.co.agena.minerva.model.Model
This is the propagation algorithm that will be used for this model.
getPropagationCalculationEstimate() - Method in class uk.co.agena.minerva.model.Model
Returns the estimated number of calculations required by the propagation algorithm.
getPropagationCallSigns() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns the array containing the propagation call signs.
getQueries() - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
getQuery() - Method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
getQuery() - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
getQueryInstance() - Method in class uk.co.agena.minerva.model.querymodel.NodeEvidence
 
getQueryParameters() - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
getQueryString() - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
getQuestionnaireList() - Method in class uk.co.agena.minerva.model.Model
Returns this Model's QuestionnaireList.
getQuestionnaires(int[]) - Method in class uk.co.agena.minerva.model.Model
Returns all Questionnaires corresponding to the supplied IDs.
getRange() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Returns the Range with which this ExtendedState is associated.
getRangesNotToBeSplit() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
getRankedSampleSize() - Static method in class uk.co.agena.minerva.model.extendedbn.RankedEN
 
getRankedSampleSize() - Method in class uk.co.agena.minerva.model.Model
 
getRelevantExtendedBNIds() - Method in class uk.co.agena.minerva.model.scenario.Scenario
Returns a list of IDs of all the ExtendedBNs that are related to this Scenario.
getReportable() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns whether the ExtendedNode can be reported on.
getResult() - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
getResult(int, int) - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
getRowMajorNPT() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the NPT of the underlying node in the CoreBN as a row major array of probabilities.
getSamplesForState(int, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
getSamplesForState(int, boolean, int) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Returns a set of samples from the range of the state in question.
getSamplesForState(int, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
Just returns the single numerical value as the only sample for the supplied state.
getSamplesForState(int, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns a set of values that are sampled from the state at the supplied index.
getSamplesForState(int, boolean, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
Returns a set of samples from the range of the state in question.
getSamplesForState(int, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.LabelledEN
Returns a set of samples from the range of the state in question.
getSamplesForState(int, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.RankedEN
 
getSampleSize() - Static method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
getSampleSize() - Method in class uk.co.agena.minerva.model.Model
 
getSavedPriors() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getScaledTargetValue() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Returns the scaled target value.
getScaledTargetValue() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Normalises the ExtendedStates so that the first one has the value 0, the next has value 1 and so on.
getScenario(int) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
Returns the Scenario with the supplied ID.
getScenarioAtIndex(int) - Method in class uk.co.agena.minerva.model.Model
Returns the Scenario at the supplied index in the model's list of Scenarios.
getScenarioAtIndex(int) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
 
getScenarioList() - Method in class uk.co.agena.minerva.model.Model
Returns this Model's ScenarioList.
getScenarioName() - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
getScenarios(int[]) - Method in class uk.co.agena.minerva.model.Model
Returns all Scenarios corresponding to the supplied IDs.
getScenarios() - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
Return the complete List of Scenarios.
getScenariosConnectedToExtendedBN(int) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
Returns a List of Scenarios that have one or more Observations within them connected to the specified Extended BN.
getScenarioWithName(String) - Method in class uk.co.agena.minerva.model.Model
Returns the Scenario with the supplied name in the list of the model's Scenarios.
getScenarioWithName(String) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
 
getShortDescription() - Method in class uk.co.agena.minerva.util.model.NameDescription
Returns the short description of the NameDescription object.
getSimulationEntropyConvergenceTolerance() - Method in class uk.co.agena.minerva.model.Model
 
getSimulationEvidenceTolerancePercent() - Method in class uk.co.agena.minerva.model.Model
 
getSimulationNoOfIterations() - Method in class uk.co.agena.minerva.model.Model
 
getSingleColumnNPT() - Method in class uk.co.agena.minerva.util.nptgenerator.Function
 
getSourceCardinality() - Method in class uk.co.agena.minerva.util.model.Connection
The cardibality attactched to the source of the connection
getStandardDeviationValue() - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
getStringValue() - Method in class uk.co.agena.minerva.util.model.StringDataPoint
 
getStructureElement() - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
getStructureRoot() - Method in class uk.co.agena.minerva.model.querymodel.ClassQueryModel
 
getsubnodecount() - Method in class uk.co.agena.minerva.model.querymodel.XmlHelper
 
getSubnodeName(int) - Method in class uk.co.agena.minerva.model.querymodel.XmlHelper
 
getSubstitution(String) - Method in class uk.co.agena.minerva.model.querymodel.ClassQueryModel
 
getSubstitution() - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
getSuitableMessagePassingNodes(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Searches through the supplied List and returns a List of ExtendedNodes that have the same number of ExtendedStates.
getSupportedFunctionTypes() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Returns a list of the function classes supported by this node type.
getSupportedFunctionTypes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns a list of the function classes supported by this node type.
getSupportedFunctionTypes() - Method in class uk.co.agena.minerva.model.extendedbn.RankedEN
Returns a list of the function classes supported by this node type.
getTableNames() - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
getTargetCardinality() - Method in class uk.co.agena.minerva.util.model.Connection
The cardibality attactched to the target of the connection
getTargetValue() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the target value for this ExtendedNode.
getTargetValueAsString() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Returns the target value of this ContinuousIntervalEN as a String.
getTargetValueAsString() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the target value as a String.
getTargetValueRange(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Returns the Range in which the target value has to lie.
getTargetValueRange(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Gets the Range in which the target value can lie.
getTargetValueRangeAsString() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns the target value range as a String for displaying to a system user.
getTitle() - Method in class uk.co.agena.minerva.util.model.ModificationLog
The title of the modification log
getTotal(int, int) - Method in class uk.co.agena.minerva.util.model.DataSet
returns the total value of all data points between the specified points, a value of -1 in a arguement will have it default to the beginning and end of the data set respectivily Thus getTotal(-1,-1) will return the total of the whole data set
getTotalAdjustedForProbabilityMass(int, int) - Method in class uk.co.agena.minerva.util.model.DataSet
This methods will return a total of the data point values between the specified points.
getTotalNumberOfExtendedFunctions() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Calculates the total number of functions in use.
getTrueOrderStateCode(List, int[], List) - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
The order in which the user selected model nodes are added to the specified list may not be the correct order in which the Model nodes exist in the reqNodeOrder List.
getType() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns the type of the ExtendedBN.
getType() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Returns the type of this ExtendedNodeFunction.
getUniqueExNodeIdWhenCreated() - Method in class uk.co.agena.minerva.model.scenario.Observation
 
getUnmarkedMessagePassingExtendedBNs() - Method in class uk.co.agena.minerva.model.Model
Gets all the ExtendedBNs that are not flagged to have been visted by the MessagePassing algorithm.
getUnmarkedTemporaryNodeOrderFlagNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Gets all the ExtendedNodes that are not flagged to have been visted by ordering algorithm.
getUnmatchedNodeNames() - Method in class uk.co.agena.minerva.model.Model
 
getUpperBound() - Method in class uk.co.agena.minerva.util.model.Range
Returns the upper bound.
getUpperPercentile() - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
getUrl() - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
getUserDefinedRelevantExtendedBNIds() - Method in class uk.co.agena.minerva.model.scenario.Scenario
Returns the user-defined ExtendedBN IDs that are deemed relevant to this Scenario.
getUserEnteredAnswer() - Method in class uk.co.agena.minerva.model.scenario.Observation
Returns the answer entered by the user if one exists.
getUserEnteredAnswerMapping() - Method in class uk.co.agena.minerva.model.scenario.Observation
Returns the mapping that is used to interpret the user-entered answer.
getValue(String) - Method in class uk.co.agena.minerva.model.querymodel.Substitution
 
getValue(String) - Method in class uk.co.agena.minerva.model.querymodel.XmlHelper
 
getValue() - Method in class uk.co.agena.minerva.util.model.DataPoint
Returns the double value encapsulated by the DataPoint.
getValue() - Method in class uk.co.agena.minerva.util.model.Variable
 
getValueToContain() - Method in exception uk.co.agena.minerva.util.nptgenerator.NPTGeneratorInsufficientStateRangeException
 
getVariable() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
This is the Variable that is added or removed.
getVariable(String) - Method in class uk.co.agena.minerva.util.model.VariableList
Finds the Variable with the supplied name.
getVariables() - Method in class uk.co.agena.minerva.util.model.VariableList
 
getVarianceValue() - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
getVersion() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
getVersion() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
 
getVersion() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
getVersion() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
 
getVersion() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
 
getVersion() - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
getVersion() - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
getVersion() - Method in class uk.co.agena.minerva.model.MarginalDataStore
 
getVersion() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
 
getVersion() - Method in class uk.co.agena.minerva.model.Model
 
getVersion() - Method in class uk.co.agena.minerva.model.scenario.Observation
 
getVersion() - Method in class uk.co.agena.minerva.model.scenario.Scenario
 
getVersion() - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
 
getVersion() - Method in class uk.co.agena.minerva.util.model.DataPoint
 
getVersion() - Method in class uk.co.agena.minerva.util.model.DataSet
 
getVersion() - Method in class uk.co.agena.minerva.util.model.ModificationLog
 
getVersion() - Method in class uk.co.agena.minerva.util.model.Note
 
getVersion() - Method in class uk.co.agena.minerva.util.model.Notes
 
getVersion() - Method in class uk.co.agena.minerva.util.model.Variable
 
getVersion() - Method in class uk.co.agena.minerva.util.model.VariableList
 
getVersion() - Method in interface uk.co.agena.minerva.util.model.Writable
Returns the version of the class.
getVersionString() - Static method in class uk.co.agena.minerva.util.BuildInformation
 
getVisible() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns whether the ExtendedNode is visible.
getVisible() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Returns whether the ExtendedState is visible.

H

hasDDNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns a boolean value that determines whether the exBN has DD nodes
hasParents() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Indicates whether this ExtendedNode has any parents.
hasRankedNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns a boolean value that determines whether the exBN has Ranked nodes
hasStatisticalNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns a boolean value that determines whether the exBN has statistical nodes
howManyFunctionsDoINeed() - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
This returns the Number of Functions that is required before we can generate the NPT.
Hypergeometric - Class in uk.co.agena.minerva.util.nptgenerator
 
Hypergeometric(List, int, int, int) - Static method in class uk.co.agena.minerva.util.nptgenerator.Hypergeometric
calculates the distribution over a defined set of ranges
Hypergeometric(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Hypergeometric
 

I

id - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
The unique integer ID for the ExtendedNode.
Identifiable - Interface in uk.co.agena.minerva.util.model
This interface is implemented by objects that have a unique integer ID.
Identifier - Class in uk.co.agena.minerva.util.model
The Identifier is a central helper class that can determine the next available ID with respect to a list of Identifiable objects.
Identifier() - Constructor for class uk.co.agena.minerva.util.model.Identifier
 
importScenarios(ScenarioList) - Method in class uk.co.agena.minerva.model.Model
Takes the supplied list of Scenarios and adds them to the Model.
InconsistentEvidenceException - Exception in uk.co.agena.minerva.model.extendedbn
 
InconsistentEvidenceException() - Constructor for exception uk.co.agena.minerva.model.extendedbn.InconsistentEvidenceException
Constructs an empty InconsistentEvidenceException.
InconsistentEvidenceException(String) - Constructor for exception uk.co.agena.minerva.model.extendedbn.InconsistentEvidenceException
Constructs an InconsistentEvidenceException with the specified message.
InconsistentEvidenceException(Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.InconsistentEvidenceException
Constructs an InconsistentEvidenceException with the specified cause.
InconsistentEvidenceException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.extendedbn.InconsistentEvidenceException
Constructs an InconsistentEvidenceException with the specified cause and message.
InconsistentEvidenceException(String, ExtendedNode, List) - Constructor for exception uk.co.agena.minerva.model.extendedbn.InconsistentEvidenceException
 
InconsistentEvidenceException(String, CoreBNInconsistentEvidenceException, ExtendedBN) - Constructor for exception uk.co.agena.minerva.model.extendedbn.InconsistentEvidenceException
 
inconsistentEvidencePropagated - Variable in class uk.co.agena.minerva.model.Propagation
We need to monitor if there has been any inconsistent evidence propagated.
increasePriority() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Increments the current priority level by one (unless the priority level is already PRIORITY_VERY_HIGH i.e.
inputNodeReceivedMarginals - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Flag to inform us if this node is an Input Node, then has it received its new Marginals via a Message Pass.
insertExtendedState(int, Range) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Inserts a state with the supplied range at the specified index.
insertExtendedState(int, Range, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Inserts a state with the supplied range at the specified index.
insertExtendedState(int, Range) - Method in class uk.co.agena.minerva.model.extendedbn.RankedEN
 
insertStatesForValues(double[], boolean, boolean, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
This method will insert these double values into this node.
IntContParseException - Exception in uk.co.agena.minerva.util.nptgenerator
This Exception is specific to the IntCont function.
IntContParseException() - Constructor for exception uk.co.agena.minerva.util.nptgenerator.IntContParseException
 
IntContParseException(String) - Constructor for exception uk.co.agena.minerva.util.nptgenerator.IntContParseException
 
IntContParseException(Throwable) - Constructor for exception uk.co.agena.minerva.util.nptgenerator.IntContParseException
 
IntContParseException(String, Throwable) - Constructor for exception uk.co.agena.minerva.util.nptgenerator.IntContParseException
 
IntegerIntervalEN - Class in uk.co.agena.minerva.model.extendedbn
This class is used to represent intervals that contain only integers; floating point numbers in between are ignored.
IntegerIntervalEN() - Constructor for class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
Creates a default DiscreteRealEN.
IntegerIntervalEN(NameDescription, String, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
 
IntegerIntervalEN(NameDescription, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
 
IntervalDataPoint - Class in uk.co.agena.minerva.util.model
This class represents DataPoints that have an interval (e.g.
IntervalDataPoint() - Constructor for class uk.co.agena.minerva.util.model.IntervalDataPoint
Default constructor.
IntervalDataPoint(double, int, double, double) - Constructor for class uk.co.agena.minerva.util.model.IntervalDataPoint
Constructs an IntervalDataPoint with the supplied value, connected object ID, lower bound and upper bound.
IntervalDataPoint(String, double, int, double, double) - Constructor for class uk.co.agena.minerva.util.model.IntervalDataPoint
Constructs an IntervalDataPoint with the supplied label, value, connected object ID, lower bound and upper bound.
IntervalDataPoint(String, double, double) - Constructor for class uk.co.agena.minerva.util.model.IntervalDataPoint
 
