Index (Algernon API documentation)

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ACTIONS - Variable in class org.algernon.aam.register.RegisterSet: Stack or queue of paths to be followed.
ACTIVATE_BC - Variable in class org.algernon.aam.OpcodeSet
ACTIVATE_BC - Variable in class org.algernon.aam.register.RegisterSet: Activation clause for forward chaining rules.
ACTIVATE_FC - Variable in class org.algernon.aam.OpcodeSet
ACTIVATE_FC - Variable in class org.algernon.aam.register.RegisterSet: Activation clause for backard chaining rules.
ALL_LABEL - Variable in class org.algernon.aam.compile.AlgernonCompiler
ALWAYS - Static variable in class org.algernon.aam.Tracer: A trace level that always prints.
ALWAYS_STRING - Static variable in class org.algernon.aam.Tracer
ANY - Variable in class org.algernon.Algernon: Used when defining a relation, indicates unlimited maximum cardinality.
ANY - Variable in class org.algernon.aam.OpcodeSet
ANY - Static variable in interface org.algernon.kb.AlgernonValueType: The Algernon Value Types All data members in interfaces are implicitly public static final
ANY - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
ANY_TYPE - Variable in class org.algernon.Algernon
APPROVE - Static variable in class org.algernon.app.j2p.gui.J2PAdviceDialog
ASK - Variable in class org.algernon.aam.OpcodeSet
ASK - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
ASK_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
ASK_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
ASK_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
ASK_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
ASSERT - Variable in class org.algernon.aam.OpcodeSet
ASSERT_MODE - Static variable in class org.algernon.aam.compile.AlgernonCompiler
ASSUME - Variable in class org.algernon.aam.OpcodeSet
ActivateBCRules - class org.algernon.aam.opcode.ActivateBCRules.: This class represents an :ACTIVATE-BC-RULES Opcode in the AAM.
ActivateBCRules(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.ActivateBCRules: Create a new AAM :ActivateBCRules Opcode.
ActivateFCRules - class org.algernon.aam.opcode.ActivateFCRules.: This class represents a Test Opcode in the AAM.
ActivateFCRules(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.ActivateFCRules: Create a new AAM :TEST Opcode.
Activation - class org.algernon.datatype.Activation.: This class represents an Activation in the AAM.
Activation(Algernon, Processor, BindingList, int, AlgernonKBSet, Rule, int, LispValue, LispValue) - Constructor for class org.algernon.datatype.Activation: Create a new AAM Activation.
AddAdviceAction - class org.algernon.app.j2p.action.AddAdviceAction.: AddAdviceAction performs the action of adding new advice.
AddAdviceAction(J2PWindow, String, String, KeyStroke, Integer) - Constructor for class org.algernon.app.j2p.action.AddAdviceAction: Creates a new SaveAdviceFileAction.
Advice - class org.algernon.app.j2p.Advice.: Advice reads and writes advice files, as well as transforming slot and class names upon request.
Advice() - Constructor for class org.algernon.app.j2p.Advice: Creates a new advice with default values.
Advice(String) - Constructor for class org.algernon.app.j2p.Advice: Creates a new set of advice from the given file.
AdviceTable - class org.algernon.app.j2p.AdviceTable.: AdviceTable stores information about slots and serves as the Data Model for displaying them in a JTable.
AdviceTable(Java2Protege, Object[]) - Constructor for class org.algernon.app.j2p.AdviceTable
Algernon - class org.algernon.Algernon.: Algernon is an inference engine for knowledge-based systems that use a relational or frame-based system representation system.
Algernon() - Constructor for class org.algernon.Algernon
Algernon(AlgernonKB) - Constructor for class org.algernon.Algernon: Create a new instance of Algernon.
Algernon(AlgernonKBSet) - Constructor for class org.algernon.Algernon: Create a new instance of Algernon.
AlgernonApplication - class org.algernon.app.AlgernonApplication.: AlgernonApplication does...
AlgernonApplication(String, int, int, int, String, String, String) - Constructor for class org.algernon.app.AlgernonApplication
AlgernonClass - interface org.algernon.kb.AlgernonClass.: This defines an interface for an Algernon Class
AlgernonCompiler - class org.algernon.aam.compile.AlgernonCompiler.: This class compiles Algernon expressions into AAM abstract machine opcodes.
AlgernonCompiler(Algernon) - Constructor for class org.algernon.aam.compile.AlgernonCompiler
AlgernonCompilerException - exception org.algernon.exception.AlgernonCompilerException.: This is a generic compiler exception to be thrown by Algernon code.
AlgernonCompilerException(String) - Constructor for class org.algernon.exception.AlgernonCompilerException: Creates a new AlgernonCompilerException
AlgernonCompilerState - class org.algernon.aam.compile.AlgernonCompilerState.: This class holds internal state during compilation.
AlgernonCompilerState(Algernon) - Constructor for class org.algernon.aam.compile.AlgernonCompilerState
AlgernonDataException - exception org.algernon.exception.AlgernonDataException.: This exception indicates a problem in the data or rules.
AlgernonDataException(String) - Constructor for class org.algernon.exception.AlgernonDataException: Creates a new AlgernonDataException
AlgernonEvent - interface org.algernon.kb.event.AlgernonEvent.: User: hewett Date: May 28, 2003 Time: 3:41:16 PM
AlgernonException - exception org.algernon.exception.AlgernonException.: This is a generic exception to be thrown by Algernon code.
AlgernonException(String) - Constructor for class org.algernon.exception.AlgernonException: Creates a new AlgernonException
AlgernonFacet - interface org.algernon.kb.AlgernonFacet.: This defines an interface for an Algernon Facet.
AlgernonFrame - interface org.algernon.kb.AlgernonFrame.: This defines an interface for an Algernon Frame.
AlgernonInstance - interface org.algernon.kb.AlgernonInstance.: This defines an interface for an Algernon Instance.
AlgernonKB - interface org.algernon.kb.AlgernonKB.: This defines an interface for an AlgernonKB.
AlgernonKBSet - class org.algernon.kb.AlgernonKBSet.: AlgernonKBSet is a class that contains a list of KBs and implements methods to be performed on them.
AlgernonKBSet(String, Algernon) - Constructor for class org.algernon.kb.AlgernonKBSet
AlgernonKBSet(AlgernonKB, Algernon) - Constructor for class org.algernon.kb.AlgernonKBSet
AlgernonListener - interface org.algernon.kb.event.AlgernonListener.: User: hewett Date: May 28, 2003 Time: 3:43:53 PM
AlgernonObject - interface org.algernon.kb.AlgernonObject.: This defines an interface for an Algernon Object.
AlgernonProtegeClass - class org.algernon.kb.okbc.protege.AlgernonProtegeClass.: This defines an interface for an AlgernonProtegeKB.
AlgernonProtegeClass(AlgernonProtegeKB, String, AlgernonClass, AlgernonClass) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Creates a new class in Protege, using the metaclass of the given superclass if the metaclass is null.
AlgernonProtegeClass(AlgernonProtegeKB, Cls) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeClass
AlgernonProtegeFacet - class org.algernon.kb.okbc.protege.AlgernonProtegeFacet.: This implements AlgernonFacet for Protege facets.
AlgernonProtegeFacet(AlgernonProtegeKB, String, Facet) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeFacet
AlgernonProtegeFacet(AlgernonProtegeKB, Facet) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeFacet
AlgernonProtegeFrame - class org.algernon.kb.okbc.protege.AlgernonProtegeFrame.: This defines an interface for an AlgernonKB.
AlgernonProtegeFrame(AlgernonProtegeKB, Instance) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeFrame
AlgernonProtegeFrame(AlgernonProtegeKB) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeFrame
AlgernonProtegeInstance - class org.algernon.kb.okbc.protege.AlgernonProtegeInstance.: This implements AlgernonInstance for Protege instances.
AlgernonProtegeInstance(AlgernonProtegeKB, String, AlgernonClass) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeInstance
AlgernonProtegeInstance(AlgernonProtegeKB, Instance) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeInstance
AlgernonProtegeKB - class org.algernon.kb.okbc.protege.AlgernonProtegeKB.: Implements a Protege KB for Algernon.
AlgernonProtegeKB(Algernon) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Creates a new in-memory Protege project.
AlgernonProtegeKB(Algernon, String) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Opens the given Protege project file.
AlgernonProtegeKB(Algernon, KnowledgeBase) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Adds a kb that is already open.
AlgernonProtegeObject - class org.algernon.kb.okbc.protege.AlgernonProtegeObject.: Defines a root object type for Protege objects.
AlgernonProtegeObject(Algernon) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeObject
AlgernonProtegeRelation - class org.algernon.kb.okbc.protege.AlgernonProtegeRelation.: This defines an Algernon relation in Protege.
AlgernonProtegeRelation(AlgernonProtegeKB, String, Object, Integer, Integer, Object, AlgernonRelation) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeRelation
AlgernonProtegeRelation(AlgernonProtegeKB, Slot) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: Creates an AlgernonProtegeRelation from an already-existing slot.
AlgernonProtegeValueType - class org.algernon.kb.okbc.protege.AlgernonProtegeValueType.: Class AlgernonProtegeGenValueType ----------------- This class provides a mapping from Algernon value types to Protege and back.