IntervalDataPoint(double, double) - Constructor for class uk.co.agena.minerva.util.model.IntervalDataPoint
 
isAllowCloning() - Method in class uk.co.agena.minerva.model.querymodel.NodeQueryMapping
 
isAllParentExtendedBNsMarkedForMessagePassing(ExtendedBN) - Method in class uk.co.agena.minerva.model.Model
 
isAllParentExtendedNodesMarkedForOrdering(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
isAllParentsSame() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Goes through and checks whether all the IDs for the parent ExtendedBNs in this MessagePassingLinks object are the same.
isCanContinueFromError() - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
Flag used by the method createFunctionListForModelNodes to indicate when throwing an exception whether it is one from which the calling method can continue from.
isChangeStatesOnInputNodeIfRequired() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
isChildExtendedBN(int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Checks whether there are any links in this MessagePassingLinks object whose children have the supplied ExtendedBN ID.
isCompile() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNEvent
 
isCompiled() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Checks whether the underlying BN has been compiled or not.
isConnectableInputNode() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns whether this ExtendedNode is a potential input node.
isConnectableOutputNode() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Returns whether this ExtendedNode is a potential output node.
isContinueToDynamicallyDiscretise() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
isDirectObservation() - Method in class uk.co.agena.minerva.model.scenario.Observation
Determines whether there is a direct Observation i.e.
isDisplayOnRiskGraphs() - Method in class uk.co.agena.minerva.model.scenario.Scenario
 
isDynamicallyDiscretisable() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
isDynamicallyDiscretisable() - Method in class uk.co.agena.minerva.model.extendedbn.RankedEN
 
isErrorFixed() - Method in class uk.co.agena.minerva.model.ModelEvent
Returns whether the error has been fixed or not.
isFireUpExtendedNodeEvent() - Method in class uk.co.agena.minerva.model.Model
 
isForceSampling() - Method in class uk.co.agena.minerva.util.nptgenerator.Function
 
isFullySpecified() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Returns whether the ExtendedNodeFunction is fully specified.
isHandlesOwnQueries() - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
isHasMultipleChildren() - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
isInputNodeReceivedMarginals() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
isInputNodeRecivedMarginalsAsEvidence() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
isMessagepassingMarkedFlag() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
isMetaDataUsed() - Method in class uk.co.agena.minerva.model.Model
 
isNoObservation(String) - Method in class uk.co.agena.minerva.model.querymodel.Substitution
 
isNptReCalcRequired() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This is a flag to monitor if the NPT needs to be Re-Calculated at any point in time.
isNptSynchronisedWithFormula() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
isOnlyUpdateOnMatchedCallSign() - Method in class uk.co.agena.minerva.model.MarginalDataItem
Attribute determines whether an update is only called when the call sign in the propagate event is matched to the call sign in the MDI, or if the uodate occurs on every occassion
isParentExtendedBN(int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Checks whether there are any links in this MessagePassingLinks object whose parents have the supplied ExtendedBN ID.
isPasteErrorCritical() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
If an error occured in the paste operation and it was of critical nature this flag will be set.
isProgressableTaskDone() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
isProgressableTaskDone() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
 
isProgressableTaskDone() - Method in class uk.co.agena.minerva.model.Propagation
When set to true the current task being monitored will have been completed.
isProgressableTaskDone() - Method in interface uk.co.agena.minerva.util.model.Progressable
 
isProgressableTaskDone() - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
When set to true the current task being monitored will have been completed.
isPropagateUsingModelScenarios() - Method in class uk.co.agena.minerva.model.Model
 
isRecursive() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Checks if this link is recursive
isReportable() - Method in class uk.co.agena.minerva.model.scenario.Scenario
Flag can be toggled by external objects to determine whether the scenario is reportable (the user is interested in seeing its results).
isSimulationLogging() - Method in class uk.co.agena.minerva.model.Model
 
isSimulationNode() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
isStateSplitable(int) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
This method checks if the state at the given stateindex is splitable.
isStateSplitable(int) - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
This method checks if the state at the given stateindex is splitable.
isStructureQuery() - Method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
isTargetValuePresent() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Indicates whether a target value is present for this ExtendedNode.
isTemporaryNodeOrderFlag() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
isUniformJustSet() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
isUpdate() - Method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
isUpdateOnAllEvidenceRetracted() - Method in class uk.co.agena.minerva.model.MarginalDataItem
this attribute determines whether the monitors should update when it recieves a all evidence retracted event from the connected extended BN.
isValidForModel(Model) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
This method will itterate over the message pass links in the message pass link object, and remove those that are connected to exBNs and exNodes that are in the connected model.
isValidLink(ExtendedNode, ExtendedBN, ExtendedNode) - Static method in class uk.co.agena.minerva.model.MessagePassingLinks
This method takes two nodes, and informs the user whether they are a valid source and target for a message parse link.
isValueSet() - Method in class uk.co.agena.minerva.util.model.Variable
 
isVisible() - Method in class uk.co.agena.minerva.model.MarginalDataItem
This attribute defines whether the results of the marginal data item should be made visible to the user (currently restricted to the visibility of the marginal plot on the monitors)

J

joinLinks(List) - Static method in class uk.co.agena.minerva.model.MessagePassingLinks
Joins the Links in the List of MessagePassingLinks.

L

label - Variable in class uk.co.agena.minerva.util.model.DataPoint
The label for this DataPoint.
LABELLED_E_N - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Constant corresponding to the LabelledEN type.
LabelledEN - Class in uk.co.agena.minerva.model.extendedbn
A LabelledEN is an ExtendedNode whose states are not numerical or in any order but simply have labels e.g.{Java, C++, C, Ada}.
LabelledEN() - Constructor for class uk.co.agena.minerva.model.extendedbn.LabelledEN
Default constructor.
LabelledEN(NameDescription, String, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.LabelledEN
Constructs a LabelledEN with the specified name, connected node ID and connected BN.
LabelledEN(NameDescription, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.LabelledEN
Constructs a LabelledEN with the specified name and connected BN.
lengthOfProgressableTask - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Represnts the current progress of any operation which is currently being monitored in this class.
lengthOfProgressableTask - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Represnts the progress of any operation which is currently being monitored in this class.
lengthOfProgressableTask - Variable in class uk.co.agena.minerva.model.Propagation
Represnts the length of the operation which is currently being monitored in this class.
lengthOfProgressableTask - Variable in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
Represnts the length of the operation which is currently being monitored in this class.
LIMIT_RULE_NUMERIC_VALUE - Static variable in class uk.co.agena.minerva.util.model.DataSet
 
LIMIT_RULE_STATENUMBER - Static variable in class uk.co.agena.minerva.util.model.DataSet
 
link(ExtendedNode, ExtendedNode) - Method in class uk.co.agena.minerva.model.Model
Links the two ExtendedNodes together, thereby linking the two containing ExtendedBNs.
linkFamilyMembers(List) - Static method in class uk.co.agena.minerva.util.model.FamilyProcessor
Links the FamilyMembers in the list based on their IDs and parent IDs.
linkFamilyMembers(List, List) - Static method in class uk.co.agena.minerva.util.model.FamilyProcessor
Links up the supplied FamilyMembers into a family tree (that can have multiple roots).
linkUp() - Method in class uk.co.agena.minerva.model.MarginalDataStore
Links the Marginal Data Item Lists to the correct BNs and nodes and then uses the temporary list of MDILs to build the node-list map.
load(String) - Static method in class uk.co.agena.minerva.model.Model
Loads the model from the supplied file.
load(XmlHelper, DataSource) - Static method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
load(XmlHelper, ClassQueryModel) - Static method in class uk.co.agena.minerva.model.querymodel.DataSource
 
load(XmlHelper, DatabaseQuery) - Static method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
loadModel(Model, String) - Method in class uk.co.agena.minerva.model.querymodel.ClassQueryModel
A base model is used as a template to define a hierarchy of types and the BNs used to instantiate those types.
loadScenariosFromCSV(List) - Method in class uk.co.agena.minerva.model.Model
Takes the supplied set of CSV strings, creates scenarios from it and loads them into the Model (replacing any existing scenarios).
loadUsingModel(Model, String) - Method in class uk.co.agena.minerva.model.querymodel.ClassQueryModel
 
LocateModelObjectsNoConnectedToMetaDataItems(boolean, boolean, boolean) - Method in class uk.co.agena.minerva.model.Model
This method will itterate over the model items (Extended BNs, scenarios and questionnaires), and add to a return list all those that are not connected to any of the meta data objects connected to the model.
Logistic - Class in uk.co.agena.minerva.util.nptgenerator
 
Logistic(List, double, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.Logistic
calculates the distribution over a defined set of ranges
Logistic(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Logistic
 
LogNormal - Class in uk.co.agena.minerva.util.nptgenerator
 
LogNormal(List, double, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.LogNormal
calculates the Distribution over a defined set of ranges given a mean and a variance.
LogNormal(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.LogNormal
 

M

main(String[]) - Static method in class uk.co.agena.minerva.util.BuildInformation
 
main(String[]) - Static method in class uk.co.agena.minerva.util.nptgenerator.Hypergeometric
 
main(String[]) - Static method in class uk.co.agena.minerva.util.nptgenerator.ProbabilityCalculator
 
main(String[]) - Method in class uk.co.agena.minerva.util.nptgenerator.TNormal
 
MarginalDataItem - Class in uk.co.agena.minerva.model
A MarginalDataItem captures all the marginal information for an ExtendedNode for a given scenario.
MarginalDataItem() - Constructor for class uk.co.agena.minerva.model.MarginalDataItem
 
MarginalDataItem(String) - Constructor for class uk.co.agena.minerva.model.MarginalDataItem
Empty constructor
MarginalDataItemList - Class in uk.co.agena.minerva.model
Stores a List of MarginalDataItems which are cleared & created before a propagation is started.
MarginalDataItemList() - Constructor for class uk.co.agena.minerva.model.MarginalDataItemList
Empty constructor
MarginalDataItemList(ExtendedBN, ExtendedNode) - Constructor for class uk.co.agena.minerva.model.MarginalDataItemList
Empty constructor
MarginalDataStore - Class in uk.co.agena.minerva.model
Stores a map of each ExtendedNode to a MarginalDataItemList object.
mean() - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
 
mean() - Method in class uk.co.agena.minerva.model.extendedbn.NumericalEN
Calculates the mean of the marginals for this ExtendedNode.
median() - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
 
median() - Method in class uk.co.agena.minerva.model.extendedbn.NumericalEN
Calculates the median of the marginals for this ExtendedNode.
merge(MarginalDataStore) - Method in class uk.co.agena.minerva.model.MarginalDataStore
Merges the entries of the specified MarginalDataStore nodeMarginalListMap in to this nodeMarginalListMap.
merge(Model, boolean, boolean, MetaDataItem) - Method in class uk.co.agena.minerva.model.Model
Merges the supplied Model into this one, by adding its Questionnaires, ExtendedBNs, Scenarios and MessagePassingLinks objects.
mergeExtendedStates(int, int) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
mergeExtendedStates(int, int, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
mergeExtendedStates(int, int) - Method in class uk.co.agena.minerva.model.extendedbn.RankedEN
 
MESSAGE_LINK_NAME - Static variable in class uk.co.agena.minerva.model.MessagePassingLinks
Constant used when storing MessagePassingLinks to file.
MESSAGE_PASSING_LINKS_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
messageParseExistsFor(int, int, int, int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Indicates whether a message-passing link exists between the two specified ExtendedNodes (that reside in the two specified ExtendedBNs).
MessagePassingLinkException - Exception in uk.co.agena.minerva.model
Throw when there are problems creating a MessagePassingLink.
MessagePassingLinkException() - Constructor for exception uk.co.agena.minerva.model.MessagePassingLinkException
Constructs an empty MessagePassingLinkException.
MessagePassingLinkException(String) - Constructor for exception uk.co.agena.minerva.model.MessagePassingLinkException
Constructs a MessagePassingLinkException with the specified message.
MessagePassingLinkException(Throwable) - Constructor for exception uk.co.agena.minerva.model.MessagePassingLinkException
Constructs a MessagePassingLinkException with the specified cause.
MessagePassingLinkException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.MessagePassingLinkException
Constructs a MessagePassingLinkException with the specified cause and message.
MessagePassingLinks - Class in uk.co.agena.minerva.model
This class should be used to setup a link between ExtendedNodes of possibly different ExtendedBNs so that message-passing can occur between them.
MessagePassingLinks() - Constructor for class uk.co.agena.minerva.model.MessagePassingLinks
Default constructor.
MessagePassingLinks(int, int, int, int) - Constructor for class uk.co.agena.minerva.model.MessagePassingLinks
Creates a MessagePassingLinks object with one initial link.
META_DATA_ITEMS_REMOVED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
midPoint() - Method in class uk.co.agena.minerva.util.model.Range
Returns the midpoint of the upper and lower bounds
MinervaClassMismatchException - Exception in uk.co.agena.minerva.util.model
Thrown whenever there there is a class mismatch or a class casting problem.
MinervaClassMismatchException() - Constructor for exception uk.co.agena.minerva.util.model.MinervaClassMismatchException
Constructs an empty MinervaClassMismatchException.
MinervaClassMismatchException(String) - Constructor for exception uk.co.agena.minerva.util.model.MinervaClassMismatchException
Constructs a MinervaClassMismatchException with the specified message.
MinervaClassMismatchException(Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaClassMismatchException
Constructs a MinervaClassMismatchException with the specified cause.
MinervaClassMismatchException(String, Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaClassMismatchException
Constructs a MinervaClassMismatchException with the specified cause and message.
MinervaIDException - Exception in uk.co.agena.minerva.util.model
Thrown whenever there are ID errors when using Minerva model classes.
MinervaIDException() - Constructor for exception uk.co.agena.minerva.util.model.MinervaIDException
Constructs an empty MinervaIDException.
MinervaIDException(String) - Constructor for exception uk.co.agena.minerva.util.model.MinervaIDException
Constructs a MinervaIDException with the specified message.
MinervaIDException(Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaIDException
Constructs a MinervaIDException with the specified cause.
MinervaIDException(String, Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaIDException
Constructs a MinervaIDException with the specified cause and message.
MinervaIndexException - Exception in uk.co.agena.minerva.util.model
Throw whenever there are index bounding errors in Minerva model classes.
MinervaIndexException() - Constructor for exception uk.co.agena.minerva.util.model.MinervaIndexException
Constructs an empty MinervaIndexException.
MinervaIndexException(String) - Constructor for exception uk.co.agena.minerva.util.model.MinervaIndexException
Constructs a MinervaIndexException with the specified message.
MinervaIndexException(Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaIndexException
Constructs a MinervaIndexException with the specified cause.
MinervaIndexException(String, Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaIndexException
Constructs a MinervaIndexException with the specified cause and message.
MinervaNumericalMappingException - Exception in uk.co.agena.minerva.util.model
Thrown whenever there are problems mapping between numbers entered as observations and either ranges or point values.
MinervaNumericalMappingException() - Constructor for exception uk.co.agena.minerva.util.model.MinervaNumericalMappingException
Constructs an empty MinervaNumericalMappingException.
MinervaNumericalMappingException(String) - Constructor for exception uk.co.agena.minerva.util.model.MinervaNumericalMappingException
Constructs a MinervaNumericalMappingException with the specified message.
MinervaNumericalMappingException(Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaNumericalMappingException
Constructs a MinervaNumericalMappingException with the specified cause.
MinervaNumericalMappingException(String, Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaNumericalMappingException
Constructs a MinervaNumericalMappingException with the specified cause and message.
MinervaPropagation - Class in uk.co.agena.minerva.model
 
MinervaPropagation(Model) - Constructor for class uk.co.agena.minerva.model.MinervaPropagation
 