AlgernonProtegeValueType(Algernon, String, ValueType) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
AlgernonProtegeValueType(Algernon, String, Class) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
AlgernonProtegeValueType(Algernon) - Constructor for class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
AlgernonRelation - interface org.algernon.kb.AlgernonRelation.: This defines an interface for a relation in Algernon.
AlgernonRuntimeException - exception org.algernon.exception.AlgernonRuntimeException.: This is a generic runtime exception to be thrown by Algernon code.
AlgernonRuntimeException(String) - Constructor for class org.algernon.exception.AlgernonRuntimeException: Creates a new AlgernonRuntimeException
AlgernonServer - class org.algernon.server.AlgernonServer.
AlgernonServer(Algernon, int) - Constructor for class org.algernon.server.AlgernonServer: Create a new AlgernonServer.
AlgernonServer.SocketConnectionHandler - class org.algernon.server.AlgernonServer.SocketConnectionHandler.: Socket connection handler runs on its thread to handle one client connection.
AlgernonServer.SocketConnectionHandler(AlgernonServer, Socket) - Constructor for class org.algernon.server.AlgernonServer.SocketConnectionHandler
AlgernonServerAction - class org.algernon.kb.okbc.protege.plugins.action.AlgernonServerAction.: User: hewett Date: Mar 7, 2003 Time: 11:50:02 AM
AlgernonServerAction(AlgernonTab, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.AlgernonServerAction: Calls back to Algernon to reload all rules.
AlgernonSettings - class org.algernon.AlgernonSettings.
AlgernonSettings() - Constructor for class org.algernon.AlgernonSettings
AlgernonStorageCardinalityException - exception org.algernon.exception.AlgernonStorageCardinalityException.: This is an exception thrown at runtime by Algernon code when a cardinality exception prevents a relation from being stored in the KB.
AlgernonStorageCardinalityException(String) - Constructor for class org.algernon.exception.AlgernonStorageCardinalityException: Creates a new AlgernonStorageCardinalityException
AlgernonStorageException - exception org.algernon.kb.AlgernonStorageException.: This exception is thrown when an error occurs during a storage operation.
AlgernonStorageException(String) - Constructor for class org.algernon.kb.AlgernonStorageException: Creates a new AlgernonStorageException.
AlgernonTab - class org.algernon.kb.okbc.protege.plugins.AlgernonTab.: This class is a Protege tab plugin that allows the user to construct and enter Algernon expressions.
AlgernonTab() - Constructor for class org.algernon.kb.okbc.protege.plugins.AlgernonTab
AlgernonTabAction - class org.algernon.kb.okbc.protege.plugins.action.AlgernonTabAction.: Abstract base class used for AlgernonTab actions.
AlgernonTabAction(AlgernonTab, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.AlgernonTabAction: Creates a new Action.
AlgernonValueType - interface org.algernon.kb.AlgernonValueType.: Description of the class
Any - class org.algernon.aam.opcode.Any.: This class represents a Test Opcode in the AAM.
Any(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Any: Create a new AAM :ANY Opcode.
Ask - class org.algernon.aam.opcode.Ask.: This class represents an ASK Opcode in the AAM.
Ask(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Ask: Create a new AAM :ASK Opcode.
AskAction - class org.algernon.kb.okbc.protege.plugins.action.AskAction.: User: hewett Date: Mar 7, 2003 Time: 11:50:02 AM
AskAction(AlgernonTab, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.AskAction: Creates a new AskAction.
Assert - class org.algernon.aam.opcode.Assert.: This class represents a Assert Opcode in the AAM.
Assert(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Assert: Create a new AAM :ASSERT Opcode.
Assume - class org.algernon.aam.opcode.Assume.: This class represents a Test Opcode in the AAM.
Assume(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Assume: Create a new AAM :TEST Opcode.
accept(File) - Method in class org.algernon.app.j2p.gui.ProtegeProjectFileFilter
actionPerformed(ActionEvent) - Method in class org.algernon.app.j2p.action.AddAdviceAction
actionPerformed(ActionEvent) - Method in class org.algernon.app.j2p.action.DeleteAdviceAction
actionPerformed(ActionEvent) - Method in class org.algernon.app.j2p.action.RunConversionAction
actionPerformed(ActionEvent) - Method in class org.algernon.app.j2p.action.SaveAdviceFileAction
actionPerformed(ActionEvent) - Method in class org.algernon.app.j2p.action.SelectAdviceFileAction
actionPerformed(ActionEvent) - Method in class org.algernon.app.j2p.action.SelectAlgernonFileAction
actionPerformed(ActionEvent) - Method in class org.algernon.app.j2p.action.SelectKBFileAction
actionPerformed(ActionEvent) - Method in class org.algernon.app.j2p.action.WriteAlgernonFileAction
actionPerformed(ActionEvent) - Method in class org.algernon.app.j2p.gui.J2PAdviceDialog
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.AlgernonServerAction
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.AskAction
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.ClearAction
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.ClearQueryHistoryAction
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.DeleteAllRulesAction
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.DeleteRulesAction
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.EditPathsAction
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.EditRulesAction
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.LoadAction
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.ReloadAllRulesAction
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.ReloadRulesAction
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.ShowResultAction
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.TellAction
actionPerformed(ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.action.TraceRulesAction
activateClosures(Clause, AlgernonKBSet, int) - Method in class org.algernon.aam.Processor: Activates rule closures from assertions or queries.
add(DefaultMutableTreeNode, J2PFrame) - Method in class org.algernon.app.j2p.FrameTree: Adds the child to the table with the given parent.
add(J2PSlot) - Method in class org.algernon.app.j2p.SlotTable
add(BindingList) - Method in class org.algernon.datatype.BindingList: Adds a new binding list to this list.
addAdvice(String, String, String, String) - Method in class org.algernon.app.Java2Protege: Processes and stores the advice.
addAdvice(String, String, String, String) - Method in class org.algernon.app.j2p.AdviceTable
addBinding(Object, Object) - Method in class org.algernon.datatype.BindingList: Adds a new pair to the binding list.
addChild(Object, Object) - Method in class org.algernon.util.SimpleTree: Adds a child to a node.
addClause(Clause) - Method in class org.algernon.datatype.Path: Adds a clause to the end of the path.
addClosure(Closure) - Method in class org.algernon.Algernon: Adds a closure to the system.
addClosure(Closure) - Method in class org.algernon.aam.Processor: Adds a closure to the system.
addClosure(Closure) - Method in class org.algernon.rule.RuleManager: Adds a closure to the system.
addCommand(LispValue, Command) - Method in class org.algernon.Algernon: Adds a new command to Algernon.
addError(String) - Method in class org.algernon.util.ErrorSet: Adds a new warning to the error set.
addEvaluator(String, ExternalLanguageEvaluator) - Method in class org.algernon.Algernon: Adds a new language evaluator.
addIfNew(BindingList) - Method in class org.algernon.datatype.BindingList: Adds the new bindings to this list if the variable is new.
addKB(AlgernonKB) - Method in class org.algernon.Algernon: Adds a new KB to the list of KBs that Algernon accesses.
addKB(AlgernonKB) - Method in class org.algernon.kb.AlgernonKBSet: Adds a KB to this KBSet.
addKBSet(AlgernonKBSet) - Method in class org.algernon.Algernon: Adds a new AlgernonKBSet to this instantiation of Algernon.
addList(BindingList) - Method in class org.algernon.datatype.BindingSet: Adds a new list to the binding set.
addMouseListenerToHeaderInTable(JTable) - Method in class org.algernon.app.j2p.TableSorter
addNotify() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
addRelation(AlgernonRelation) - Method in interface org.algernon.kb.AlgernonClass: Adds a new relation to this class.
addRelation(AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Adds a new relation to this class.
addRelationValue(AlgernonRelation, Object) - Method in interface org.algernon.kb.AlgernonFrame: Adds the given value to the relation on this Frame.
addRelationValue(AlgernonRelation, Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Adds the given value to the relation on this Frame.
addRule(Rule, AlgernonFrame) - Method in class org.algernon.Algernon: Adds a rule to the system.
addRule(Rule, AlgernonFrame) - Method in class org.algernon.aam.Processor: Adds a new rule.
addRule(Rule) - Method in class org.algernon.rule.RuleManager: Stores one rule of the given direction and type.
addRule(Rule, AlgernonFrame) - Method in class org.algernon.rule.RuleManager: Stores one rule of the given direction and type, associated with the given frame (which should be a class or slot, as appropriate.
addSubClass(J2PClass) - Method in class org.algernon.app.j2p.J2PClass: Adds a subclass
addSuperClass(J2PClass) - Method in class org.algernon.app.j2p.J2PClass: Adds a superclass.
addToActionQueue(Processor, LispValue) - Method in class org.algernon.Algernon: Adds an activation to the action queue.
addToActionQueue(Activation) - Method in class org.algernon.aam.Processor: Forwards to Algernon.
addToCache(Object, Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Adds a pairing of frames to the frame cache.
addToDisplayNameCache(String, AlgernonFrame) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Adds a mapping from a DisplayName to an AlgernonFrame to the display name frame cache.
addWarning(String) - Method in class org.algernon.util.ErrorSet: Adds a new warning to the error set.
algernon - Variable in class org.algernon.test.InitializeAlgernonTwice
append(LispValue) - Method in class org.algernon.aam.register.BindingsRegister: Appends the given value onto the end of the register.
append(LispValue) - Method in class org.algernon.aam.register.GeneralRegister: Appends the given value onto the end of the register.
append(LispValue) - Method in interface org.algernon.aam.register.Register: Appends the given value onto the end of the register.
appendRegisterValue(LispValue, LispValue) - Method in class org.algernon.aam.Processor: Pushes the given value onto the end of the register.
appendRegisterValue(LispValue, LispValue) - Method in class org.algernon.aam.register.RegisterSet: Appends the given value onto the end of the register.
argumentToClass(AlgernonKB, LispValue) - Method in class org.algernon.aam.Opcode: Utility method to convert an argument to an AlgernonClass.
argumentToClass(AlgernonKBSet, LispValue) - Method in class org.algernon.aam.Opcode: Utility method to convert an argument to an AlgernonClass.
argumentToFacet(AlgernonKB, LispValue) - Method in class org.algernon.aam.Opcode: Utility method to convert an argument to an AlgernonFacet.
argumentToFacet(AlgernonKBSet, LispValue) - Method in class org.algernon.aam.Opcode: Utility method to convert an argument to an AlgernonFacet.
argumentToFrame(AlgernonKB, LispValue) - Method in class org.algernon.aam.Opcode: Utility method to convert an argument to an AlgernonFrame.
argumentToFrame(AlgernonKBSet, LispValue) - Method in class org.algernon.aam.Opcode: Utility method to convert an argument to an AlgernonFrame.
argumentToInstance(AlgernonKB, AlgernonClass, LispValue) - Method in class org.algernon.aam.Opcode: Utility method to convert an argument to an AlgernonInstance.
argumentToInstance(AlgernonKB, LispValue) - Method in class org.algernon.aam.Opcode: Utility method to convert an argument to an AlgernonInstance.
argumentToInstance(AlgernonKBSet, LispValue) - Method in class org.algernon.aam.Opcode: Utility method to convert an argument to an AlgernonInstance.
argumentToRelation(AlgernonKB, LispValue) - Method in class org.algernon.aam.Opcode: Utility method to convert an argument to an AlgernonClass.
argumentToRelation(AlgernonKBSet, LispValue) - Method in class org.algernon.aam.Opcode: Utility method to convert an argument to an AlgernonClass.
arrayToString(Object[]) - Static method in class org.algernon.util.StringUtil: Converts an array into a printable string.
ascending - Variable in class org.algernon.app.j2p.TableSorter
ask(String) - Method in class org.algernon.Algernon: Processes the path in QUERY mode.
ask(String, AlgernonKB) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
ask(String, ErrorSet) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
ask(String, AlgernonKB, ErrorSet) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
ask(String, AlgernonKB, ErrorSet, BindingList) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
ask(String, AlgernonKBSet) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
ask(String, AlgernonKBSet, String) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
ask(String, AlgernonKBSet, String, ErrorSet) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
ask(String, AlgernonKBSet, String, ErrorSet, BindingList, AlgernonSettings) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
ask(Path, AlgernonKBSet, String, ErrorSet, BindingList, AlgernonSettings) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
ask(String, Algernon) - Method in class org.algernon.test.MultipleAlgernonObjTestCase: Receives commands strings.
ask(String, Algernon) - Method in class org.algernon.test.SubclassInclusive: Receives commands strings.
askForValue(String, LispValue, Collection) - Method in class org.algernon.Algernon: Requires the user to enter an item from the set of possibleValues.
askYorN(String) - Method in class org.algernon.Algernon: Asks the user to confirm whether the query is true.
ask_testFile - Variable in class org.algernon.test.MiscellanyTest

B

BACKWARD - Variable in class org.algernon.rule.Rule
BACKWARD_CHAIN - Static variable in class org.algernon.rule.RuleManager
BEST_FIRST - Static variable in class org.algernon.Algernon: Controls how the set of activations is processed.
BIND - Variable in class org.algernon.aam.OpcodeSet
BINDINGS - Variable in class org.algernon.aam.register.RegisterSet: Stack of binding lists.
BOOLEAN - Static variable in interface org.algernon.kb.AlgernonValueType
BOOLEAN - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
BOOLEAN_TYPE - Variable in class org.algernon.Algernon
BRANCH - Variable in class org.algernon.aam.OpcodeSet
BRANCH_USER - Variable in class org.algernon.aam.OpcodeSet
BREADTH_FIRST - Static variable in class org.algernon.Algernon: Controls how the set of activations is processed.
BackwardTest - class org.algernon.test.BackwardTest.: Tests basic execution functionality of Algernon.
BackwardTest() - Constructor for class org.algernon.test.BackwardTest
BasicTest - class org.algernon.test.BasicTest.: Tests basic execution functionality of Algernon.
BasicTest() - Constructor for class org.algernon.test.BasicTest
Bind - class org.algernon.aam.opcode.Bind.: This class represents a Test Opcode in the AAM.
Bind(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Bind: Create a new AAM :TEST Opcode.
BindingList - class org.algernon.datatype.BindingList.: This is a list of variable bindings.
BindingList(Algernon) - Constructor for class org.algernon.datatype.BindingList: Create a new BindingList.
BindingList(Algernon, LispValue) - Constructor for class org.algernon.datatype.BindingList: Create a new BindingList from an association list.
BindingSet - class org.algernon.datatype.BindingSet.: This is a set of BindingLists.
BindingSet(Algernon) - Constructor for class org.algernon.datatype.BindingSet: Create a new BindingSet.
BindingSet(Algernon, BindingList) - Constructor for class org.algernon.datatype.BindingSet: Create a new BindingSet containing one binding list.
BindingsRegister - class org.algernon.aam.register.BindingsRegister.: This class represents a register that holds BindingSets in the AAM.
BindingsRegister(Processor, String, RegisterSet) - Constructor for class org.algernon.aam.register.BindingsRegister: Creates a new AAM register that holds a binding set.
Branch - class org.algernon.aam.opcode.Branch.: This class represents a Branch Opcode in the AAM.
Branch(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Branch: Create a new AAM :BRANCH Opcode.
BranchByUser - class org.algernon.aam.opcode.BranchByUser.: This class represents a BranchByUser Opcode in the AAM.
BranchByUser(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.BranchByUser: Create a new AAM :BRANCH Opcode.
bind(LispValue, LispValue, LispValue) - Method in class org.algernon.datatype.BindingSet
bind_testFile - Variable in class org.algernon.test.MiscellanyTest
bindingTerm(LispValue) - Static method in class org.algernon.datatype.BindingSet
bindingVar(LispValue) - Static method in class org.algernon.datatype.BindingSet
bindingsCount() - Method in class org.algernon.datatype.BindingSet: Returns the number of bindings across all binding lists in the set.

C

CANCEL - Static variable in class org.algernon.app.j2p.gui.J2PAdviceDialog
CHILD - Variable in class org.algernon.aam.OpcodeSet
CHILD_ERROR_COLOR - Variable in class org.algernon.app.j2p.J2PFrame
CHILD_ERROR_STRING - Static variable in class org.algernon.app.Java2Protege
CLASS - Variable in class org.algernon.aam.OpcodeSet
CLASS_TYPE - Variable in class org.algernon.Algernon
CLAUSE - Variable in class org.algernon.aam.OpcodeSet
CLAUSE - Variable in class org.algernon.aam.register.RegisterSet: The clause currently being executed.
CLEAR_LABEL_FONT_SIZE - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
CLEAR_QUERY_HISTORY_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
CLEAR_QUERY_HISTORY_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
CLEAR_QUERY_HISTORY_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
CLEAR_QUERY_HISTORY_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
CLEAR_RELATION - Variable in class org.algernon.aam.OpcodeSet
CLEAR_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
CODE - Variable in class org.algernon.aam.register.RegisterSet: Code register (like a Program Counter).
CODE - Static variable in class org.algernon.datatype.Activation
CONJ_BRANCH - Variable in class org.algernon.aam.OpcodeSet
CONJ_CLEAR - Variable in class org.algernon.aam.OpcodeSet
CONTEXT - Variable in class org.algernon.aam.register.RegisterSet: Stack of execution contexts.
CONTINUATION - Variable in class org.algernon.aam.OpcodeSet
CONVERT_TAB_INDEX - Static variable in class org.algernon.app.j2p.gui.J2PWindow
COUNT - Variable in class org.algernon.aam.OpcodeSet
COUNTER - Static variable in class org.algernon.datatype.Closure
CREATE_CLASS - Variable in class org.algernon.aam.OpcodeSet
CREATE_FACET - Variable in class org.algernon.aam.OpcodeSet
CREATE_INSTANCE - Variable in class org.algernon.aam.OpcodeSet
CREATE_RELATION - Variable in class org.algernon.aam.OpcodeSet
CREATE_RULES - Variable in class org.algernon.aam.OpcodeSet
CREATE_SLOT_RULES - Variable in class org.algernon.aam.OpcodeSet
Child - class org.algernon.aam.opcode.Child.: Child expects a clause of the form (:CHILD parent child).
Child(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Child
ClassOp - class org.algernon.aam.opcode.ClassOp.: This class implements the CLASS Opcode in the AAM.
ClassOp(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.ClassOp: Create a new AAM Opcode.
Clause - class org.algernon.aam.opcode.Clause.: This class represents a CLAUSE Opcode in the AAM.
Clause(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Clause: Create a new AAM :CLAUSE Opcode.
Clause - class org.algernon.datatype.Clause.
Clause(Algernon, String) - Constructor for class org.algernon.datatype.Clause: Creates a new clause.