MinervaRangeException - Exception in uk.co.agena.minerva.util.model
Thrown whenever there are index range errors in Minerva model classes.
MinervaRangeException() - Constructor for exception uk.co.agena.minerva.util.model.MinervaRangeException
Constructs an empty MinervaRangeException.
MinervaRangeException(String) - Constructor for exception uk.co.agena.minerva.util.model.MinervaRangeException
Constructs a MinervaRangeException with the specified message.
MinervaRangeException(Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaRangeException
Constructs a MinervaRangeException with the specified cause.
MinervaRangeException(String, Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaRangeException
Constructs a MinervaRangeException with the specified cause and message.
MinervaReadWriteException - Exception in uk.co.agena.minerva.util.model
Thrown whenever there are problems reading or writing Writable objects.
MinervaReadWriteException() - Constructor for exception uk.co.agena.minerva.util.model.MinervaReadWriteException
Constructs an empty MinervaReadWriteException.
MinervaReadWriteException(String) - Constructor for exception uk.co.agena.minerva.util.model.MinervaReadWriteException
Constructs a MinervaReadWriteException with the specified message.
MinervaReadWriteException(Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaReadWriteException
Constructs a MinervaReadWriteException with the specified cause.
MinervaReadWriteException(String, Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaReadWriteException
Constructs a MinervaReadWriteException with the specified cause and message.
MinervaVariableException - Exception in uk.co.agena.minerva.util.model
Thrown whenever there are problems e.g.
MinervaVariableException() - Constructor for exception uk.co.agena.minerva.util.model.MinervaVariableException
Constructs an empty MinervaVariableException.
MinervaVariableException(String) - Constructor for exception uk.co.agena.minerva.util.model.MinervaVariableException
Constructs a MinervaVariableException with the specified message.
MinervaVariableException(Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaVariableException
Constructs a MinervaVariableException with the specified cause.
MinervaVariableException(String, Throwable) - Constructor for exception uk.co.agena.minerva.util.model.MinervaVariableException
Constructs a MinervaVariableException with the specified cause and message.
mode() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Calculates the mode of the marginals for this ExtendedNode.
Model - Class in uk.co.agena.minerva.model
This class encapsulates all of the ExtendedBNs, Scenarios and Questionnaires in an application and mediates all interaction between them.
Model() - Constructor for class uk.co.agena.minerva.model.Model
Default constructor.
model - Variable in class uk.co.agena.minerva.model.Propagation
This is the Model on which to do the propagation.
ModelAdapter - Class in uk.co.agena.minerva.model
Defines an adapter for Models.
ModelAdapter() - Constructor for class uk.co.agena.minerva.model.ModelAdapter
 
modelChanged(ModelEvent) - Method in class uk.co.agena.minerva.model.DynDiscPropagation
 
modelChanged(ModelEvent) - Method in class uk.co.agena.minerva.model.MarginalDataStore
 
modelChanged(ModelEvent) - Method in class uk.co.agena.minerva.model.ModelAdapter
 
modelChanged(ModelEvent) - Method in interface uk.co.agena.minerva.model.ModelListener
Called whenever a Model changes.
ModelEvent - Class in uk.co.agena.minerva.model
A list of the model event types, including the contents of the array passed as part of the event ------------------------------------------------------------------------------------------ QUESTIONNAIRE_REMOVED array(0) = The questionaire that was removed ------------------------------------------------------------------------------------------ EXTENDEDBN_NAME_CHANGED array(0) = ExtendedBNEvent ------------------------------------------------------------------------------------------ SCENERIO ATTRIBUTE CHANGED EVENT array(0) = ScenarioEvent array(1) = Integer (class version): attribute that changed (constants available in the ScenarioEvent class) ------------------------------------------------------------------------------------------ EXTENDEDNODE_ATTRIBUTE_CHANGED EVENT array(0) = Extended Node event ------------------------------------------------------------------------------------------ QUESTION_ATTRIBUTE_CHANGED EVENT array(0) = Question event ------------------------------------------------------------------------------------------ EXTENDEDNODE_CLONED EVENT array(0) = Orginal node array(1) = new cloned node ------------------------------------------------------------------------------------------ EXTENDED_NODES_DELETED array(0..X) = List of nodes that were deleted ------------------------------------------------------------------------------------------ QUESTION_REMOVED array(0) = Question removed event array(1) = List of removed questions ------------------------------------------------------------------------------------------ QUESTION_ADDED array(0) = List of the new questions added ------------------------------------------------------------------------------------------ EXTENDEDBNS_REMOVED array(0) = A List of the extended Bns that were removed ------------------------------------------------------------------------------------------ SCENARIOS_IMPORTED array(0) = List containing two items.
ModelEvent(Model) - Constructor for class uk.co.agena.minerva.model.ModelEvent
Constructs a new ModelEvent relating to the supplied Model.
ModelEvent(Model, int) - Constructor for class uk.co.agena.minerva.model.ModelEvent
Constructs a new ModelEvent relating to the supplied Model.
ModelEvent(Model, int, List) - Constructor for class uk.co.agena.minerva.model.ModelEvent
Constructs a new ModelEvent relating to the supplied Model.
ModelEvent(Model, String, boolean) - Constructor for class uk.co.agena.minerva.model.ModelEvent
Constructs a new ModelEvent relating to the supplied Model, with the supplied error information.
ModelException - Exception in uk.co.agena.minerva.model
Throw when there are problems using more than one component of the Minerva model in conjunction.
ModelException() - Constructor for exception uk.co.agena.minerva.model.ModelException
Constructs an empty ModelException.
ModelException(String) - Constructor for exception uk.co.agena.minerva.model.ModelException
Constructs a ModelException with the specified message.
ModelException(Throwable) - Constructor for exception uk.co.agena.minerva.model.ModelException
Constructs a ModelException with the specified cause.
ModelException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.ModelException
Constructs a ModelException with the specified cause and message.
modelInconsistentEvidencePropagated(ModelEvent) - Method in class uk.co.agena.minerva.model.MarginalDataStore
 
modelInconsistentEvidencePropagated(ModelEvent) - Method in class uk.co.agena.minerva.model.ModelAdapter
 
modelInconsistentEvidencePropagated(ModelEvent) - Method in interface uk.co.agena.minerva.model.ModelListener
Called whenever inconsistent evidence is propagated in one of the ExtendedBNs in a Model.
modelInconsistentEvidencePropagated(ModelEvent) - Method in class uk.co.agena.minerva.model.Propagation
 
ModelListener - Interface in uk.co.agena.minerva.model
Defines a listener for ModelEvents.
ModelNotFoundException - Exception in uk.co.agena.minerva.model
Throw when the requested Model is not found.
ModelNotFoundException() - Constructor for exception uk.co.agena.minerva.model.ModelNotFoundException
Constructs an empty ModelNotFoundException.
ModelNotFoundException(String) - Constructor for exception uk.co.agena.minerva.model.ModelNotFoundException
Constructs a ModelNotFoundException with the specified message.
ModelNotFoundException(Throwable) - Constructor for exception uk.co.agena.minerva.model.ModelNotFoundException
Constructs a ModelNotFoundException with the specified cause.
ModelNotFoundException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.ModelNotFoundException
Constructs a ModelNotFoundException with the specified cause and message.
modelPropagationFinished(ModelEvent, boolean) - Method in class uk.co.agena.minerva.model.DynDiscPropagation
 
modelPropagationFinished(ModelEvent, boolean) - Method in class uk.co.agena.minerva.model.MarginalDataStore
 
modelPropagationFinished(ModelEvent, boolean) - Method in class uk.co.agena.minerva.model.ModelAdapter
 
modelPropagationFinished(ModelEvent, boolean) - Method in interface uk.co.agena.minerva.model.ModelListener
Called whenever the propagation has finished.
modelPropagationStarting(ModelEvent) - Method in class uk.co.agena.minerva.model.DynDiscPropagation
 
modelPropagationStarting(ModelEvent) - Method in class uk.co.agena.minerva.model.MarginalDataStore
 
modelPropagationStarting(ModelEvent) - Method in class uk.co.agena.minerva.model.ModelAdapter
 
modelPropagationStarting(ModelEvent) - Method in interface uk.co.agena.minerva.model.ModelListener
Called whenever the propagation is about to start.
MODELS_MERGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
MODIFICATION_LOGS_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
ModificationLog - Class in uk.co.agena.minerva.util.model
 
ModificationLog() - Constructor for class uk.co.agena.minerva.util.model.ModificationLog
empty constructor
ModificationLog.ModificationLogItem - Class in uk.co.agena.minerva.util.model
Inner class for the items which go into the modification log
ModificationLog.ModificationLogItem(NameDescription) - Constructor for class uk.co.agena.minerva.util.model.ModificationLog.ModificationLogItem
Basic constructor

N

name - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
The name of the ExtendedNode.
Nameable - Interface in uk.co.agena.minerva.util.model
Nameable objects have a NameDescription
NameDescription - Class in uk.co.agena.minerva.util.model
The NameDescription class is used to encapsulate name and description information for objects in Minerva.
NameDescription() - Constructor for class uk.co.agena.minerva.util.model.NameDescription
Default constructor.
NameDescription(String, String) - Constructor for class uk.co.agena.minerva.util.model.NameDescription
Constructs a NameDescription with the specified short and long descriptions.
NAMEDESCRIPTION_NAME_CHANGED - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
NamedFamilyMember - Interface in uk.co.agena.minerva.util.model
 
NEGATIVE_STATE_NAMES - Static variable in class uk.co.agena.minerva.model.extendedbn.BooleanEN
List of possible negative names for Boolean states.
NegativeBinomial - Class in uk.co.agena.minerva.util.nptgenerator
 
NegativeBinomial(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.NegativeBinomial
 
NegativeBinomial(List, int, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.NegativeBinomial
calculates the NegativeBinomial over a defined set of ranges given a mean and a variance.
NEW_LINE_REPLACEMENT - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
When saving the parameters of an expression it is not possible to save user entered new lines as these adversly affect subsequent loading of the expression.
NEWLINE - Static variable in class uk.co.agena.minerva.util.nptgenerator.Function
 
next() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Increments the iterator counter.
NODE_EDGE_ADDED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
NODE_ENTROPY_CONVERGENCE_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
NODE_NPT_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
NODE_STATES_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
NODE_TYPE_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
nodeChanged(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Called whenever a node changes (for selected events)
nodeChanged(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Called whenever a node changes (for selected events)
nodeChanged(ExtendedNodeEvent) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeAdapter
 
nodeChanged(ExtendedNodeEvent) - Method in interface uk.co.agena.minerva.model.extendedbn.ExtendedNodeListener
Called whenever a node changes (for selected events)
NODEEVENT_NODEATTRIBUTECHANGED - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedBNEvent
 
NodeEvidence - Class in uk.co.agena.minerva.model.querymodel
 
NodeEvidence(String, QueryInstance, NodeQueryMapping) - Constructor for class uk.co.agena.minerva.model.querymodel.NodeEvidence
 
NodeQueryMapping - Class in uk.co.agena.minerva.model.querymodel
 
NodeQueryMapping(String, QueryInstance, boolean, String, int) - Constructor for class uk.co.agena.minerva.model.querymodel.NodeQueryMapping
 
Normal - Class in uk.co.agena.minerva.util.nptgenerator
Example use of NPT Generator with Normal Function is as follows for a Given net with parents p1,p2 and p3 of a node named "child": ExtendedBN ebn = (ExtendedBN) this.currentModel.getExtendedBNList().getExtendedBNs().get(0); List possibileNodes = ebn.getExtendedNodes("child"); ContinuousIntervalEN enode = (ContinuousIntervalEN)possibileNodes.get(0); // Upto here we are just getting the Interval Node with name "child" // Now define a Normal on this node with the ExtendedBN and the equation for mean // and variance using the parents names.
Normal(ExtendedNode, List, String[]) - Constructor for class uk.co.agena.minerva.util.nptgenerator.Normal
 
Normal(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Normal
Will Generate a normal using the node and its parent nodes.
Normal(List, double, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.Normal
calculates the normal over a defined set of ranges given a mean and a variance.
normal(double, double, double, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.ProbabilityCalculator
 
normalise() - Method in class uk.co.agena.minerva.util.model.DataSet
Normalises this DataSet that the values of all the DataPoints add up to one.
Note - Class in uk.co.agena.minerva.util.model
Created by IntelliJ IDEA.
Note(String, String) - Constructor for class uk.co.agena.minerva.util.model.Note
 
Note() - Constructor for class uk.co.agena.minerva.util.model.Note
 
Notes - Class in uk.co.agena.minerva.util.model
 
Notes() - Constructor for class uk.co.agena.minerva.util.model.Notes
Empty constructor
NPT_MODE_CHANGED - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
NPTGenerator - Class in uk.co.agena.minerva.util.nptgenerator
This class holds a list of functions for generating an NPT for a node.
NPTGenerator(ExtendedBN, ExtendedNode) - Constructor for class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
 
NPTGeneratorException - Exception in uk.co.agena.minerva.util.nptgenerator
 
NPTGeneratorException() - Constructor for exception uk.co.agena.minerva.util.nptgenerator.NPTGeneratorException
Constructs an empty NPTGeneratorException.
NPTGeneratorException(String) - Constructor for exception uk.co.agena.minerva.util.nptgenerator.NPTGeneratorException
Constructs a NPTGeneratorException with the specified message.
NPTGeneratorException(Throwable) - Constructor for exception uk.co.agena.minerva.util.nptgenerator.NPTGeneratorException
Constructs a NPTGeneratorException with the specified cause.
NPTGeneratorException(String, Throwable) - Constructor for exception uk.co.agena.minerva.util.nptgenerator.NPTGeneratorException
Constructs a NPTGeneratorException with the specified cause and message.
NPTGeneratorInsufficientStateRangeException - Exception in uk.co.agena.minerva.util.nptgenerator
 
NPTGeneratorInsufficientStateRangeException() - Constructor for exception uk.co.agena.minerva.util.nptgenerator.NPTGeneratorInsufficientStateRangeException
Constructs an empty NPTGeneratorInsufficientStateRangeException.
NPTGeneratorInsufficientStateRangeException(String) - Constructor for exception uk.co.agena.minerva.util.nptgenerator.NPTGeneratorInsufficientStateRangeException
Constructs a NPTGeneratorInsufficientStateRangeException with the specified message.
NPTGeneratorInsufficientStateRangeException(Throwable) - Constructor for exception uk.co.agena.minerva.util.nptgenerator.NPTGeneratorInsufficientStateRangeException
Constructs a NPTGeneratorInsufficientStateRangeException with the specified cause.
NPTGeneratorInsufficientStateRangeException(String, Throwable) - Constructor for exception uk.co.agena.minerva.util.nptgenerator.NPTGeneratorInsufficientStateRangeException
Constructs a NPTGeneratorInsufficientStateRangeException with the specified cause and message.
NPTGeneratorInsufficientStateRangeException(String, ExtendedNode, double) - Constructor for exception uk.co.agena.minerva.util.nptgenerator.NPTGeneratorInsufficientStateRangeException
Constructs a NPTGeneratorInsufficientStateRangeException with the specified message and set the insufficient range node with out of bounds value on.
nptReCalcRequired - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This is a flag to monitor if the NPT needs to be Re-Calculated at any point in time.
nptSynchronisedWithFormula - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This is a flag to monitor if the npt is correct with respect to the formula entered.
NUM_ITERATIONS_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
NUMERICAL_E_N - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Constant corresponding to the NumericalEN type.
NumericalEN - Class in uk.co.agena.minerva.model.extendedbn
This is an abstract class representing all ExtendedNodes that have numerical states.
NumericalEN() - Constructor for class uk.co.agena.minerva.model.extendedbn.NumericalEN
Default constructor.
NumericalEN(NameDescription, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.NumericalEN
Constructs a NumericalEN with the specified name and connected BN.
NumericalEN(NameDescription, String, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.NumericalEN
Constructs a NumericalEN with the specified name, connected node ID and connected BN.

O

Observation - Class in uk.co.agena.minerva.model.scenario
An Observation stores evidence that has been entered on a node in a BN.
Observation() - Constructor for class uk.co.agena.minerva.model.scenario.Observation
Default constructor.
Observation(int, int, int, DataSet, int, String) - Constructor for class uk.co.agena.minerva.model.scenario.Observation
Creates a fully specified Observation.
Observation(int, int, int, DataSet, int, String, String, int) - Constructor for class uk.co.agena.minerva.model.scenario.Observation
Creates a fully specified Observation including unique ID of connected node and number of states of connected node.
OBSERVATION_ADDED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
OBSERVATION_REMOVED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
OBSERVATION_TYPE_EXPRESSION_VARIABLE - Static variable in class uk.co.agena.minerva.model.scenario.Observation
 
OBSERVATION_TYPE_LONG_ANSWER - Static variable in class uk.co.agena.minerva.model.scenario.Observation
Represents an Observation that has been made using the long name of an Answer.
OBSERVATION_TYPE_NUMERIC - Static variable in class uk.co.agena.minerva.model.scenario.Observation
Represents an Observation that has been made using a numerical value.
OBSERVATION_TYPE_SHORT_ANSWER - Static variable in class uk.co.agena.minerva.model.scenario.Observation
Represents an Observation that has been made using the short name of an Answer.
ObservationNotDirectException - Exception in uk.co.agena.minerva.model.scenario
Thrown whenever an Observation is incorrectly treated as direct.
ObservationNotDirectException() - Constructor for exception uk.co.agena.minerva.model.scenario.ObservationNotDirectException
Constructs an empty ObservationNotDirectException.
ObservationNotDirectException(String) - Constructor for exception uk.co.agena.minerva.model.scenario.ObservationNotDirectException
Constructs an ObservationNotDirectException with the specified message.
ObservationNotDirectException(Throwable) - Constructor for exception uk.co.agena.minerva.model.scenario.ObservationNotDirectException
Constructs an ObservationNotDirectException with the specified cause.
ObservationNotDirectException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.scenario.ObservationNotDirectException
Constructs an ObservationNotDirectException with the specified cause and message.
ObservationNotFoundException - Exception in uk.co.agena.minerva.model.scenario
Thrown whenever a requested Observation is not found in a Scenario or List.
ObservationNotFoundException() - Constructor for exception uk.co.agena.minerva.model.scenario.ObservationNotFoundException
Constructs an empty ObservationNotFoundException.
ObservationNotFoundException(String) - Constructor for exception uk.co.agena.minerva.model.scenario.ObservationNotFoundException
Constructs an ObservationNotFoundException with the specified message.
ObservationNotFoundException(Throwable) - Constructor for exception uk.co.agena.minerva.model.scenario.ObservationNotFoundException
Constructs an ObservationNotFoundException with the specified cause.
ObservationNotFoundException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.scenario.ObservationNotFoundException
Constructs an ObservationNotFoundException with the specified cause and message.
ObservationNotInitialisedException - Exception in uk.co.agena.minerva.model.scenario
Thrown whenever an Observation is queried but has not been initialised with data.
ObservationNotInitialisedException() - Constructor for exception uk.co.agena.minerva.model.scenario.ObservationNotInitialisedException
Constructs an empty ObservationNotInitialisedException.
ObservationNotInitialisedException(String) - Constructor for exception uk.co.agena.minerva.model.scenario.ObservationNotInitialisedException
Constructs an ObservationNotInitialisedException with the specified message.
ObservationNotInitialisedException(Throwable) - Constructor for exception uk.co.agena.minerva.model.scenario.ObservationNotInitialisedException
Constructs an ObservationNotInitialisedException with the specified cause.
ObservationNotInitialisedException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.scenario.ObservationNotInitialisedException
Constructs an ObservationNotInitialisedException with the specified cause and message.
observationsAdded(ScenarioEvent, List, boolean) - Method in class uk.co.agena.minerva.model.Model
Gets the Observations from the supplied ScenarioEvent and enters them into the relevant ExtendedBN.
observationsAdded(ScenarioEvent, List, boolean) - Method in interface uk.co.agena.minerva.model.scenario.ScenarioListener
Invoked whenever an Observation has been added to a Scenario.
observationsRemoved(ScenarioEvent, List, boolean) - Method in class uk.co.agena.minerva.model.Model
Gets the Observations from the supplied ScenarioEvent and removes them from the current relevant ExtendedBNs in the model.
observationsRemoved(ScenarioEvent, List, boolean) - Method in interface uk.co.agena.minerva.model.scenario.ScenarioListener
Invoked whenever an Observation has been removed from a Scenario.
ONLY_PROPAGATE_MODIFIED_EXTENDEDBNS - Static variable in class uk.co.agena.minerva.model.Propagation
Propagation will only deal with ExtendedBN's which have been modified if this flag is true.

P

pad(double, int, String, int) - Method in class uk.co.agena.minerva.util.model.DataSet
Creates multiple identical DataPoints and adds them to this DataSet.
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Arithmetic
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Beta
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Binomial
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.ChiSquared
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Comparative
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Exponential
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.ExtremeValue
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Gamma
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Geometric
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Hypergeometric
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Logistic
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.LogNormal
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.NegativeBinomial
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Normal
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Poisson
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Student
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.TNormal
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Triangle
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Uniform
 
parameterDisplayNames - Static variable in class uk.co.agena.minerva.util.nptgenerator.Weibull
 
PARENT_ADDED - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
parseNodeMapping(ClassQueryModel, XmlHelper) - Static method in class uk.co.agena.minerva.model.querymodel.NodeQueryMapping
 
paste(List, List, ExtendedBN, String, Map) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Based on the specified List of ExtendedNodes and List of connections between these nodes this method creates clones of the ExtendedNodes and adds them to the ExtendedBN with the required connections between the cloned nodes.
pathToRoot() - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
Returns the object path between this node and the root node.
percentile(double) - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
 
percentile(double) - Method in class uk.co.agena.minerva.model.extendedbn.NumericalEN
Calculates the specified percentile of the marginals for this ExtendedNode.
performSplit(Range, int) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
performSplit(Range, int) - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
 
Poisson - Class in uk.co.agena.minerva.util.nptgenerator
 
Poisson(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Poisson
 
Poisson(List, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.Poisson
calculates the poisson over a defined set of ranges given a mean.
populateStateCombinationArray(int[][], int, List) - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
Builds up an array of ints that can be used to uniquly represent each possible state combination for all the specifed parents.
POSITIVE_STATE_NAMES - Static variable in class uk.co.agena.minerva.model.extendedbn.BooleanEN
List of possible positive names for Boolean states.
printJunctionTreeReport() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
PRIORITY_HIGH - Static variable in class uk.co.agena.minerva.model.MessagePassingLinks
Constant used to indicate high priority.
PRIORITY_LOW - Static variable in class uk.co.agena.minerva.model.MessagePassingLinks
Constant used to indicate low priority.
PRIORITY_MEDIUM - Static variable in class uk.co.agena.minerva.model.MessagePassingLinks
Constant used to indicate medium priority.
PRIORITY_VERY_HIGH - Static variable in class uk.co.agena.minerva.model.MessagePassingLinks
Constant used to indicate very high priority.
PRIORITY_VERY_LOW - Static variable in class uk.co.agena.minerva.model.MessagePassingLinks
Constant used to indicate very low priority.
ProbabilityCalculator - Class in uk.co.agena.minerva.util.nptgenerator
Temporary Class used to test various Probability Distibution Calculators using the Colt API.
ProbabilityCalculator() - Constructor for class uk.co.agena.minerva.util.nptgenerator.ProbabilityCalculator
 
PROBS_NOT_EDITABLE - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
If the ExtendedNode's functionMode has this value, its probability values cannot be edited at all.
processExtraFields(StringTokenizer, double) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
processExtraFields(StringTokenizer, double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This should be overridden by any subclass of ExtendedNode that has additional fields that need to be read in.
progress - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Represnts the length of the operation which is currently being monitored in this class.
progress - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Represnts the length of the operation which is currently being monitored in this class.
progress - Variable in class uk.co.agena.minerva.model.Propagation
Represnts the current progress of any operation which is currently being monitored in this class.
progress - Variable in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
Represnts the current progress of any operation which is currently being monitored in this class.
Progressable - Interface in uk.co.agena.minerva.util.model
Classes in which progress needs to be monitored in any way must implement this class.
PROGRESSABLE_GENERATE_NPT - Static variable in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
To indicate we are monitoring the GenerateNPT operation.
PROGRESSABLE_PASTE - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
To indicate we are monitoring the Paste operation.
PROGRESSABLE_RECALC_NPTS - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
To indicate we are monitoring the ReCalculate all NPT's operation.
progressableTaskDone - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
When set to true the current task being monitored will have been completed.
progressableTaskDone - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
When set to true the current task being monitored will have been completed.
progressableTaskDone - Variable in class uk.co.agena.minerva.model.Propagation
When set to true the current task being monitored will have been completed.
progressableTaskDone - Variable in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
When set to true the current task being monitored will have been completed.
propagate(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Propagates the underlying BN.
propagate(List, List) - Method in class uk.co.agena.minerva.model.Model
This method should be called to propagate the model.
propagateAllExtendedBNs(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Propagates all the ExtendedBNs in the list.
propagateAllExtendedBNs(boolean) - Method in class uk.co.agena.minerva.model.Model
Propagates all ExtendedBNs in this Model's ExtendedBNList.
propagateDDAlgorithm(List) - Method in class uk.co.agena.minerva.model.Model
This method will propagate all extendedBNs as normal.
propagateDDAlgorithm(List, List, boolean, boolean) - Method in class uk.co.agena.minerva.model.Model
This method will be call the DD propagation after deriving which ExtendedBNs to actually propagate dependent on its arguments.
propagateScenario(List, Scenario, boolean, int) - Method in class uk.co.agena.minerva.model.DynDiscPropagation
 
propagateScenario(List, Scenario, boolean, int) - Method in class uk.co.agena.minerva.model.MinervaPropagation
This is the method which does the application of the scenarios.
propagateScenario(List, Scenario, boolean, int) - Method in class uk.co.agena.minerva.model.Propagation
 
Propagation - Class in uk.co.agena.minerva.model
This class encapsulates propagation algorithms in which multiple Scenarios may be applied in different ways to a set of ExtendedBNs over a sequence of time periods.
Propagation(Model) - Constructor for class uk.co.agena.minerva.model.Propagation
Contructs a Propagation object that relates to the specified Model.
Propagation.PropagationEventGenerator - Class in uk.co.agena.minerva.model
The PropagationEventGenerator is used to inform listeners of events relating to propagation.
Propagation.PropagationEventGenerator() - Constructor for class uk.co.agena.minerva.model.Propagation.PropagationEventGenerator
 
PropagationEvent - Class in uk.co.agena.minerva.model
A PropagationEvent encapsulates information about a Model that has changed its state in some way.
PropagationEvent(Object) - Constructor for class uk.co.agena.minerva.model.PropagationEvent
Constructs a new PropagationEvent with the supplied source as its point of origin.
propagationEventGenerator - Variable in class uk.co.agena.minerva.model.Propagation
Event generator used for firing events relating to propagation.
PropagationException - Exception in uk.co.agena.minerva.model
Throw when an error occurs during Propgation
PropagationException() - Constructor for exception uk.co.agena.minerva.model.PropagationException
Constructs an empty PropagationException.
PropagationException(String) - Constructor for exception uk.co.agena.minerva.model.PropagationException
Constructs a PropagationException with the specified message.
PropagationException(Throwable) - Constructor for exception uk.co.agena.minerva.model.PropagationException
Constructs a PropagationException with the specified cause.
PropagationException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.PropagationException
Constructs a PropagationException with the specified cause and message.
propagationIncremented(PropagationEvent, int) - Method in class uk.co.agena.minerva.model.Model
 
propagationIncremented(PropagationEvent, int) - Method in interface uk.co.agena.minerva.model.PropagationListener
Fired whenever a cycle of a Propagation has finished.
PropagationListener - Interface in uk.co.agena.minerva.model
Defines a listener for PropagationEvents.
PropagationTerminatedException - Exception in uk.co.agena.minerva.model
Throw when Propagation is terminated prematurely.
PropagationTerminatedException() - Constructor for exception uk.co.agena.minerva.model.PropagationTerminatedException
Constructs an empty PropagationTerminatedException.
PropagationTerminatedException(String) - Constructor for exception uk.co.agena.minerva.model.PropagationTerminatedException
Constructs a PropagationTerminatedException with the specified message.
PropagationTerminatedException(Throwable) - Constructor for exception uk.co.agena.minerva.model.PropagationTerminatedException
Constructs a PropagationTerminatedException with the specified cause.
PropagationTerminatedException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.PropagationTerminatedException
Constructs a PropagationTerminatedException with the specified cause and message.