Clause(Algernon, LispValue) - Constructor for class org.algernon.datatype.Clause: Creates a new clause.
ClearAction - class org.algernon.kb.okbc.protege.plugins.action.ClearAction.: Executed when the user presses a CLEAR button for a text component.
ClearAction(JTextComponent, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.ClearAction: Creates a new ClearAction.
ClearQueryHistoryAction - class org.algernon.kb.okbc.protege.plugins.action.ClearQueryHistoryAction.: Action to clear the query history.
ClearQueryHistoryAction(AlgernonTab, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.ClearQueryHistoryAction: Calls back to Algernon to clear the query history in Algernon.
ClearRelation - class org.algernon.aam.opcode.ClearRelation.: This class represents a ClearRelation Opcode in the AAM.
ClearRelation(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.ClearRelation: Create a new AAM :CLEAR-RELATION Opcode.
Closure - class org.algernon.datatype.Closure.: A closure encapsulates a rule that is ready to execute.
Closure(Algernon, Rule, BindingList, AlgernonFrame, LispValue, LispValue) - Constructor for class org.algernon.datatype.Closure
CollectionUtil - class org.algernon.util.CollectionUtil.
CollectionUtil() - Constructor for class org.algernon.util.CollectionUtil
Command - class org.algernon.datatype.Command.: Command represents a user-level command in Algernon.
Command(Algernon, LispValue, Opcode, boolean, boolean, boolean) - Constructor for class org.algernon.datatype.Command: Creates a new command.
Command(Algernon, LispValue, Opcode, boolean, boolean) - Constructor for class org.algernon.datatype.Command: Creates a new command.
ConjunctiveBranch - class org.algernon.aam.opcode.ConjunctiveBranch.: This class represents a ConjunctiveBranch Opcode in the AAM.
ConjunctiveBranch(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.ConjunctiveBranch: Create a new AAM :CONJ-BRANCH Opcode.
ConjunctiveClear - class org.algernon.aam.opcode.ConjunctiveClear.: This class represents a ConjunctiveClear Opcode in the AAM.
ConjunctiveClear(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.ConjunctiveClear: Create a new AAM :CONJ-CLEAR Opcode.
Continuation - class org.algernon.aam.opcode.Continuation.: This class represents a Test Opcode in the AAM.
Continuation(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Continuation: Create a new AAM :TEST Opcode.
Count - class org.algernon.aam.opcode.Count.: This class implements the COUNT Opcode in the AAM.
Count(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Count: Create a new AAM Count Opcode.
CreateClass - class org.algernon.aam.opcode.CreateClass.: This class represents a Test Opcode in the AAM.
CreateClass(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.CreateClass: Create a new AAM :TEST Opcode.
CreateFacet - class org.algernon.aam.opcode.CreateFacet.: This class represents a Test Opcode in the AAM.
CreateFacet(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.CreateFacet: Create a new AAM :TEST Opcode.
CreateInstance - class org.algernon.aam.opcode.CreateInstance.: This class represents a Test Opcode in the AAM.
CreateInstance(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.CreateInstance: Create a new AAM :TEST Opcode.
CreateRelation - class org.algernon.aam.opcode.CreateRelation.: This opcode creates a new relation in the KB..
CreateRelation(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.CreateRelation: Create a new AAM :ADD-Relation Opcode.
CreateRelationRules - class org.algernon.aam.opcode.CreateRelationRules.: This class represents a CreateRelationRules Opcode in the AAM.
CreateRelationRules(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.CreateRelationRules: Create a new AAM :TEST Opcode.
CreateRules - class org.algernon.aam.opcode.CreateRules.: This class represents a CreateRules Opcode in the AAM.
CreateRules(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.CreateRules: Create a new AAM :CREATE-RULES Opcode.
canAssignToValueType(Object, LispValue) - Method in interface org.algernon.kb.AlgernonKB: Check if you can assign an Object o to a slot having a ValueType vt
canAssignToValueType(Object, LispValue) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Check if you can assign a Java Object o to a Protege slot having a ValueType vt
canAssignToValueType(Object, AlgernonValueType) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType: Returns true if the Object o can be assigned to a slot having a ValueType vt.
checkForDuplicateFrames(String) - Method in class org.algernon.app.Java2Protege: Adds an error to classes if they have the same name as the given slot.
checkForObsoleteMacro(LispValue, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: check for obsolete macro - puts a warning message in the error set.
checkModel() - Method in class org.algernon.app.j2p.TableSorter
checkSlotDomainAndRange(J2PSlot) - Method in class org.algernon.app.Java2Protege
childHasError() - Method in class org.algernon.app.j2p.J2PFrame
children() - Method in class org.algernon.app.j2p.J2PClass: Returns an enumeration of the children of this class.
children() - Method in class org.algernon.app.j2p.J2PFrame: Creates and returns a forward-order enumeration of this node's children.
children() - Method in class org.algernon.app.j2p.J2PSlot: Returns an enumeration of the children of this class.
classesToAlgernon(FrameTree, String) - Method in class org.algernon.app.Java2Protege: Creates Algernon taxonomy from stored information about class structure.
clear() - Method in class org.algernon.aam.register.BindingsRegister: Initializes the register contents to NIL.
clear() - Method in class org.algernon.aam.register.GeneralRegister: Initializes the register contents to NIL.
clear() - Method in interface org.algernon.aam.register.Register: Initializes the register contents to an appropriate value, usually NIL or the empty set.
clear() - Method in class org.algernon.app.j2p.FrameTree: Empties the FrameTree.
clear() - Method in class org.algernon.datatype.BindingList: Removes all entries from the Binding List.
clear() - Method in class org.algernon.datatype.BindingSet: Removes all entries from the BindingSet.
clear() - Method in class org.algernon.rule.RuleManager: Removes all rules and rule continuations.
clear() - Method in class org.algernon.util.ErrorSet
clearAllRules() - Method in class org.algernon.Algernon: Removes all known rules and rule continuations.
clearErrors() - Method in class org.algernon.util.ErrorSet
clearHistoricalQueries(LispValue, LispValue) - Method in class org.algernon.aam.Processor: Clears the query history for the given frame and relation.
clearHistoricalQueries() - Method in class org.algernon.aam.Processor: Clears all of the query history.
clearHistoricalQueries(AlgernonFrame) - Method in class org.algernon.aam.Processor: Clears the query history for the given frame.
clearHistoricalQuery(Clause) - Method in class org.algernon.aam.Processor: Clears one query from the history.
clearQueries(LispValue, LispValue) - Method in class org.algernon.aam.QueryHistory
clearQueries(AlgernonFrame) - Method in class org.algernon.aam.QueryHistory
clearQuery(Clause) - Method in class org.algernon.aam.QueryHistory: Clears the query from the history.
clearQueryHistory() - Method in class org.algernon.Algernon: Clears the entire list of historical queries.
clearWarnings() - Method in class org.algernon.util.ErrorSet
close() - Method in interface org.algernon.kb.AlgernonKB: Closes a KB.
close() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Closes a KB.
codeToString(LispValue) - Method in class org.algernon.aam.OpcodeSet: Prints the AAM opcodes as in an assembly language printout to a string.
collectionToNumberedList(Collection) - Static method in class org.algernon.util.CollectionUtil: Returns a numbered, indented list with the values and an index number.
collectionToString(Collection) - Static method in class org.algernon.util.StringUtil: Converts a collection of String into a single comma-delimited string
collectionToString(Collection, String) - Static method in class org.algernon.util.StringUtil
commandList - Variable in class org.algernon.app.j2p.gui.J2PAdviceDialog
compare(int, int) - Method in class org.algernon.app.j2p.TableSorter
compareRowsByColumn(int, int, int) - Method in class org.algernon.app.j2p.TableSorter
compares - Variable in class org.algernon.app.j2p.TableSorter
compile(Path, AlgernonKBSet, int, ErrorSet) - Method in class org.algernon.Algernon: Compiles a path (which may be a rule declaration, a query, an assert or part of a rule) and returns the AAM opcodes for the path.
compile(String, AlgernonKBSet, int, ErrorSet) - Method in class org.algernon.Algernon: Compiles a path (which may be a rule declaration, a query, an assert or part of a rule) and returns the AAM opcodes for the path.
compile(Path, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: Returns a list of AAM machine code to be executed.
compileAssert(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: compile-assert
compileClause(Clause, AlgernonKBSet, int, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: compiles one clause
compileMacro(Clause, AlgernonKBSet, int, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler
compileOpAddClass(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: create a new frame and assert the path for that variable.
compileOpAddInstance(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler
compileOpAllPaths(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler
compileOpAny(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler
compileOpAsk(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler
compileOpCount(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: This compiles the :COUNT macro.
compileOpDelete(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler
compileOpFail(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: This compiles the :FAIL and :UNP macros (which are synonyms of each other).
compileOpFire(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler
compileOpFor(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: This compiles the :FOR macro.
compileOpForcClass(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler
compileOpForcInstance(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler
compileOpLimit(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: This compiles the :LIMIT macro.
compileOpOr(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler
compileOpPrint(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet, boolean) - Method in class org.algernon.aam.compile.AlgernonCompiler: compileOpPrint - compiles the PRINT and PRINTLN macros.
compileOpTheClass(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler
compileOpTheInstance(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler
compilePath(Path, AlgernonKBSet, int, int, BindingList, Map, Rule, AlgernonCompilerState, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: compilePath compiles an Algernon path into abstract machine code.