Q

QueryException - Exception in uk.co.agena.minerva.model.querymodel
 
QueryException() - Constructor for exception uk.co.agena.minerva.model.querymodel.QueryException
 
QueryException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.querymodel.QueryException
 
QueryException(String) - Constructor for exception uk.co.agena.minerva.model.querymodel.QueryException
 
QueryException(Throwable) - Constructor for exception uk.co.agena.minerva.model.querymodel.QueryException
 
QueryInstance - Class in uk.co.agena.minerva.model.querymodel
A QueryInstance is an instance of a DatabaseQuery.
QueryInstance(DatabaseQuery, String, Object[]) - Constructor for class uk.co.agena.minerva.model.querymodel.QueryInstance
 
QueryObjectNode - Class in uk.co.agena.minerva.model.querymodel
Keeps track of objects created by queries.
QueryObjectNode(StructureElement, String, Object[], QueryObjectNode) - Constructor for class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
QUESTION_ATTRIBUTE_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
QUESTION_REMOVED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
questionAdded(QuestionnaireEvent, Question) - Method in class uk.co.agena.minerva.model.Model
This event is fired whenever a new question is added to the questionnaire
questionEventFired(QuestionnaireEvent, QuestionEvent, int) - Method in class uk.co.agena.minerva.model.Model
This event is fired up to the questionnaire listeners when the questionnaire receives an event from one of its questions.
QUESTIONNAIRE_NAME_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
QUESTIONNAIRE_REMOVED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
questionnaireChanged(QuestionnaireEvent) - Method in class uk.co.agena.minerva.model.Model
Event fired by questionnaires
questionnaireIDChanged(QuestionnaireEvent) - Method in class uk.co.agena.minerva.model.Model
Informs all Observations within this Model when the ID for a connected Questionnaire changes.
QUESTIONNAIRES_ADDED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
QUESTIONNAIRES_REPLACED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
QUESTIONS_ADDED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
questionsRemoved(QuestionnaireEvent, List) - Method in class uk.co.agena.minerva.model.Model
 

R

Range - Class in uk.co.agena.minerva.util.model
This class encapsulates a lower bound and upper bound that together define a numerical range.
Range() - Constructor for class uk.co.agena.minerva.util.model.Range
Creates a new Range.
Range(double, double) - Constructor for class uk.co.agena.minerva.util.model.Range
Creates a new Range with the specified lower and upper bounds.
RANKED_SAMPLE_SIZE_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
RankedEN - Class in uk.co.agena.minerva.model.extendedbn
This class is used to represent nodes whose states are in a ranked order e.g.
RankedEN() - Constructor for class uk.co.agena.minerva.model.extendedbn.RankedEN
Creates a default RankedEN.
RankedEN(NameDescription, String, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.RankedEN
 
RankedEN(NameDescription, CoreBN) - Constructor for class uk.co.agena.minerva.model.extendedbn.RankedEN
 
read(List, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
read(List, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
 
read(List, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
read(List, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
 
read(List, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
 
read(List, int) - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
read(List, int) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
read(List, int) - Method in class uk.co.agena.minerva.model.MarginalDataStore
 
read(List, int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
 
read(List, int) - Method in class uk.co.agena.minerva.model.Model
 
read(List, int) - Method in class uk.co.agena.minerva.model.scenario.Observation
 
read(List, int) - Method in class uk.co.agena.minerva.model.scenario.Scenario
 
read(List, int) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
 
read(List, int) - Method in class uk.co.agena.minerva.util.model.DataPoint
 
read(List, int) - Method in class uk.co.agena.minerva.util.model.DataSet
 
read(List, int) - Method in class uk.co.agena.minerva.util.model.ModificationLog
 
read(List, int) - Method in class uk.co.agena.minerva.util.model.Note
 
read(List, int) - Method in class uk.co.agena.minerva.util.model.Notes
 
read(List, int) - Method in class uk.co.agena.minerva.util.model.Variable
 
read(List, int) - Method in class uk.co.agena.minerva.util.model.VariableList
 
read(List, int) - Method in interface uk.co.agena.minerva.util.model.Writable
 
readRestOfFields(StringTokenizer) - Method in class uk.co.agena.minerva.util.model.DataPoint
 
readRestOfFields(StringTokenizer) - Method in class uk.co.agena.minerva.util.model.IntervalDataPoint
 
readRestOfFields(StringTokenizer) - Method in class uk.co.agena.minerva.util.model.StringDataPoint
 
recalculateConnStateIndices() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
regenerateNPT(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Regenerates the NPT for the supplied node if it has an expression or partitioned expressions defined on it.
regenerateNPT(ExtendedNode, boolean, boolean, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
This method will take the function properties of this node (i.e.
regenerateNPTforEveryExtendedNode(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Re-generates the NPT for every node in every BN using the formulae defined for that node..
regenerateProblemNPTs() - Method in class uk.co.agena.minerva.model.Model
Checks the list of problem nodes and, if there are any, regenerates their NPTs.
reinitialise(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
They will multiply back in all NPTs to build new cliques and sepsets and then message pass to make the BN consistent.
reinitialiseAllExtendedBNs() - Method in class uk.co.agena.minerva.model.Model
Reinitialises all ExtendedBNs in this Model's ExtendedBNList.
reinitiliseAllEvidenceOnAllExtendedBNs(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Re-initlise all ExtendedBNs, that is, multiply back in all their NPTs to build new cliques and sepsets and message pass to make consistent.
removeAllConnBNs() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Removes the CoreBNs connected to each ExtendedBN in the List from memory.
removeAllDataForNode(ExtendedBN, ExtendedNode) - Method in class uk.co.agena.minerva.model.MarginalDataStore
Removes all items in the MDS related to the supplied node.
removeAllExtendedNodes() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Removes all ExtendedNodes from the ExtendedBN's List.
removeAllFurtherSavedPriors(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Reomves the priors stored at the given index and all subsequent priors too.
removeAllMessageParsesBetweenBNs(ExtendedBN, ExtendedBN) - Method in class uk.co.agena.minerva.model.Model
This method removes all MessagePassingLinks objects that exist between the two specified ExtendedBNs.
removeAllMessagePassesForBN(int) - Method in class uk.co.agena.minerva.model.Model
Given the ID of an ExtendedBN, this method will then remove all the MessagePassingLinks objects that are associated with it.
removeAllMessagePassLinks() - Method in class uk.co.agena.minerva.model.Model
Removes all message passing links
removeAllNotes() - Method in class uk.co.agena.minerva.util.model.Notes
Removes all notes from the note collection
removeAllRelatedMessagePassLinks(int, int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Removes all message passing links where the supplied BN/Node ID combination features as child or parent.
removeAllScenarios() - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
Removes all the Scenarios in this ScenarioList.
removeAllTracesOfExtendedNode(ExtendedBN, ExtendedNode) - Method in class uk.co.agena.minerva.model.Model
Removes the supplied ExtendedNode from its ExtendedBN.
removeAllVariables() - Method in class uk.co.agena.minerva.util.model.VariableList
Removes all Variables from the List.
removeCoreBNListeners() - Method in class uk.co.agena.minerva.model.Propagation
Removes this as a Listener to each of the CoreBN's associated with the ExtendedBN's in the current models ExtendedBNList.
removeCrossMDIMessagePassingLinks() - Method in class uk.co.agena.minerva.model.Model
This method will remove all Message Passing links that exist between ExtendedBNs of 2 different Metadataitems.
removeDataPointAtOrderPosition(int) - Method in class uk.co.agena.minerva.util.model.DataSet
Removes the DataPoint at the specified order position in the DataSet.
removeDataSetsForConnObject(int) - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Removes the DataSets associated with the specified connected object ID from this DataSetGrouping.
removeDataSetVars(DataSet) - Method in class uk.co.agena.minerva.util.nptgenerator.ExpressionParser
Removes from the parser variables with names matching those in the supplied List.
removeDataSetWithId(int) - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Removes the DataSets with the specified ID from this DataSetGrouping.
removeExpressionVariable(ExtendedNode, Variable) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Removes the specified Variable from the VariableList of the specified ExtendedNode if it is actually a member that ExtendedNodes VariableList.
removeExpressionVariable(Variable) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Removes the specified Variable from the VariableList if it is a Member of this ExtendedNodes VariableList.
removeExtendedBN(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Removes the ExtendedBN with the supplied ID if it is found.
removeExtendedBNListener(ExtendedBNListener) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Removes an object no longer interested in ExtendedBNEvents from the List of ExtendedBNListeners (actually held by an internal ExtendedBNEventGenerator).
removeExtendedBNs(List, boolean) - Method in class uk.co.agena.minerva.model.Model
Removes a specified ExtendedBN from this Model.
removeExtendedBNs(ExtendedBN, boolean) - Method in class uk.co.agena.minerva.model.Model
Convinence method for the remove extended BNs, takes a single BN, calls the list based remove extended Bns
removeExtendedNode(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Removes the ExtendedNode from the this ExtendedBN.
removeExtendedNodeListener(ExtendedNodeListener) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Removes an object no longer interested in ExtendedNodeEvents from the List of ExtendedNodeListeners (actually held by an internal ExtendedNodeEventGenerator).
removeExtendedState(int) - Method in class uk.co.agena.minerva.model.extendedbn.BooleanEN
 
removeExtendedState(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Removes the ExtendedState with the specified ID from the ExtendedNode's List.
removeExtendedStateListener(ExtendedStateListener) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Removes an object no longer interested in ExtendedStateEvents from the List of ExtendedStateListeners (actually held by an internal ExtendedStateEventGenerator).
removeMessageParseLinks(ExtendedNode, ExtendedNode) - Method in class uk.co.agena.minerva.model.Model
Removes all message parsing links between the specified nodes
removeMessagePassingLinkByIndex(int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
This will remove the message passing links that are located in the argument index.
removeMessagePassLink(int, int, int, int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Removes the first link in this MessagePassingLinks object that has the specified child/parent ExtendedBN/ExtendedNode IDs.
removeMessagePassLink(int, int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Removes all links between the specified ExtendedBNs.
removeMessagePassLink(int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Removes all links involving the specified Extended BN.
removeModelListener(ModelListener) - Method in class uk.co.agena.minerva.model.Model
Removes an object no longer interested in ModelEvents from the List of ModelListeners (actually held by an internal ModelEventGenerator).
removeModificationLogsFoeExBNs(List) - Method in class uk.co.agena.minerva.model.Model
This method will remove the inconsitency logs for the specified BNs
removeNonNumericObservationsForNode(int, int) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
Removes all Non-numeric Observations from any Scenarios that are related to the supplied ExtendedBN and ExtendedNode IDs.
removeNote(Note) - Method in class uk.co.agena.minerva.util.model.Notes
Removes the specified note from the list of notes
removeObservation(Observation, boolean) - Method in class uk.co.agena.minerva.model.scenario.Scenario
This method will remove the specified Observations from the Scenario.
removeObservationsForExtendedBN(int) - Method in class uk.co.agena.minerva.model.scenario.Scenario
This method will remove all the observations from the scenario that are contaiend within the specified extended BN
removeObservationsForExtendedBN(ExtendedBN) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
This method will remove all observations that are connected to the specified extended BN from the scenarios contained within the list.
removeObservationsForNode(int, int, int[], boolean) - Method in class uk.co.agena.minerva.model.scenario.Scenario
This method will remove all Observations in the Scenario that are related to the specified ExtendedNode (determined by its ID, and the ID of the ExtendedBN in which it resides).
removeObservationsForNode(int, int) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
Removes all Observations from any Scenarios that are related to the supplied ExtendedBN and ExtendedNode IDs.
removeObservationsForNodeExpression(int, int, String) - Method in class uk.co.agena.minerva.model.scenario.Scenario
This method will remove all observations for the specified node that have the same parameter name as the one specified in the third argument
removeObservationsForNodeWithParameter(int, int, String) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
This method will remove all observations that are connected to the specified node and have the specified expression name from the scebario list
removePropagationListener(PropagationListener) - Method in class uk.co.agena.minerva.model.Propagation
Removes an object no longer interested in PropagationEvents from the List of PropagationListeners (actually held by an internal PropagationEventGenerator).
removeQuestionnaire(Questionnaire) - Method in class uk.co.agena.minerva.model.Model
This method will remove the selected questionnaire from the model.
removeRelationship(ExtendedNode, ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Removes the CoreBN relationship between the two specified nodes.
removeScenario(Scenario) - Method in class uk.co.agena.minerva.model.Model
 
removeScenario(int) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
Removes the Scenario with the supplied ID if it is found.
removeScenario(Scenario) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
Removes the specified scenario from the model
removeScenarioListener(ScenarioListener) - Method in class uk.co.agena.minerva.model.scenario.Scenario
Removes an object no longer interested in ScenarioEvents from the List of ScenarioListeners (actually held by an internal ScenarioEventGenerator).
removeStringVars(List) - Method in class uk.co.agena.minerva.util.nptgenerator.ExpressionParser
Removes from the parser variables with names matching those in the supplied List.
removeVariable(Variable) - Method in class uk.co.agena.minerva.util.model.VariableList
Removes the specified Variable from the list of Variables if it is a member of the List.
removeVariableVars(List) - Method in class uk.co.agena.minerva.util.nptgenerator.ExpressionParser
Removes from the parser variables with names matching those in the supplied List.
reorderByPriority(List) - Static method in class uk.co.agena.minerva.model.MessagePassingLinks
Takes the supplied list of MessagePassingLinks objects, orders them by priority level and then returns them.
replaceState(int, int) - Method in class uk.co.agena.minerva.model.extendedbn.BooleanEN
Takes the state at the specified index and replaces it with the required number of new states.
replaceState(int, int) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Takes the state at the specified index and replaces it with the required number of new states.
replaceState(int, int, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Takes the state at the specified index and replaces it with the required number of new states.
replaceState(int, int) - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
Takes the state at the specified index and replaces it with the required number of new states.
replaceState(int, int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Takes the state at the specified index and replaces it with the required number of new states.
replaceState(int, int) - Method in class uk.co.agena.minerva.model.extendedbn.LabelledEN
Takes the state at the specified index and replaces it with the required number of new states.
replicateNodeStates(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This method will take the states from the argument extended node and copy them to this node.
replicateNodeStates(ExtendedNode) - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
This method will take the states from the argument extended node and copy them to this node.
reportable - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Whether the ExtendedNode should be reported on.
requiresSampling() - Method in class uk.co.agena.minerva.util.nptgenerator.Function
We can check if this function needs sampling or not by taking each expression and testing to see if it contains the names of any of the parents of this node.
resetAllScenarios() - Method in class uk.co.agena.minerva.model.Model
Removes all Observations from all Scenarios.
resetAllScenarios() - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
Removes all Observations from all Scenarios.
resetModificationLog() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Clears the modification log on the exBN.
resetParserCache() - Static method in class uk.co.agena.minerva.util.nptgenerator.Function
Resets the cache of parsed expressions.
resetProgressableTask() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Should be invoked at the end of the task to reset all required attributes used in the monitoring of the task.
resetProgressableTask() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Should be invoked at the end of the task to reset all required attributes used in the monitoring of the task.
resetProgressableTask() - Method in class uk.co.agena.minerva.model.Propagation
Reset the variables used in the monitoring of the current propagation.
resetProgressableTask() - Method in interface uk.co.agena.minerva.util.model.Progressable
Should be invoked at the end of the task to reset all required attributes used in the monitoring of the task.
resetProgressableTask() - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
Reset the variables used in the monitoring of the current task.
resetRangesNotToBeSplitList() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Clears the list of ranges that should not be split.
restartConnection() - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
restartDataCollectionStore(boolean, List) - Method in class uk.co.agena.minerva.model.Propagation
This method should be called always at the start of the simulate method to restart the data collection store.
restartSavedPriors() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
retractAllEvidence(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Retracts all evidence from the underlying BN.
retractAllEvidence() - Method in class uk.co.agena.minerva.model.Model
Retracts evidence from all ExtendedBNs in this Model.
retractAllEvidenceOnAllExtendedBNs(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Retracts all evidence from all the ExtendedBNs in the list.
revert2savedPrior(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the NPT for the node to the savedPrior at the given index if it exists.
revertAllExtendedBNsToSavedMarginals(int) - Method in class uk.co.agena.minerva.model.Propagation
Returns all ExtendedBNs to a state stored during propagation if there is one.
revertToSavedPriors(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Makes all the relevant nodes revert their priors back to the saved priors at the given index.
rollBackCores() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
This will roll back the cores to their original states and not inform anybosy about it.
rollBackCores() - Method in class uk.co.agena.minerva.model.Propagation
 
rollbackToLastMarginalDataItems() - Method in class uk.co.agena.minerva.model.MarginalDataItemList
This method will replace the current marginal data item with the previous one.
runDataQueries(QueryObjectNode) - Method in class uk.co.agena.minerva.model.querymodel.StructureElement
Runs the data queries used to populate nodes with data.
runStructureQueries() - Method in class uk.co.agena.minerva.model.querymodel.ClassQueryModel
 
runStructureQuery(QueryObjectNode) - Method in class uk.co.agena.minerva.model.querymodel.StructureElement
Builds the object hierarchy using the queries specified in the structure hierarchy.

S

save(String) - Method in class uk.co.agena.minerva.model.Model
Saves the model to the specified file
saveCreationTimestamp(String) - Method in class uk.co.agena.minerva.model.Model
Stores a time stamp in the each of the CoreBN's associated with this model.
savePrior() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Add the current marginals of this node as saved priors (before touchTable or setNPT is called).
Scenario - Class in uk.co.agena.minerva.model.scenario
A Scenario contains a collection of Observations that have been made by a user on an ExtendedBN.
Scenario() - Constructor for class uk.co.agena.minerva.model.scenario.Scenario
Default constructor.
Scenario(NameDescription) - Constructor for class uk.co.agena.minerva.model.scenario.Scenario
Creates a Scenario with the specified name.
SCENARIO_ATTRIBUTE_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
SCENARIO_IMPORT_NODE_NOT_FOUND - Static variable in class uk.co.agena.minerva.model.Model
 
SCENARIO_IMPORT_WRONG_NODE_ID - Static variable in class uk.co.agena.minerva.model.Model
 
SCENARIO_IMPORT_WRONG_STATES_UNWORKABLE - Static variable in class uk.co.agena.minerva.model.Model
 
SCENARIO_IMPORT_WRONG_STATES_WORKABLE - Static variable in class uk.co.agena.minerva.model.Model
 
scenarioAttributeChanged(ScenarioEvent, int) - Method in class uk.co.agena.minerva.model.Model
Fired whenever an attribute of the scenario is modified
scenarioAttributeChanged(ScenarioEvent, int) - Method in interface uk.co.agena.minerva.model.scenario.ScenarioListener
Fired whenever an attribute of the scenario is modified.
ScenarioEvent - Class in uk.co.agena.minerva.model.scenario
ScenarioEvent is used to notify interested parties that a Scenario has changed in some way.
ScenarioEvent(Scenario, List) - Constructor for class uk.co.agena.minerva.model.scenario.ScenarioEvent
Constructs a new ScenarioEvent.
ScenarioException - Exception in uk.co.agena.minerva.model.scenario
Thrown whenever there is a general problem with Scenario.
ScenarioException() - Constructor for exception uk.co.agena.minerva.model.scenario.ScenarioException
Constructs an empty ScenarioException.
ScenarioException(String) - Constructor for exception uk.co.agena.minerva.model.scenario.ScenarioException
Constructs an ScenarioException with the specified message.
ScenarioException(Throwable) - Constructor for exception uk.co.agena.minerva.model.scenario.ScenarioException
Constructs an ScenarioException with the specified cause.
ScenarioException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.scenario.ScenarioException
Constructs an ScenarioException with the specified cause and message.
ScenarioList - Class in uk.co.agena.minerva.model.scenario
This class holds a list of Scenarios.
ScenarioList() - Constructor for class uk.co.agena.minerva.model.scenario.ScenarioList
Creates an empty ScenarioList.
ScenarioList(List) - Constructor for class uk.co.agena.minerva.model.scenario.ScenarioList
Creates a new ScenarioList with the supplied List of Scenarios.
ScenarioListener - Interface in uk.co.agena.minerva.model.scenario
A listener for ScenarioEvents.
ScenarioNotFoundException - Exception in uk.co.agena.minerva.model.scenario
Thrown whenever a requested Scenario is not found in a List.
ScenarioNotFoundException() - Constructor for exception uk.co.agena.minerva.model.scenario.ScenarioNotFoundException
Constructs an empty ScenarioNotFoundException.
ScenarioNotFoundException(String) - Constructor for exception uk.co.agena.minerva.model.scenario.ScenarioNotFoundException
Constructs a ScenarioNotFoundException with the specified message.
ScenarioNotFoundException(Throwable) - Constructor for exception uk.co.agena.minerva.model.scenario.ScenarioNotFoundException
Constructs a ScenarioNotFoundException with the specified cause.
ScenarioNotFoundException(String, Throwable) - Constructor for exception uk.co.agena.minerva.model.scenario.ScenarioNotFoundException
Constructs a ScenarioNotFoundException with the specified cause and message.
SCENARIOS_ADDED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
SCENARIOS_IMPORTED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
SCENARIOS_REMOVED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
SCENARIOS_REPLACED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
setAbsoluteValue(double) - Method in class uk.co.agena.minerva.util.model.AbsoluteDataPoint
Sets the absolute "x" value.
setActOnMarginalsChangedEvent(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setAnswerable(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets whether the ExtendedNode is answerable.
setAttributeChanaged(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
Stores the integer value if the attribute changed event was triggered
setCallSignToUpdateOn(String) - Method in class uk.co.agena.minerva.model.MarginalDataItem
This attribute is matched against the call sign passed during a propagation event invoked by the connected extended BN.
setChangeStatesOnInputNodeIfRequired(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setChildren(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
setChildren(List) - Method in class uk.co.agena.minerva.model.Model
Sets the children for this Model.
setChildren(List) - Method in interface uk.co.agena.minerva.util.model.FamilyMember
Sets the children of this FamilyMember to those in the supplied list of FamilyMembers.
setConfidenceInterval(double) - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
setConnBN(CoreBN) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Sets the connected BN of the ExtendedBN to that specified.
setConnBn(CoreBN) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the underlying BN to which this ExtendedNode is connected.
setConnCoreFileName(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Sets the name of file in which the connected CoreBN is stored.
setConnectableInputNode(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets whether this ExtendedNode is a potential input node.
setConnectableOutputNode(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets whether this ExtendedNode is a potential output node.
setConnectionType(int) - Method in class uk.co.agena.minerva.util.model.Connection
Defines the nature of the connection, which must take one of the constant values defined on this class
setConnExtendedBNId(int) - Method in class uk.co.agena.minerva.model.scenario.Observation
Sets the ID of the ExtendedBN to which the Observation is connected.
setConnExtendedNodeId(int) - Method in class uk.co.agena.minerva.model.scenario.Observation
Sets the ID of the ExtendedNode to which the Observation is connected.
setConnNodeId(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setConnObjectId(int) - Method in class uk.co.agena.minerva.util.model.DataPoint
Sets the connected object ID of the DataPoint to the ID specified.
setConnObjectId(int) - Method in class uk.co.agena.minerva.util.model.DataSet
Sets the connected object ID of the DataSet to the ID specified.
setConnObjectId(int) - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Sets the connected object ID of the DataSetGrouping to the ID specified.
setConnQuestionnaireId(int) - Method in class uk.co.agena.minerva.model.scenario.Observation
Sets the ID of the Questionnaire to which the Observation is connected.
setConnStateIndex(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Sets the index of the underlying state to which this ExtendedState is connected.
setContinueToDynamicallyDiscretise(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
setCoreFilenamesToCoreBNs(Map) - Method in class uk.co.agena.minerva.model.Model
 
setCurrentNodeFunction(ExtendedNodeFunction) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the current node function for this ExtendedNode.
setCurrentParentModelNodeAltId(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setCurrentPartitionedModelNodeFunctions(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setCurrentPartitionedParentModelNodeAltIds(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setCurrentPartitionedParentModelNodes(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setDataPoints(List) - Method in class uk.co.agena.minerva.util.model.DataSet
Assigns a List of DataPoints to the DataSet.
setDataset(DataSet) - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
setDataSet(DataSet) - Method in class uk.co.agena.minerva.model.scenario.Observation
Sets the DataSet containing the actual observation data.
setDataSets(List) - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Assigns the supplied List of DataSets to this DataSetGrouping.
setDataSources(Vector) - Method in class uk.co.agena.minerva.model.querymodel.ClassQueryModel
 
setDdRelativeSumWidthEntropyErrors(double[]) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
setDefaultNodeFunction(ExtendedNodeFunction) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the default node function for this ExtendedNode.
setDefaultParentModelNodeAltId(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setDefaultPartitionedModelNodeFunctions(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setDefaultPartitionedParentModelNodeAltIds(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setDefaultPartitionedParentModelNodes(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setDefaultScenario() - Method in class uk.co.agena.minerva.model.Model
Creates scenarios for each of the metadataitems extendedbns for those which do not have any connected scenarios.
setDefaultValue(double) - Method in class uk.co.agena.minerva.util.model.Variable
 
setDescription(String) - Method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
setDescription(NameDescription) - Method in class uk.co.agena.minerva.util.model.ModificationLog.ModificationLogItem
A description of the change that caused this log to be created
setDisplayNode(FamilyTreeNode) - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
setDisplayOnRiskGraphs(boolean) - Method in class uk.co.agena.minerva.model.scenario.Scenario
 
setDriver(String) - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
setDynamicallyDiscretisable(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
setEntropyConvergenceThreshold(double) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
setEventAttributes(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
setEventAttributes(List) - Method in class uk.co.agena.minerva.model.ModelEvent
 
setEventType(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeEvent
 
setEventType(int) - Method in class uk.co.agena.minerva.model.ModelEvent
 
setExactProbabilityOnState(double) - Method in class uk.co.agena.minerva.util.nptgenerator.Arithmetic
This method is added for http://bugzilla.agena.co.uk/show_bug.cgi?id=2309 It will find the state that has the exact state value (hopefully a discrete point, and enter probability value 1 for it.
setExBN(ExtendedBN) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
setExNode(ExtendedNode) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
setExpression(ExtendedNodeFunction) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the expression on this node.
setExpressionVariableName(String) - Method in class uk.co.agena.minerva.model.scenario.Observation
 
setExpressionVariables(VariableList) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setExtendedBNID(int) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
setExtendedBnList(List) - Method in class uk.co.agena.minerva.model.Model
Sets the ExtendedBNs for this Model.
setExtendedNodeID(int) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
setExtendedNodes(List, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Reinitialises the ExtendedBN's List of ExtendedNodes with those in the supplied List.
setExtendedStates(List, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Reinitialises the ExtendedNode's List of ExtendedStates with those in the supplied List.
setExtendedStates(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setFireUpExtendedNodeEvent(boolean) - Method in class uk.co.agena.minerva.model.Model
 
setForceSampling(boolean) - Method in class uk.co.agena.minerva.util.nptgenerator.Function
 
setFunctionMode(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the function mode of this ExtendedNode.
setFunctions(Function[]) - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
Sets the functions used for this node.
setFunctions(String, List) - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
Convience method, applys the specified function to the NPT generator, using the specified parameters.
setId(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Sets the unique ID of the ExtendedBN to the ID specified.
setId(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the unique ID of the ExtendedNode to the ID specified.
setId(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Sets the unique ID of the ExtendedState to the ID specified.
setId(int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
 
setId(int) - Method in class uk.co.agena.minerva.model.Model
Sets the ID of this Model.
setId(int) - Method in class uk.co.agena.minerva.model.scenario.Observation
Sets the unique ID of the Observation to the ID specified.
setId(int) - Method in class uk.co.agena.minerva.model.scenario.Scenario
Sets the unique ID of the Scenario to the ID specified.
setId(int) - Method in class uk.co.agena.minerva.util.model.DataSet
Sets the unique ID of the DataSet to the ID specified.
setId(int) - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Sets the unique ID of the DataSetGrouping to the ID specified.
setInputNodeReceivedMarginals(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setInputNodeRecivedMarginalsAsEvidence(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setInputNodeRecivedMarginalsAsEvidenceDS(DataSet) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setIntervalLowerBound(double) - Method in class uk.co.agena.minerva.util.model.IntervalDataPoint
Sets the lower bound of the "x" interval.
setIntervalUpperBound(double) - Method in class uk.co.agena.minerva.util.model.IntervalDataPoint
Sets the upper bound of the "x" interval.
setIterationChildExtendedBNId(int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Sets the child ExtendedBN ID at the index specified by the current value of the iterator counter.
setIterationChildExtendedNodeId(int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Sets the child ExtendedNode ID at the index specified by the current value of the iterator counter.
setIterationParentExtendedBNId(int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Sets the parent ExtendedBN ID at the index specified by the current value of the iterator counter.
setIterationParentExtendedNodeId(int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Sets the parent ExtendedNode ID at the index specified by the current value of the iterator counter.
setLabel(String) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
setLabel(String) - Method in class uk.co.agena.minerva.util.model.DataPoint
Sets the label of the DataPoint to the label specified.
setLongDescription(String) - Method in class uk.co.agena.minerva.util.model.NameDescription
Sets the long description of the NameDescription object.
setLowerBound(double) - Method in class uk.co.agena.minerva.util.model.Range
Sets the lower bound.
setMarginalDataStore(MarginalDataStore) - Method in class uk.co.agena.minerva.model.Model
 
setMaximumValueReached(double) - Method in class uk.co.agena.minerva.util.nptgenerator.Function
 
setMdi(MetaDataItem) - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
setMessagePassingLinks(List) - Method in class uk.co.agena.minerva.model.Model
Sets the MessagePassingLinks objects associated with this Model.
setMessagepassingMarkedFlag(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
setMetaData(MetaData) - Method in class uk.co.agena.minerva.model.Model
 
setMetaDataUsed(boolean) - Method in class uk.co.agena.minerva.model.Model
 
setMinimumValueReached(double) - Method in class uk.co.agena.minerva.util.nptgenerator.Function
 
setModel(Model) - Method in class uk.co.agena.minerva.model.MarginalDataStore
 
setModificationItems(List) - Method in class uk.co.agena.minerva.util.model.ModificationLog
A list of the modifications for the log
setName(NameDescription) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Sets the name of the ExtendedBN to the name specified.
setName(NameDescription) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the name of the ExtendedNode to the name specified.
setName(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
 
setName(NameDescription) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Sets the name of the ExtendedState to the name specified.
setName(NameDescription) - Method in class uk.co.agena.minerva.model.Model
Sets the name of this Model.
setName(String) - Method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
setName(String) - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
setName(String) - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
setName(NameDescription) - Method in class uk.co.agena.minerva.model.scenario.Scenario
Sets the name of the Scenario to the name specified.
setName(NameDescription) - Method in class uk.co.agena.minerva.util.model.DataSet
Sets the name of the DataSet to the name specified.
setName(NameDescription) - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Sets the name of the DataSetGrouping to the name specified.
setName(NameDescription) - Method in interface uk.co.agena.minerva.util.model.Nameable
 
setName(String) - Method in class uk.co.agena.minerva.util.model.Variable
 
setNameOfIntervalDataPoint(IntervalDataPoint) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
setNameOfIntervalDataPoint(IntervalDataPoint) - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
 
setNameOfStateUsingRange(ExtendedState, Range) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
setNameOfStateUsingRange(ExtendedState, Range) - Method in class uk.co.agena.minerva.model.extendedbn.IntegerIntervalEN
 
setNd(NameDescription) - Method in class uk.co.agena.minerva.util.model.Note
The name description that holds the contents of the note
setNetFileAestheticData(List) - Method in class uk.co.agena.minerva.model.Model
 