compilePathAux(Path, AlgernonKBSet, int, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: compilePathAux is an internal routine that compiles a path.
compilePathNoReturn(Path, AlgernonKBSet, int, int, BindingList, Map, Rule, AlgernonCompilerState, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: compilePathAux is an internal routine that compiles a path.
compileQuery(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: compileQuery
compileRule(Rule, AlgernonKBSet) - Method in class org.algernon.Algernon: Compiles the given rule and returns the compiled code.
compileRule(Rule, AlgernonKBSet) - Method in class org.algernon.aam.Processor: Compiles the given rule and returns it.
compileRule(Rule, AlgernonKBSet, BindingList, Map, AlgernonCompilerState, int, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: Compiles a rule.
compileSpecial(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: compileSpecial - general-purpose routine for special MACROS whose details are handled by the opcode.
compileSpecialWithFail(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: compileSpecialWithFail - general-purpose routine for special MACROS that need to check for failure afterward.
compileSpecialWithFailAndMerge(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: compileSpecialWithFailAndMerge - general-purpose routine for special MACROS that need to check for failure afterward.
compileSpecialWithMerge(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: compileSpecialWithMerge - general-purpose routine for special MACROS that need to do a merge-bindings afterward.
compileSubroutine(LispValue, Path, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: compiles a subroutine.
compileVerify(Clause, AlgernonKBSet, int, BindingList, Map, Rule, AlgernonCompilerState, LispValue, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: compileVerify
concatenateStrings(Collection, String) - Static method in class org.algernon.util.StringUtil: Converts the objects in a Collection into strings and concatenates them, with an separator string between the interior divisions.
consolidateBindings(Processor, LispValue, Object) - Method in class org.algernon.aam.opcode.Subroutine: Consolidates a list of results into one binding set.
constantTypeEQ(AlgernonKBSet, LispValue, Set, Clause, AlgernonCompilerState, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler
contains(Clause) - Method in class org.algernon.aam.QueryHistory: Returns true if the QueryHistory contains the query or a generalization of it.
containsClause(Clause, int) - Method in interface org.algernon.kb.AlgernonKB: State is
containsClause(Clause) - Method in class org.algernon.kb.AlgernonKBSet: Returns true if the KBSet contains the given clause.
containsClause(Clause, int) - Method in class org.algernon.kb.AlgernonKBSet: Returns true if the KBSet contains the given clause.
containsClause(Clause, int) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: State is Algernon.NEGATED or something else.
containsVariable(Object) - Method in class org.algernon.datatype.BindingList: Retrieves the binding for a variable.
continuationRuleName(int) - Method in class org.algernon.rule.Rule: Returns a string containing the name of a continuation rule.
continuationRuleName(Rule, int) - Method in class org.algernon.rule.RuleManager: Returns a string containing the name of a continuation rule.
convertFromAlgernon(Collection) - Method in interface org.algernon.kb.AlgernonKB: Converts a collection of Algernon objects to a collection of KB implementation-level objects, if possible.
convertFromAlgernon(Object) - Method in interface org.algernon.kb.AlgernonKB: Converts an Algernon object to an implementation-level object, if possible.
convertFromAlgernon(Collection) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Converts a collection of Algernon objects to a collection of Protege objects, if possible.
convertFromAlgernon(Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Converts an Algernon object to a Protege object, if possible.
convertRelationRange(Class, String, Class) - Method in class org.algernon.app.Java2Protege: Converts a Java type to a Protege type.
convertToAlgernon(Collection) - Method in interface org.algernon.kb.AlgernonKB: Converts a collection of KB objects to a collection of Algernon objects, if possible.
convertToAlgernon(Object) - Method in interface org.algernon.kb.AlgernonKB: Converts a KB object to an Algernon object, if possible.
convertToAlgernon(Collection) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Converts a collection of Protege objects to a collection of Algernon objects, if possible.
convertToAlgernon(Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Converts a Protege object to a ProtegeAlgernon object, if possible.
convertToAlgernonValueType(Object) - Method in interface org.algernon.kb.AlgernonValueType: Convert a given value type (such as Protege's ValueType) to an AlgernonValueType.
convertToAlgernonValueType(Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType: Convert a given value type (such as Protege's ValueType) to an AlgernonValueType.
copy() - Method in class org.algernon.aam.Processor: Returns a new processor that contains the same global variable bindings as this one.
copy() - Method in class org.algernon.aam.compile.AlgernonCompilerState
copyBindingList() - Method in class org.algernon.datatype.BindingList: Copys this binding list and returns a new one.
copyClause() - Method in class org.algernon.datatype.Clause: Returns a new clause that is a copy of this one.
countNameUses(String) - Method in class org.algernon.app.Java2Protege: Returns the number of times the name is used.
count_testFile - Variable in class org.algernon.test.MiscellanyTest
createAdviceTable() - Method in class org.algernon.app.Java2Protege
createButtons() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
createClass(String, AlgernonClass) - Method in interface org.algernon.kb.AlgernonKB: Creates a new frame in the storage.
createClass(String, AlgernonClass, AlgernonClass) - Method in interface org.algernon.kb.AlgernonKB: Creates a new frame in the storage.
createClass(LispValue, AlgernonClass) - Method in class org.algernon.kb.AlgernonKBSet: Creates a new class in the given KB.
createClass(AlgernonKB, LispValue, AlgernonClass) - Method in class org.algernon.kb.AlgernonKBSet: Creates a new class in the given KB.
createClass(String, AlgernonClass) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Creates a new frame in the storage.
createClass(String, AlgernonClass, AlgernonClass) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Creates a new frame in the storage.
createClassDataStructures(SimpleTree) - Method in class org.algernon.app.Java2Protege: Creates the data structures for storing potential classes.
createClassDataStructuresAux(Class, J2PClass, SimpleTree) - Method in class org.algernon.app.Java2Protege: Recursive method to create class and subclass data structures.
createFacet(String) - Method in interface org.algernon.kb.AlgernonKB: Creates a new facet in the storage.
createFacet(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Creates a new facet in the storage.
createHelpTab() - Method in class org.algernon.app.j2p.gui.J2PWindow: Creates the Help Tab
createInputArea() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
createInstance(LispValue, AlgernonClass) - Method in class org.algernon.aam.Processor: Forwards to the current KBSet.
createInstance(String) - Method in interface org.algernon.kb.AlgernonClass: Creates an instance with the given name.
createInstance(String, String) - Method in interface org.algernon.kb.AlgernonClass: Creates an instance with the given name and stores the "pretty" name in the display name slot.
createInstance(String, AlgernonClass) - Method in interface org.algernon.kb.AlgernonKB: Creates a new instance in the storage.
createInstance(String, AlgernonClass) - Method in class org.algernon.kb.agent.google.GoogleKB: Creates a new instance in the storage.
createInstance(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Creates an instance with the given name.
createInstance(String, String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Creates an instance with the given name and stores the "pretty" name in the display name slot.
createInstance(String, AlgernonClass) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Creates a new instance in the storage.
createInstanceAux(String, int) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: auxiliary function to handle duplicate name problems.
createInstances() - Static method in class org.algernon.test.ProtegeTest
createInstances(KnowledgeBase, String, int) - Static method in class org.algernon.test.ProtegeTest: Creates n instances of the given class.
createKB(Clause) - Method in class org.algernon.Algernon: Called by the USE-KB opcode to create a new KB.
createLabels() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
createMenu() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
createMessageArea() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
createOutputArea() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
createPanels() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
createPathBuilder() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
createRelation(AlgernonKB, String, Set, Set, Integer, Integer, Object, AlgernonRelation) - Method in class org.algernon.Algernon: Creates a new relation in the given KB.
createRelation(AlgernonKB, String, Set, Set, Integer, Integer, Object, AlgernonRelation) - Method in class org.algernon.aam.Processor: Creates a new relation in the given KB.
createRelation(String, Set, Set, Integer, Integer, Object, AlgernonRelation) - Method in interface org.algernon.kb.AlgernonKB: Creates a new relation in the storage.
createRelation(String, LispValue, LispValue, Integer, Integer, Object, AlgernonRelation) - Method in interface org.algernon.kb.AlgernonKB: Helper method that creates a set around single domain and range to pass into the actual createRelation method.
createRelation(String, LispValue, LispValue, Integer, Integer, Object, AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Helper method that creates a set around single domain and range to pass into the actual createRelation method.
createRelation(String, Set, Set, Integer, Integer, Object, AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Creates a new relation in this KB.
createReviewTab() - Method in class org.algernon.app.j2p.gui.J2PWindow: Creates the Review Tab
createRule(Rule, AlgernonKBSet, AlgernonFrame) - Method in class org.algernon.Algernon: Send in a rule instance.
createRule(Rule, AlgernonKBSet, AlgernonFrame) - Method in class org.algernon.aam.Processor: Creates a new rule - adds it to the RuleManager, compiles it, creates continuations and compiles them.
createSaveTab() - Method in class org.algernon.app.j2p.gui.J2PWindow: Creates the Save tab
createSetupTab() - Method in class org.algernon.app.j2p.gui.J2PWindow: Creates the setup tab
createSlotDataStructures(SimpleTree) - Method in class org.algernon.app.Java2Protege: Creates the data structures for storing potential slots.
createSlotDataStructuresAux(Class) - Method in class org.algernon.app.Java2Protege: Helper method for createSlotDataStructures.
createSlotTable() - Method in class org.algernon.app.Java2Protege
createTextAreas() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab

D

DATE - Variable in class org.algernon.aam.OpcodeSet
DBTest - class org.algernon.test.DBTest.: Tests basic delete functionality of Algernon.