setNotes(Notes) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the note object of the node
setNotes(Notes) - Method in class uk.co.agena.minerva.model.Model
Tne notes set connected to the model
setNPT(double[][], List, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the NPT of the underyling nod ein the CoreBN using the supplied two-dimensional array of probabilities.
setNPT(double[]) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the NPT of a node with no parents.
setNPT(double[][], List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the NPT of a node with parents.
setNPTForSingleModelParentNode(double[][], ExtendedNode, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This is used to set a NPT on this node if the NPT has only been generated for a single parent node as a model node.
setNptReCalcRequired(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This is a flag to monitor if the NPT needs to be Re-Calculated at any point in time.
setNptSynchronisedWithFormula(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setNumericalValue(double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Sets the point value with which this ExtendedState is associated.
setNumExNodeStatesWhenCreated(int) - Method in class uk.co.agena.minerva.model.scenario.Observation
 
setObjectName(String) - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
setOldExtendedBNId(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNEvent
 
setOnlyUpdateOnMatchedCallSign(boolean) - Method in class uk.co.agena.minerva.model.MarginalDataItem
Attribute determines whether an update is only called when the call sign in the propagate event is matched to the call sign in the MDI, or if the uodate occurs on every occassion
setParameters(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
 
setParent(QueryObjectNode) - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
setParentId(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
setParentId(int) - Method in class uk.co.agena.minerva.model.Model
Sets the parent ID of this Model.
setParentId(int) - Method in interface uk.co.agena.minerva.util.model.FamilyMember
Sets the ID of this FamilyMember's parent.
setPartitionedExpressionModelNodes(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the partitioned expression model nodes on this node.
setPartitionedExpressions(List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the partitioned expressions on this node.
setPossibleMaxOrMinVaule(double) - Method in class uk.co.agena.minerva.util.nptgenerator.Function
Given a value this function will test and assign it to the relative Max or Min Value attained for this function.
setPriorityLevel(int) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Sets the current priority level of this MessagePassingLinks object with respect to any other MessagePassingLinks objects that are being navigated.
setProblemNodes(List) - Method in class uk.co.agena.minerva.model.Model
 
setProgressableTaskDone(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
 
setPropagateUsingModelScenarios(boolean) - Method in class uk.co.agena.minerva.model.Model
 
setPropagationAlgorithm(Propagation) - Method in class uk.co.agena.minerva.model.Model
This is the propagation algorithm that will be used for this model.
setPropagationCallSigns(String[]) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Sets the array containing the propagation call signs.
setQueries(Vector) - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
setQuery(String) - Method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
setQuery(DatabaseQuery) - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
setQueryParameters(Object[]) - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
setQuestionnaireList(List) - Method in class uk.co.agena.minerva.model.Model
Sets the Questionnaires for this Model.
setRange(Range) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Sets the Range with which this ExtendedState is associated.
setRankedSampleSize(int) - Static method in class uk.co.agena.minerva.model.extendedbn.RankedEN
 
setRankedSampleSize(int) - Method in class uk.co.agena.minerva.model.Model
 
setReportable(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets whether the ExtendedNode can be reported on or not.
setReportable(boolean) - Method in class uk.co.agena.minerva.model.scenario.Scenario
Flag can be toggled by external objects to determine whether the scenario is reportable (the user is interested in seeing its results).
setSampleSize(int) - Static method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
setSampleSize(int) - Method in class uk.co.agena.minerva.model.Model
 
setSavedPriors(DataSetGrouping) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setScenarioList(List) - Method in class uk.co.agena.minerva.model.Model
Sets this Model's ScenarioList
setScenarioName(String) - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
setScenarios(List) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
Set the list of Scenarios that this holds.
setShortDescription(String) - Method in class uk.co.agena.minerva.util.model.NameDescription
Sets the short description of the NameDescription object.
setSimulationEntropyConvergenceTolerance(double) - Method in class uk.co.agena.minerva.model.Model
 
setSimulationEvidenceTolerancePercent(double) - Method in class uk.co.agena.minerva.model.Model
 
setSimulationLogging(boolean) - Method in class uk.co.agena.minerva.model.Model
 
setSimulationNode(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Sets (or unsets) this node as a simulation node.
setSimulationNoOfIterations(int) - Method in class uk.co.agena.minerva.model.Model
 
setSourceCardinality(Range) - Method in class uk.co.agena.minerva.util.model.Connection
The cardibality attactched to the source of the connection
setStringValue(String) - Method in class uk.co.agena.minerva.util.model.StringDataPoint
 
setStructureElement(StructureElement) - Method in class uk.co.agena.minerva.model.querymodel.QueryObjectNode
 
setStructureQuery(boolean) - Method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
setSubstitution(Substitution) - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
setTargetCardinality(Range) - Method in class uk.co.agena.minerva.util.model.Connection
The cardibality attactched to the target of the connection
setTargetValue(double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the target value for this ExtendedNode.
setTargetValueFromString(String) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Sets the target value of this ContinuousIntervalEN using the supplied String.
setTargetValueFromString(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets the target value using the supplied String.
setTargetValuePresent(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets whether the target value is present or not.
setTemporaryNodeOrderFlag(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setText(String, String) - Method in class uk.co.agena.minerva.util.model.Note
Sets the text in the connected name / description
setTitle(String) - Method in class uk.co.agena.minerva.util.model.ModificationLog
The title of the modification log
setType(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Sets the type of the ExtendedBN to the value specified.
setType(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Sets the type of this ExtendedNodeFunction to the value specified.
setUniform() - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Sets the ExtendedNodeFunction to be a simple Uniform.
setUniformJustSet(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
setUniqueExNodeIdWhenCreated(String) - Method in class uk.co.agena.minerva.model.scenario.Observation
 
setUnmatchedNodeNames(List) - Method in class uk.co.agena.minerva.model.Model
 
setupActionForMarginalsChangedEvent(int, boolean, boolean, boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This configures the ExtendedNode so that it reacts correctly when it receives a MarginalsChangedEvent.
setUpdate(boolean) - Method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
setUpdateOnAllEvidenceRetracted(boolean) - Method in class uk.co.agena.minerva.model.MarginalDataItem
this attribute determines whether the monitors should update when it recieves a all evidence retracted event from the connected extended BN.
setupEntropyErrors(List) - Method in class uk.co.agena.minerva.model.DynDiscPropagation
Ensures that the DD flags are set correctly, and the entropy errors list is empty to start with
setupExpressionVariableNodesFromScenario(Scenario, ExtendedBNList) - Method in class uk.co.agena.minerva.model.Propagation
 
setupMessagePasses(MessagePassingLinks, int, boolean) - Method in class uk.co.agena.minerva.model.Propagation
Sets up parameter passes among ExtendedNodes as defined in the supplied MessagePassingLinks object.
setUpMetaData(MetaData, List, Map) - Method in class uk.co.agena.minerva.model.Model
 
setupNonRecursiveParameterPasses(MessagePassingLinks, int, boolean, boolean, boolean) - Method in class uk.co.agena.minerva.model.Model
Same as setupParameterPasses but only for non recursive links
setupParameterPasses(MessagePassingLinks, int, boolean, boolean, boolean) - Method in class uk.co.agena.minerva.model.Model
Connects the two supplied ExtendedBNs together so that information can be passed between them.
setUpperBound(double) - Method in class uk.co.agena.minerva.util.model.Range
Sets the upper bound.
setupRecursiveParameterPasses(MessagePassingLinks, int, boolean, boolean, boolean) - Method in class uk.co.agena.minerva.model.Model
Same as setupParameterPasses but only for recursive links
setUpScenarios() - Method in class uk.co.agena.minerva.model.Model
Ensures that Scenarios are set up correctly once a Model has been loaded in.
setUrl(String) - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
setUserDefinedRelevantExtendedBNIds(int[]) - Method in class uk.co.agena.minerva.model.scenario.Scenario
Sets the user-defined ExtendedBN IDs that are deemed relevant to this Scenario.
setUserEnteredAnswer(String) - Method in class uk.co.agena.minerva.model.scenario.Observation
Sets the user-entered answer for this Observation.
setUserEnteredAnswerMapping(int) - Method in class uk.co.agena.minerva.model.scenario.Observation
Sets the mapping that is used to interpret the user-entered answer.
setValue(double) - Method in class uk.co.agena.minerva.util.model.DataPoint
Sets the value of the DataPoint to the value specified.
setValue(double) - Method in class uk.co.agena.minerva.util.model.Variable
 
setValueSet(boolean) - Method in class uk.co.agena.minerva.util.model.Variable
 
setVariables(List) - Method in class uk.co.agena.minerva.util.model.VariableList
 
setVersion(double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
setVersion(double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
 
setVersion(double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
setVersion(double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
 
setVersion(double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
 
setVersion(double) - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
setVersion(double) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
setVersion(double) - Method in class uk.co.agena.minerva.model.MarginalDataStore
 
setVersion(double) - Method in class uk.co.agena.minerva.model.MessagePassingLinks
 
setVersion(double) - Method in class uk.co.agena.minerva.model.Model
 
setVersion(double) - Method in class uk.co.agena.minerva.model.scenario.Observation
 
setVersion(double) - Method in class uk.co.agena.minerva.model.scenario.Scenario
 
setVersion(double) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
 
setVersion(double) - Method in class uk.co.agena.minerva.util.model.DataPoint
 
setVersion(double) - Method in class uk.co.agena.minerva.util.model.DataSet
 
setVersion(double) - Method in class uk.co.agena.minerva.util.model.ModificationLog
 
setVersion(double) - Method in class uk.co.agena.minerva.util.model.Note
 
setVersion(double) - Method in class uk.co.agena.minerva.util.model.Notes
 
setVersion(double) - Method in class uk.co.agena.minerva.util.model.Variable
 
setVersion(double) - Method in class uk.co.agena.minerva.util.model.VariableList
 
setVersion(double) - Method in interface uk.co.agena.minerva.util.model.Writable
Sets the version number of the class.
setVisible(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Sets whether the ExtendedNode is visible.
setVisible(boolean) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
Sets whether the ExtendedState is visible.
setVisible(boolean) - Method in class uk.co.agena.minerva.model.MarginalDataItem
This attribute defines whether the results of the marginal data item should be made visible to the user (currently restricted to the visibility of the marginal plot on the monitors)
shiftQuestionnaireInModelList(Questionnaire, Questionnaire, int) - Method in class uk.co.agena.minerva.model.Model
This method will reorder the specified questionnaire in the model list of questionnaires and reorder it in the connected meta data layer
simulate(List, List) - Method in class uk.co.agena.minerva.model.Propagation
Propagates using a given list of scenarios if the model allows this.
simulate(List) - Method in class uk.co.agena.minerva.model.Propagation
 
simulateCheckPoint() - Method in class uk.co.agena.minerva.model.Propagation
This method should be used to check if the marginals have changed from the last propagation, and if it should continue to Dynamically Discretise Nodes before it starts doing so.
SIMULATION_STATUS_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
simulationFinished(PropagationEvent, boolean, List) - Method in class uk.co.agena.minerva.model.Model
 
simulationFinished(PropagationEvent, boolean, List) - Method in interface uk.co.agena.minerva.model.PropagationListener
Fired whenever an execution of a Propagation has finished.
simulationStarted(PropagationEvent) - Method in class uk.co.agena.minerva.model.Model
 
simulationStarted(PropagationEvent) - Method in interface uk.co.agena.minerva.model.PropagationListener
Fired whenever an execution of a Propagation is about to be Started.
size() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Returns the size of the ExtendedBNList.
size() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Returns the number of links stored in this MessagePassingLinks object.
size() - Method in class uk.co.agena.minerva.util.model.DataSet
 
size() - Method in class uk.co.agena.minerva.util.model.Range
Calculates the size of the range.
size() - Method in class uk.co.agena.minerva.util.model.VariableList
Returns the number of Variables in the List.
splitStatesForNodeWithEvidence(ContinuousEN, double, Range, DataSet, int, ExtendedBN) - Method in class uk.co.agena.minerva.model.DynDiscPropagation
AKA Log serach/split This function will split a State into X new States based upon the log of the current States range.
standardDeviation() - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
 
standardDeviation() - Method in class uk.co.agena.minerva.model.extendedbn.NumericalEN
Calculates the standard deviation of the marginals for this ExtendedNode.
startDataCollection(List) - Method in class uk.co.agena.minerva.model.MarginalDataItemList
for each of the scenarios it creates a MarginalDataItem
startDataCollection(boolean, List) - Method in class uk.co.agena.minerva.model.MarginalDataStore
This method will restart the data collections store.
startIterator() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
Starts an iterator for the links in this MessagePassingLinks object.
STAT_SAMPLE_SIZE_CHANGED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
storeFunctionsCorrectly(List, double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Stores the supplied List of functions in their correct fields within the ExtendedNode object.
StringDataPoint - Class in uk.co.agena.minerva.util.model
A DataPoint represents a single numerical value.
StringDataPoint() - Constructor for class uk.co.agena.minerva.util.model.StringDataPoint
Default constructor.
StringDataPoint(String, double, int, String) - Constructor for class uk.co.agena.minerva.util.model.StringDataPoint
Creates a DataPoint with the specified label, connected object ID (e.g.
StringDataPoint(String, int, String) - Constructor for class uk.co.agena.minerva.util.model.StringDataPoint
 
StructureElement - Class in uk.co.agena.minerva.model.querymodel
Reads in a element from an exterprise XML file.
StructureElement(ClassQueryModel, Model, StructureElement, XmlHelper) - Constructor for class uk.co.agena.minerva.model.querymodel.StructureElement
 
Student - Class in uk.co.agena.minerva.util.nptgenerator
 
Student(List, int) - Static method in class uk.co.agena.minerva.util.nptgenerator.Student
calculates the distribution over a defined set of ranges
Student(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Student
 
Substitution - Class in uk.co.agena.minerva.model.querymodel
 
Substitution(XmlHelper) - Constructor for class uk.co.agena.minerva.model.querymodel.Substitution
 
successfulSimulationCompletion - Static variable in interface uk.co.agena.minerva.model.PropagationListener
This boolean should be set to true if the simulation is completed sucessfully, false otherwise.
supportedFunctionTypes - Static variable in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
 
supportedFunctionTypes - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
supportedFunctionTypes - Static variable in class uk.co.agena.minerva.model.extendedbn.RankedEN
 
synchroniseQuestionAnswersToNodeStates(ExtendedBN, ExtendedNode) - Method in class uk.co.agena.minerva.model.Model
This method will locate all questions connected to the specified node, and ensure that if the question is configured to auto synchronise the answers to the states in the connected node then it there is indeed a 1-1 mapping

T

TAB - Static variable in class uk.co.agena.minerva.util.nptgenerator.Function
 
targetValue - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
A threshold value for the node that can be used to represent an upper or lower limit on the node's value about which warning should be given.
targetValuePresent - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
This indicates whether a target value is currently valid for a node.
terminateProgressableTask - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
When set to true the current operation can be cancelled / terminated.
terminateProgressableTask() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Invoked when the user has requested the task to be terminated.
terminateProgressableTask - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
When set to true the current operation can be cancelled/terminated.
terminateProgressableTask() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Invoked when the user has requested the task to be terminated.
terminateProgressableTask - Variable in class uk.co.agena.minerva.model.Propagation
When set to true the current propagation will be terminated/cancelled.
terminateProgressableTask() - Method in class uk.co.agena.minerva.model.Propagation
Stop the current propagation.
terminateProgressableTask() - Method in interface uk.co.agena.minerva.util.model.Progressable
Invoked when the user has requested the task to be terminated.
terminateProgressableTask - Variable in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
When set to true the current propagation will be terminated/cancelled.
terminateProgressableTask() - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
Stop the current progressable task.
TNormal - Class in uk.co.agena.minerva.util.nptgenerator
 