DBTest() - Constructor for class org.algernon.test.DBTest
DEBUG - Static variable in class org.algernon.aam.Tracer: A trace level for debugging.
DEBUG - Variable in class org.algernon.aam.compile.AlgernonCompiler
DEBUG_STRING - Static variable in class org.algernon.aam.Tracer
DEFAULT - Variable in class org.algernon.Algernon: Used when defining a relation.
DEFAULT_HEIGHT - Static variable in class org.algernon.app.j2p.gui.J2PWindow
DEFAULT_IMPORTANT_SUPERSET_SLOTNAME - Static variable in class org.algernon.kb.AlgernonKBSet
DEFAULT_KBSET_NAME - Static variable in class org.algernon.Algernon
DEFAULT_LIST_SIZE - Static variable in class org.algernon.aam.QueryHistory
DEFAULT_MAX_RESULTS - Static variable in class org.algernon.kb.agent.google.GoogleKB
DEFAULT_ROOT_CLASS - Static variable in class org.algernon.app.Java2Protege
DEFAULT_ROWS - Static variable in class org.algernon.app.j2p.AdviceTable
DEFAULT_RULE_CLASS_NAME - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
DEFAULT_SERVER_PORT_NUMBER - Static variable in class org.algernon.Algernon: Default port number when Algernon is running in Server mode.
DEFAULT_SIZE - Static variable in class org.algernon.aam.QueryHistory
DEFAULT_TEXT_FIELD_WIDTH - Static variable in class org.algernon.app.j2p.gui.J2PWindow
DEFAULT_WIDTH - Static variable in class org.algernon.app.j2p.gui.J2PWindow
DELETE_ALL_RULES_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
DELETE_ALL_RULES_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
DELETE_ALL_RULES_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
DELETE_ALL_RULES_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
DELETE_CLASS - Variable in class org.algernon.aam.OpcodeSet
DELETE_CLAUSE - Variable in class org.algernon.aam.OpcodeSet
DELETE_FACET - Variable in class org.algernon.aam.OpcodeSet
DELETE_FRAME - Variable in class org.algernon.aam.OpcodeSet
DELETE_INSTANCE - Variable in class org.algernon.aam.OpcodeSet
DELETE_RELATION - Variable in class org.algernon.aam.OpcodeSet
DELETE_RULES_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
DELETE_RULES_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
DELETE_RULES_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
DELETE_RULES_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
DEPTH_FIRST - Static variable in class org.algernon.Algernon: Controls how the set of activations is processed.
DETAIL - Static variable in class org.algernon.aam.Tracer: Trace level that prints detailed information.
DETAIL_STRING - Static variable in class org.algernon.aam.Tracer
DIRECT_CLASS - Variable in class org.algernon.aam.OpcodeSet
DIRECT_INSTANCE - Variable in class org.algernon.aam.OpcodeSet
DIRECT_SUBCLASS - Variable in class org.algernon.aam.OpcodeSet
DIRECT_SUPERCLASS - Variable in class org.algernon.aam.OpcodeSet
DOMAIN_POSITION - Static variable in class org.algernon.app.j2p.SlotTable
Date - class org.algernon.aam.opcode.Date.: This class implements the Date Opcode in the AAM.
Date(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Date: Create a new AAM Date Opcode.
DeleteAdviceAction - class org.algernon.app.j2p.action.DeleteAdviceAction.: DeleteAdviceAction performs the action of deleting an advice.
DeleteAdviceAction(J2PWindow, String, String, KeyStroke, Integer) - Constructor for class org.algernon.app.j2p.action.DeleteAdviceAction: Creates a new SaveAdviceFileAction.
DeleteAllRulesAction - class org.algernon.kb.okbc.protege.plugins.action.DeleteAllRulesAction.: User: hewett Date: Mar 7, 2003 Time: 11:50:02 AM
DeleteAllRulesAction(AlgernonTab, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.DeleteAllRulesAction: Calls back to Algernon to clear all rules installed in Algernon.
DeleteClass - class org.algernon.aam.opcode.DeleteClass.: This opcode deletes a class from the KB.
DeleteClass(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.DeleteClass
DeleteClause - class org.algernon.aam.opcode.DeleteClause.: This class represents a Test Opcode in the AAM.
DeleteClause(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.DeleteClause: Create a new AAM :DELETE-CLAUSE Opcode.
DeleteFacet - class org.algernon.aam.opcode.DeleteFacet.: This opcode deletes a facet from the KB.
DeleteFacet(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.DeleteFacet
DeleteFrame - class org.algernon.aam.opcode.DeleteFrame.: This opcode deletes a frame from the KB.
DeleteFrame(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.DeleteFrame
DeleteInstance - class org.algernon.aam.opcode.DeleteInstance.: This opcode deletes an instance from the KB.
DeleteInstance(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.DeleteInstance
DeleteRelation - class org.algernon.aam.opcode.DeleteRelation.: This opcode deletes a relation from the KB.
DeleteRelation(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.DeleteRelation
DeleteRulesAction - class org.algernon.kb.okbc.protege.plugins.action.DeleteRulesAction.: User: hewett Date: Mar 7, 2003 Time: 11:50:02 AM
DeleteRulesAction(AlgernonTab, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.DeleteRulesAction: Calls back to Algernon to pop up a dialog to delete selected rules.
DeleteTest - class org.algernon.test.DeleteTest.: Tests basic delete functionality of Algernon.
DeleteTest() - Constructor for class org.algernon.test.DeleteTest
DirectClass - class org.algernon.aam.opcode.DirectClass.: This opcode confirms or retrieves the direct class of an instance.
DirectClass(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.DirectClass
DirectInstance - class org.algernon.aam.opcode.DirectInstance.: This opcode confirms or retrieves the direct instances of a class.
DirectInstance(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.DirectInstance
DirectSubclass - class org.algernon.aam.opcode.DirectSubclass.: This opcode confirms or retrieves the direct instances of a class.
DirectSubclass(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.DirectSubclass
DirectSuperclass - class org.algernon.aam.opcode.DirectSuperclass.: This opcode confirms or retrieves the direct instances of a class.
DirectSuperclass(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.DirectSuperclass
Displayable - interface org.algernon.io.Displayable.
data - Variable in class org.algernon.app.j2p.SlotTableIterator
date1() - Static method in class org.algernon.test.MiscellanyTest
date_testFile - Variable in class org.algernon.test.MiscellanyTest
deleteAdvice(Vector) - Method in class org.algernon.app.Java2Protege: See documentation below.
deleteAdvice(String, String, String, String) - Method in class org.algernon.app.j2p.AdviceTable
deleteAllRelationValues(AlgernonRelation) - Method in interface org.algernon.kb.AlgernonFrame: Deletes all values on the given slot for this frame.
deleteAllRelationValues(AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Deletes all values on the given slot for this frame.
deleteClass(AlgernonClass) - Method in interface org.algernon.kb.AlgernonKB: Deletes a class and all of its relations from storage.
deleteClass(AlgernonClass) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Deletes a frame and all of its relations from storage.
deleteClauses(Clause) - Method in interface org.algernon.kb.AlgernonKB: Deletes one or more clauses from the storage.
deleteClauses(Clause, AlgernonFacet) - Method in interface org.algernon.kb.AlgernonKB: Deletes one or more clauses from the storage.
deleteClauses(Clause) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Deletes one or more clauses from the storage.
deleteClauses(Clause, AlgernonFacet) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Deletes one or more clauses from the storage.
deleteEntry(String, String, String, String) - Method in class org.algernon.app.j2p.Advice: Deletes an entry from the advice list.
deleteFacet(AlgernonFacet) - Method in interface org.algernon.kb.AlgernonKB: Deletes a frame and all of its relations from storage.
deleteFacet(AlgernonFacet) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Deletes a frame and all of its relations from storage.
deleteFrame(AlgernonFrame) - Method in interface org.algernon.kb.AlgernonKB: Deletes a frame and all of its relations from storage.
deleteFrame(AlgernonFrame) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Deletes a frame and all of its relations from storage.
deleteInstance(AlgernonInstance) - Method in interface org.algernon.kb.AlgernonKB: Deletes a frame and all of its relations from storage.
deleteInstance(AlgernonInstance) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Deletes a frame and all of its relations from storage.
deleteRelation(AlgernonRelation) - Method in interface org.algernon.kb.AlgernonKB: Deletes a frame and all of its relations from storage.
deleteRelation(AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Deletes a relation from storage.
deleteRelationValue(AlgernonRelation, Object) - Method in interface org.algernon.kb.AlgernonFrame: Deletes one value of a relation on this frame.
deleteRelationValue(AlgernonRelation, Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Deletes one value of a relation on this frame.
deleteRelationValues(AlgernonRelation, Collection) - Method in interface org.algernon.kb.AlgernonFrame: Calls deleteRelationValue for each value in the Collection.
deleteRelationValues(AlgernonRelation, Collection) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Calls deleteRelationValue for each value in the Collection.
delete_testFile - Variable in class org.algernon.test.DeleteTest
deprecationWarning(LispValue, String, LispValue) - Method in class org.algernon.aam.compile.AlgernonCompiler: General deprecation warning for old operators.
dereferenceExpression(LispValue, LispValue, LispValue) - Method in class org.algernon.datatype.BindingSet: Follows bindings to a non-variable or unbound variable.
dereferencePattern(LispValue, LispValue) - Static method in class org.algernon.datatype.BindingSet: Follows bindings to a non-variable or unbound variable.
display(PrintStream) - Method in class org.algernon.datatype.Clause: Displayable interface
display(PrintStream) - Method in class org.algernon.datatype.Path: Displayable interface
display(PrintStream) - Method in interface org.algernon.io.Displayable: If the outputstream is specified, the string is written to the output AND returned in a String.
display(PrintStream) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: implements the Displayable interface
display(PrintStream) - Method in class org.algernon.rule.Rule: Displayable interface.
displayByGene(List) - Method in class org.algernon.test.BasicTest
displayByStudyCenter(List) - Method in class org.algernon.test.BasicTest
displayResults(List, List) - Method in class org.algernon.test.BasicTest
doAddAdvice(ActionEvent) - Method in class org.algernon.app.j2p.gui.J2PWindow: Adds new advice.
doAskOrTell(int, ActionEvent) - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
doBackwardChaining - Variable in class org.algernon.AlgernonSettings: true if the processor should activate backward chaining rules during execution.
doBackwardChaining - Variable in class org.algernon.aam.compile.AlgernonCompilerState: This is true if backward chaining rules should be activated.
doCheckErrors(FrameTree, SlotTable) - Method in class org.algernon.app.Java2Protege: Checks for errors (usually duplicate names) and stores errors on each frame.
doCheckSlotDomains - Variable in class org.algernon.aam.compile.AlgernonCompilerState: true if the compiler should check slot domains.
doClearQueryHistory() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
doConversion(String, String, String, String) - Method in class org.algernon.app.Java2Protege: Performs the conversion.
doConversion(ActionEvent) - Method in class org.algernon.app.j2p.gui.J2PWindow: Runs the conversion
doCreateAdviceView() - Method in class org.algernon.app.j2p.gui.J2PWindow: Creates the tabular view of the classes.
doCreateClassView() - Method in class org.algernon.app.j2p.gui.J2PWindow: Creates the tree view of the classes
doCreateSlotView() - Method in class org.algernon.app.j2p.gui.J2PWindow: Creates the tabular view of the classes.
doDeleteAdvice(ActionEvent) - Method in class org.algernon.app.j2p.gui.J2PWindow: Deletes a line of advice.
doDeleteAllRules() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab: Causes all rules to be deleted.
doDeleteRules() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab: Pops up a dialog that lets the user selected rules to be deleted.
doEditPaths() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab: Pops up the path editor window.
doEditRules() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab: Pops up the rule editor window.
doForwardChaining - Variable in class org.algernon.AlgernonSettings: true if the processor should activate forward chaining rules during execution.
doForwardChaining - Variable in class org.algernon.aam.compile.AlgernonCompilerState: This is true if forward chaining rules should be activated.
doLoad() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
doLoadRulesFromKB() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab: Loads all rules that are instances of a specified class in the KB.
doMakeContinuations - Variable in class org.algernon.aam.compile.AlgernonCompilerState: true if the compiler should output code to create a continuation while a rule is firing.
doManageServer() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab: Enables and disables the Algernon server.
doReloadAllRules() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab: Causes all rules to be deleted and then reloaded from the KB.
doReloadRules() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab: Pops up a dialog that lets the user select rules to be reloaded, then deletes them and reloads them from the KB.
doSaveAdviceFile(ActionEvent) - Method in class org.algernon.app.j2p.gui.J2PWindow: Saves the advice file.
doSelectAdviceFile(ActionEvent) - Method in class org.algernon.app.j2p.gui.J2PWindow
doSelectAlgernonFile(ActionEvent) - Method in class org.algernon.app.j2p.gui.J2PWindow
doSelectKB(ActionEvent) - Method in class org.algernon.app.j2p.gui.J2PWindow
doShowResult(int) - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
doTaxonomyPreprocess(LispValue, LispValue, BindingList) - Method in class org.algernon.aam.compile.AlgernonCompiler: This turns the TAXONOMY form into the :CLASS and :INSTANCE pseudo-code that is processed by makeTaxonomyCommands.
doTraceRules() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab: Pops up a dialog to let the user trace or untrace Rules.
doWriteAdviceFile(String) - Method in class org.algernon.app.Java2Protege: Writes the contents of the advice to a file.
doWriteAlgernonFile(String, String) - Method in class org.algernon.app.Java2Protege: Writes everything to an Algernon file.
doWriteAlgernonFile(ActionEvent) - Method in class org.algernon.app.j2p.gui.J2PWindow
domainMismatchWarning(Clause, LispValue, Set, Set) - Method in class org.algernon.aam.compile.AlgernonCompiler: Returns an error about type mismatch on variables.
dontSubstituteForFrame - Variable in class org.algernon.aam.compile.AlgernonCompilerState: Causes the opcode SUBSTITUTE1 to be used instead of SUBSTITUTE.
dumpWindowBranch(Component, int) - Static method in class org.algernon.util.WindowUtil
dumpWindowHierarchy(Component) - Static method in class org.algernon.util.WindowUtil: Prints an indented list of Window components to System.err.

E

EDIT_PATHS_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
EDIT_PATHS_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
EDIT_PATHS_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
EDIT_PATHS_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
EDIT_RULES_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
EDIT_RULES_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
EDIT_RULES_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
EDIT_RULES_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
END_LABEL - Variable in class org.algernon.aam.compile.AlgernonCompiler
ERROR_COLOR - Variable in class org.algernon.app.j2p.J2PFrame
EVAL - Variable in class org.algernon.aam.OpcodeSet
EXAMPLE_TEXT - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
EditPathsAction - class org.algernon.kb.okbc.protege.plugins.action.EditPathsAction.: Action for editing paths in AlgernonTab.
EditPathsAction(AlgernonTab, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.EditPathsAction: Calls back to AlgernonTab to open the path editor.
EditRulesAction - class org.algernon.kb.okbc.protege.plugins.action.EditRulesAction.: Action to edit rules in AlgernonTab.
EditRulesAction(AlgernonTab, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.EditRulesAction: Calls back to Algernon to pop up the rule editor.
ErrorSet - class org.algernon.util.ErrorSet.: This class collects errors during compilation and processing.
ErrorSet() - Constructor for class org.algernon.util.ErrorSet
Eval - class org.algernon.aam.opcode.Eval.: This class represents an Eval Opcode in the AAM.
Eval(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Eval: Create a new AAM :EVAL Opcode.
ExternalLanguageEvaluator - interface org.algernon.lang.ExternalLanguageEvaluator.: Created by IntelliJ IDEA.
equals(AlgernonProtegeValueType) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType: Returns true if the implementation is equal to the implementation of the argument.
evaluateExpression(String, LispValue) - Method in class org.algernon.Algernon: Evaluates a method in the given language.
evaluateExpression(String, LispValue) - Method in class org.algernon.aam.Processor: Evaluates a method in the given language.
evaluateExpression(LispValue, Algernon) - Method in interface org.algernon.lang.ExternalLanguageEvaluator: Evaluates an expression written in the given language..
evaluateExpression(LispValue, Algernon) - Method in class org.algernon.lang.java.JavaEvaluator: Evaluates a method call.
evaluateExpression(LispValue, Algernon) - Method in class org.algernon.lang.lisp.JathaEvaluator: Evaluates a LISP expression.
evaluateExpression(LispValue, Algernon) - Method in class org.algernon.lang.shell.GenericUnixShellEvaluator: Makes a call to the UNIX shell.
evaluateExpressionAsBoolean(String, LispValue) - Method in class org.algernon.Algernon: Evaluates a method in the given language.
evaluateExpressionAsBoolean(String, LispValue) - Method in class org.algernon.aam.Processor: Evaluates a method in the given language.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.Opcode: Executes this opcode, using information in the given processor.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.ActivateBCRules: Executes the Activate BC opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.ActivateFCRules: Executes the Activate FC opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Any: If there is more than one binding list in the topmost binding-set of the *BINDINGS* register, pick one at random and throw the rest away.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Ask: Executes the ASK opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Assert: Executes the ASSERT opcode, which stores a clause in the KB.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Assume: Executes the TEST opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Bind: Executes the BIND opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Branch: Executes the BRANCH opcode.