TNormal(ExtendedNode, List, String[]) - Constructor for class uk.co.agena.minerva.util.nptgenerator.TNormal
 
TNormal(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.TNormal
Will Generate a normal using the node and its parent nodes.
TNormal(List, double, double, double, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.TNormal
calculates the normal over a defined set of ranges given a mean and a variance.
toHTMLString(boolean, String) - Method in class uk.co.agena.minerva.util.model.DataPoint
This method will render the data set to an HTML string.
toHTMLString(boolean, boolean, String) - Method in class uk.co.agena.minerva.util.model.DataSet
This method will render the data set to an HTML string.
toIntString() - Method in class uk.co.agena.minerva.util.model.Range
Rounds the range to integers and then represents as a string.
toString() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Returns a String representation of the ExtendedNode.
toString() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
toString() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Returns a String representation of the ExtendedNodeFunction.
toString() - Method in class uk.co.agena.minerva.model.querymodel.DatabaseQuery
 
toString() - Method in class uk.co.agena.minerva.model.querymodel.DataSource
 
toString() - Method in class uk.co.agena.minerva.model.querymodel.QueryInstance
 
toString() - Method in class uk.co.agena.minerva.model.scenario.Scenario
Returns a String representation of this Scenario.
toString() - Method in class uk.co.agena.minerva.util.model.DataPoint
Returns a string representation of the DataPoint in the format: [LABEL] = [VALUE]
toString(String) - Method in class uk.co.agena.minerva.util.model.DataPoint
This method will render the data set to a string.
toString() - Method in class uk.co.agena.minerva.util.model.DataSet
Returns a String representation of the DataSet.
toString(boolean, String) - Method in class uk.co.agena.minerva.util.model.DataSet
This method will format the data set to a sting, it includes line breaks between data points :
toString() - Method in class uk.co.agena.minerva.util.model.DataSetGrouping
Returns a String representation of this DataSetGrouping which consists of its name and String representations of the DataSets contained in it.
toString() - Method in class uk.co.agena.minerva.util.model.IntervalDataPoint
Returns a String representation of the IntervalDataPoint.
toString() - Method in class uk.co.agena.minerva.util.model.ModificationLog.ModificationLogItem
 
toString() - Method in class uk.co.agena.minerva.util.model.ModificationLog
returns the log as a string
toString() - Method in class uk.co.agena.minerva.util.model.NameDescription
Creates a String representation of the NameDescription.
toString() - Method in class uk.co.agena.minerva.util.model.Note
Overrides the to string method and returns the short description of th note
toString() - Method in class uk.co.agena.minerva.util.model.Range
Returns a String representation of the Range in the following format: [LOWERBOUND] - [UPPERBOUND]
toString() - Method in class uk.co.agena.minerva.util.model.StringDataPoint
Returns a string representation of the DataPoint in the format: [LABEL] = [VALUE]
toString() - Method in class uk.co.agena.minerva.util.model.Variable
Creates a String representation of the Variable.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Arithmetic
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Beta
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Binomial
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.ChiSquared
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Comparative
 
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Exponential
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.ExtremeValue
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Function
Default toString method.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Gamma
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Geometric
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Hypergeometric
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Logistic
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.LogNormal
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.NegativeBinomial
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Normal
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Poisson
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Student
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.TNormal
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Triangle
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Uniform
Returns a String representation of the object.
toString() - Method in class uk.co.agena.minerva.util.nptgenerator.Weibull
Returns a String representation of the object.
Triangle - Class in uk.co.agena.minerva.util.nptgenerator
 
Triangle(List, double, double, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.Triangle
 
Triangle(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Triangle
 
truncateStates(double, double) - Method in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
Manipulates the ExtendedStates so that the new first one has the specified lower bound and the last one has the specified upper bound.

U

uk.co.agena.minerva.model - package uk.co.agena.minerva.model
This package contains all the subpackages and classes that are needed for creating Minerva models.
uk.co.agena.minerva.model.extendedbn - package uk.co.agena.minerva.model.extendedbn
This package contains classes that act as an extended "wrapper" around Bayesian Networks.
uk.co.agena.minerva.model.querymodel - package uk.co.agena.minerva.model.querymodel
 
uk.co.agena.minerva.model.scenario - package uk.co.agena.minerva.model.scenario
This package contains classes that encapsulate the evidence that a user enters into an ExtendedBN.
uk.co.agena.minerva.util - package uk.co.agena.minerva.util
This package contains various classes (broken down into four subpackages) that are used throughout Minerva: helper classes, IO classes, domain modelling classes and classes for generating NPTs.
uk.co.agena.minerva.util.model - package uk.co.agena.minerva.util.model
This package contains various common classes that are used to represent domain data in Minerva.
uk.co.agena.minerva.util.nptgenerator - package uk.co.agena.minerva.util.nptgenerator
This package contains classes that can be used for generating NPTs from standard statistical functions and mathematical expressions (e.g.
Uniform - Class in uk.co.agena.minerva.util.nptgenerator
 
Uniform(ExtendedNode, List, String[]) - Constructor for class uk.co.agena.minerva.util.nptgenerator.Uniform
 
Uniform(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Uniform
Will Generate a normal using the node and its parent nodes.
Uniform(List, double, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.Uniform
calculates the normal over a defined set of ranges given a mean and a variance.
uniformJustSet - Variable in class uk.co.agena.minerva.model.extendedbn.ContinuousEN
This flag monitors whether a uniform distribution has just been automatically set on a node after it's type was changed and/or DD was enabled.
unmarkExpressionVariableNodes(Map) - Method in class uk.co.agena.minerva.model.Propagation
 
updateConnNodeId(ExtendedNode, String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Updates the ID of the underlying Core Node for the specified ExtendedNode.
updateConnNodeId(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Updates the ID of the underlying connected node.
updateCurrentProgress(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
Increment the currentProgress by the specified value.
updateCurrentProgress(int) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
Increment the currentProgress by the specified value.
updateCurrentProgress(int) - Method in class uk.co.agena.minerva.model.Propagation
Increment the currentProgress by the specified value.
updateCurrentProgress(int) - Method in class uk.co.agena.minerva.util.nptgenerator.NPTGenerator
Increment the currentProgress by the specified value.
updateCurrentProgressForSimulationNode(ExtendedNode) - Method in class uk.co.agena.minerva.model.DynDiscPropagation
Update the currentProgress after the supplied node has been discritised.
updateDataSet(ExtendedNode) - Method in class uk.co.agena.minerva.model.MarginalDataItem
invoked when a propagation or retraction event (depending on how the data item is set up).
updateExpressionParameterName(int, int, String, String) - Method in class uk.co.agena.minerva.model.scenario.Scenario
This method updates all observatins connected to the specified node with the specified parameter expression name, with the new name of the parameter
updateExpressionVariable(ExtendedNode, Variable, String, double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
For the ExtendedNodes VariableList the specified Variable is updated to have the new Name and Default Value.
updateExpressionVariable(Variable, String, double) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Updates the specified Variable to have the new Name and Default Value.
updateExtendedNodesDuringPasteFollowingCut(List, ExtendedBN, List) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
When ExtendedNodes which have been 'Cut' from another ExtendedBN are being pasted we must remove any references to the ExtendedNodes in the source ExtendedBN and CoreBN.
updateFunctionsParentConnNodeId(String, String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Need to update the Functions in the ExtendedNodeFunction of this node.
updateFunctionType(CoreBN, String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Updated the tyope of function that can be added to this node dependant on the parent configurstion.
UpdateInstance - Class in uk.co.agena.minerva.model.querymodel
A subclass of a QueryInstance used to provide some extra functionality for updates and to override the execute method.
UpdateInstance(DatabaseQuery, String, Object[]) - Constructor for class uk.co.agena.minerva.model.querymodel.UpdateInstance
 
updateNewAndImportedBNsTimestamps(List) - Method in class uk.co.agena.minerva.model.Model
The CoreBN's being added/imported into this model need to have the creation timestamps set to be identical to those CoreBN's currently in the Model.
updateParameterExpressionName(int, int, String, String) - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
This method will update all observations that are connected to the specified parameter in the specified node with the latest name of the parameter
updateParameterStrings(String, String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
Updates the parameter strings with the new function name for the nodes involved.
updateStats(ExtendedNode) - Method in class uk.co.agena.minerva.model.MarginalDataItem
extracts the stats from the connected node if they are available
updateUserDefinedRelevantExtendedBNIds(int, int) - Method in class uk.co.agena.minerva.model.scenario.Scenario
Updates an ExtendedBN ID in the array of relevant ones with the new value.
updateUserDefinedRelevantExtendedBNIds(int[], int[]) - Method in class uk.co.agena.minerva.model.scenario.Scenario
Updated the User defined relevant extended BN ids with the two argument arrays.
updateVariable(Variable, String, double) - Method in class uk.co.agena.minerva.util.model.VariableList
Updates the specified Variable to have the new Name and Default Value that have been specified.
usedInCurrentExpression(String) - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Check the parameters of the current Expression(s) for the occurance of the String s, which must be as a whole word/variable.

V

validateMarginalDataStoreAgainstModel() - Method in class uk.co.agena.minerva.model.MarginalDataStore
This method will validate the marginal data store against the connected model.
value - Variable in class uk.co.agena.minerva.util.model.DataPoint
The actual value encapsulated by this DataPoint.
Variable - Class in uk.co.agena.minerva.util.model
This class encapsulates any data that consists, fundamentally, of a name, a numerical value and a default numerical value.
Variable() - Constructor for class uk.co.agena.minerva.util.model.Variable
Default constructor.
Variable(String, double, double) - Constructor for class uk.co.agena.minerva.util.model.Variable
Creates a fully specified Variable.
Variable(String, double) - Constructor for class uk.co.agena.minerva.util.model.Variable
Creates a Variable with a name and an initial default value.
Variable(String) - Constructor for class uk.co.agena.minerva.util.model.Variable
Creates a Variable with a name and an initial default value and actual value of 0.
VARIABLE_ADDED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
VARIABLE_REMOVED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
VARIABLE_UPDATED - Static variable in class uk.co.agena.minerva.model.ModelEvent
 
VariableList - Class in uk.co.agena.minerva.util.model
This class encapsulates a List of Variables and provides various convenience methods for using the underlying List.
VariableList() - Constructor for class uk.co.agena.minerva.util.model.VariableList
Default Constructor.
variance() - Method in class uk.co.agena.minerva.model.extendedbn.DiscreteRealEN
 
variance() - Method in class uk.co.agena.minerva.model.extendedbn.NumericalEN
Calculates the variance of the marginals for this ExtendedNode.
VARIANCE_MAP - Static variable in class uk.co.agena.minerva.util.nptgenerator.Function
 
version - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
version - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
 
version - Static variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
version - Static variable in class uk.co.agena.minerva.model.MarginalDataItem
 
version - Static variable in class uk.co.agena.minerva.model.MarginalDataItemList
 
version - Static variable in class uk.co.agena.minerva.model.MarginalDataStore
 
version - Static variable in class uk.co.agena.minerva.model.MessagePassingLinks
 
version - Static variable in class uk.co.agena.minerva.model.Model
 
version - Static variable in class uk.co.agena.minerva.model.scenario.Observation
 
version - Static variable in class uk.co.agena.minerva.model.scenario.Scenario
 
version - Static variable in class uk.co.agena.minerva.model.scenario.ScenarioList
 
VERSION - Static variable in class uk.co.agena.minerva.util.BuildInformation
This will be replaced by Ant at build stage; if it is not replaced, then no version number will be returned
version - Static variable in class uk.co.agena.minerva.util.model.DataPoint
 
version - Static variable in class uk.co.agena.minerva.util.model.DataSet
 
version - Static variable in class uk.co.agena.minerva.util.model.ModificationLog
 
version - Static variable in class uk.co.agena.minerva.util.model.Variable
 
visible - Variable in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
Whether the ExtendedNode should be displayed in an application.

W

Weibull - Class in uk.co.agena.minerva.util.nptgenerator
 
Weibull(List, double, double) - Static method in class uk.co.agena.minerva.util.nptgenerator.Weibull
calculates the Distribution over a defined set of ranges given a mean and a variance.
Weibull(ExtendedNode, List, List) - Static method in class uk.co.agena.minerva.util.nptgenerator.Weibull
 
WEIGHTED_FUNCTIONS - Static variable in class uk.co.agena.minerva.util.nptgenerator.Function
 
Writable - Interface in uk.co.agena.minerva.util.model
This interface allows Objects to write themselves out to Strings (and allows Objects to be created from such Strings).
write() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBN
 
write() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedBNList
 
write() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNode
 
write() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedNodeFunction
 
write() - Method in class uk.co.agena.minerva.model.extendedbn.ExtendedState
 
write() - Method in class uk.co.agena.minerva.model.MarginalDataItem
 
write() - Method in class uk.co.agena.minerva.model.MarginalDataItemList
 
write() - Method in class uk.co.agena.minerva.model.MarginalDataStore
 
write() - Method in class uk.co.agena.minerva.model.MessagePassingLinks
 
write() - Method in class uk.co.agena.minerva.model.Model
 
write() - Method in class uk.co.agena.minerva.model.scenario.Observation
 
write() - Method in class uk.co.agena.minerva.model.scenario.Scenario
 
write() - Method in class uk.co.agena.minerva.model.scenario.ScenarioList
 
write() - Method in class uk.co.agena.minerva.util.model.DataPoint
 
write() - Method in class uk.co.agena.minerva.util.model.DataSet
 
write() - Method in class uk.co.agena.minerva.util.model.ModificationLog
 
write() - Method in class uk.co.agena.minerva.util.model.Note
 
write() - Method in class uk.co.agena.minerva.util.model.Notes
 
write() - Method in class uk.co.agena.minerva.util.model.Variable
 
write() - Method in class uk.co.agena.minerva.util.model.VariableList
 
write() - Method in interface uk.co.agena.minerva.util.model.Writable
Writes the object in question to a List of Strings.
writeMarginalsToCSV() - Method in class uk.co.agena.minerva.model.Model
Writes the marginals in the model to a List of CSV strings that can be saved to a file.
writeRestOfFields(StringBuffer) - Method in class uk.co.agena.minerva.util.model.DataPoint
 
writeRestOfFields(StringBuffer) - Method in class uk.co.agena.minerva.util.model.IntervalDataPoint
 
writeRestOfFields(StringBuffer) - Method in class uk.co.agena.minerva.util.model.StringDataPoint
 

X

XmlHelper - Class in uk.co.agena.minerva.model.querymodel
Handles all the tedious XML parsing.
XmlHelper(String) - Constructor for class uk.co.agena.minerva.model.querymodel.XmlHelper
 
XmlHelper(Node) - Constructor for class uk.co.agena.minerva.model.querymodel.XmlHelper
 

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