execute(Processor, AlgernonKBSet, boolean) - Method in class org.algernon.aam.opcode.Branch: Executes the BRANCH opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.BranchByUser: Executes the BranchByUser opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Child: Executes the Child opcode, which verifies that a pair of frames are parent and child.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.ClassOp: Executes the CLASS opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Clause: Sets the CLAUSE register to the given value.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.ClearRelation: Executes the ClearRelation opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.ConjunctiveBranch: Executes the ConjunctiveBranch opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.ConjunctiveClear: Executes the ConjunctiveClear opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Continuation: Executes the CONTINUATION opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Count: Executes the Count opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.CreateClass: Executes the CREATE-CLASS opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.CreateFacet: Executes the CreateFacet opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.CreateInstance: Executes the CreateInstance opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.CreateRelation: Creates a new relation in the KB.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.CreateRelationRules: Executes the CreateRelationRules opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.CreateRules: Executes the :ADD-RULES macro.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Date: Executes the Date opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.DeleteClass: Executes the DeleteClass opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.DeleteClause: Executes the DeleteClause opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.DeleteFacet: Executes the DeleteFacet opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.DeleteFrame: Executes the DeleteFrame opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.DeleteInstance: Executes the DeleteInstance opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.DeleteRelation: Executes the DeleteRelation opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.DirectClass: Executes the DirectClass opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.DirectInstance: Executes the DirectInstance opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.DirectSubclass: Executes the DirectInstance opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.DirectSuperclass: Executes the DirectInstance opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Eval: Executes the :EVAL opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Fire: Executes the FIRE opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.For: Executes the For opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Instance: Executes the INSTANCE opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.IsClass: Executes the IsClass opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.IsFacet: Executes the IsFacet opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.IsFrame: Executes the IsFrame opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.IsInstance: Executes the IsInstance opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.IsRelation: Executes the IsRelation opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Label: Executes the TEST opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.LeafClass: Executes the LeafClass opcode, which collects all direct and indirect subclasses of a class that are leaves.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.LeastCommonSuperclass: Executes the LeastCommonSuperclass opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Limit: Executes the Limit opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.MergeBindings: Executes the :MERGE-BINDINGS opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Name: Executes the NAME opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.NotEqual: Executes the NotEqual opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Parent: Executes the Parent opcode, which verifies that a pair of frames are parent and child.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Pop: Executes the TEST opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Print: Executes the PRINT and PRINTLN macros.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Push: Executes the PUSH opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Query: Executes the QUERY opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Return: Executes the RETURN opcode, which ends a stream of Algernon processing.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.RootClass: Executes the RootClass opcode, which collects all the root classes of a class.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Save: Executes the SAVE opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Select: Executes the SELECT opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Show: Executes the SHOW opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.ShowCode: Executes the SHOW-CODE opcode.
execute(Processor, AlgernonKBSet, LispValue) - Method in class org.algernon.aam.opcode.Skip: Pops the CODE register until reaching the label.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Skip: Pops the CODE register until reaching the label.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Stop: Executes the STOP opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Subclass: Executes the Subclass opcode, which collects all direct and indirect subclasses of a class.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Subroutine: Executes the SUBROUTINE opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.SubstituteBindings: Executes the SUBSTITUTE opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.SubstituteBindings1: Executes the SUBSTITUTE1 opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Superclass: Executes the Superclass opcode, which collects all direct and indirect subclasses of a class.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.TemplateRelation: Executes the TEMPLATE-RELATION opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.TestBound: Checks the variable in the clause and sets result to T if it is bound, where it is checked by the :FAIL operator.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.TestFail: Executes the TEST-FAIL opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.TestKnown: Executes the :KNOWN opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.TestSucceed: Executes the TEST-SUCCEED opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.TestTrue: Executes the TEST opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.TestUnbound: Checks the variable in the clause and sets result to NIL if it is bound, where it is checked by the :FAIL operator.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.TestUnique: This opcode is like TestSucceed except that it only aborts the computation if there are multiple bindings for the given variable.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Trace: Executes the Trace opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.UseKB: Executes the UseKB opcode.
execute(Processor, AlgernonKBSet) - Method in class org.algernon.aam.opcode.Verify: Executes the VERIFY opcode.

F

FAILED - Variable in class org.algernon.datatype.BindingSet
FAILURE - Variable in class org.algernon.aam.Processor
FAIL_LABEL - Variable in class org.algernon.aam.compile.AlgernonCompiler
FALSE - Variable in class org.algernon.Algernon: Boolean false = :FALSE.
FIRE - Variable in class org.algernon.aam.OpcodeSet
FLOAT - Static variable in interface org.algernon.kb.AlgernonValueType
FLOAT - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
FLOAT_TYPE - Variable in class org.algernon.Algernon
FOR - Variable in class org.algernon.aam.OpcodeSet
FORC_MODE - Static variable in class org.algernon.aam.compile.AlgernonCompiler
FOREIGN - Static variable in interface org.algernon.kb.AlgernonValueType
FOREIGN - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
FOREIGN_TYPE - Variable in class org.algernon.Algernon
FORWARD - Variable in class org.algernon.rule.Rule
FORWARD_CHAIN - Static variable in class org.algernon.rule.RuleManager
FRAME - Static variable in interface org.algernon.kb.AlgernonValueType
FRAME - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
FRAME_CREATE_EVENT - Static variable in interface org.algernon.kb.event.KnowledgeBaseEvent
FRAME_DELETE_EVENT - Static variable in interface org.algernon.kb.event.KnowledgeBaseEvent
FRAME_MODIFY_EVENT - Static variable in interface org.algernon.kb.event.KnowledgeBaseEvent
FRAME_RULE - Static variable in class org.algernon.rule.RuleManager
Fire - class org.algernon.aam.opcode.Fire.: This class represents a Fire Opcode in the AAM.
Fire(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Fire: Create a new AAM :FIRE Opcode.
For - class org.algernon.aam.opcode.For.: This class implements the FOR Opcode in the AAM.
For(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.For: Create a new AAM For Opcode.
ForwardTest - class org.algernon.test.ForwardTest.: Tests basic execution functionality of Algernon.
ForwardTest() - Constructor for class org.algernon.test.ForwardTest
FrameTree - class org.algernon.app.j2p.FrameTree.: FrameTree does...
FrameTree(Java2Protege, String) - Constructor for class org.algernon.app.j2p.FrameTree
f_AdviceFileField - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_ClassCapitalize - Variable in class org.algernon.app.j2p.Advice
f_ClassIgnore - Variable in class org.algernon.app.j2p.Advice
f_ClassLowercase - Variable in class org.algernon.app.j2p.Advice
f_ClassPrefixes - Variable in class org.algernon.app.j2p.Advice
f_ClassReplacements - Variable in class org.algernon.app.j2p.Advice
f_ClassSuffixes - Variable in class org.algernon.app.j2p.Advice
f_ClassUppercase - Variable in class org.algernon.app.j2p.Advice
f_DrugProject - Variable in class org.algernon.test.PharmGKBTest2
f_ID - Variable in class org.algernon.datatype.Activation
f_MeshProject - Variable in class org.algernon.test.PharmGKBTest2
f_ProtegeProject - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_SlotCapitalize - Variable in class org.algernon.app.j2p.Advice
f_SlotIgnore - Variable in class org.algernon.app.j2p.Advice
f_SlotLowercase - Variable in class org.algernon.app.j2p.Advice
f_SlotPrefixes - Variable in class org.algernon.app.j2p.Advice
f_SlotReplacements - Variable in class org.algernon.app.j2p.Advice
f_SlotSuffixes - Variable in class org.algernon.app.j2p.Advice
f_SlotUppercase - Variable in class org.algernon.app.j2p.Advice
f_ValueType - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
f_addAdviceButton - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_advice - Variable in class org.algernon.app.j2p.AdviceTable
f_adviceFile - Variable in class org.algernon.app.Java2Protege
f_adviceFile - Variable in class org.algernon.app.j2p.Advice
f_adviceHasChanged - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_adviceJTable - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_advicePanel - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_adviceTable - Variable in class org.algernon.app.Java2Protege
f_adviceTable - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_adviceTableColumnNames - Static variable in class org.algernon.app.Java2Protege
f_algernonMenu - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_algernonRuleClassName - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_algernonRuleClassNames - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_algy - Variable in class org.algernon.aam.Opcode
f_algy - Variable in class org.algernon.aam.OpcodeSet
f_algy - Variable in class org.algernon.aam.Processor
f_algy - Variable in class org.algernon.aam.compile.AlgernonCompiler
f_algy - Variable in class org.algernon.aam.compile.AlgernonCompilerState
f_algy - Variable in class org.algernon.aam.register.GeneralRegister
f_algy - Variable in class org.algernon.app.Java2Protege
f_algy - Variable in class org.algernon.datatype.Activation
f_algy - Variable in class org.algernon.datatype.BindingList
f_algy - Variable in class org.algernon.datatype.BindingSet
f_algy - Variable in class org.algernon.datatype.Clause
f_algy - Variable in class org.algernon.datatype.Closure
f_algy - Variable in class org.algernon.datatype.Path
f_algy - Variable in class org.algernon.datatype.Result
f_algy - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeObject
f_algy - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_algy - Variable in class org.algernon.rule.Rule
f_algy - Variable in class org.algernon.rule.RuleManager
f_algy - Variable in class org.algernon.server.AlgernonServer
f_algy - Variable in class org.algernon.test.BackwardTest
f_algy - Variable in class org.algernon.test.BasicTest
f_algy - Variable in class org.algernon.test.PharmGKBTest2
f_algy - Variable in class org.algernon.test.SimpleAlgernonExample
f_allCommands - Variable in class org.algernon.Algernon
f_app - Variable in class org.algernon.app.j2p.AdviceTable
f_app - Variable in class org.algernon.app.j2p.FrameTree
f_app - Variable in class org.algernon.app.j2p.action.Java2ProtegeAction
f_app - Variable in class org.algernon.app.j2p.gui.J2PFrameRenderer
f_app - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_askButton - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_associatedFrame - Variable in class org.algernon.datatype.Closure
f_bindings - Variable in class org.algernon.datatype.BindingSet
f_bindings - Variable in class org.algernon.datatype.Closure
f_cancelButton - Variable in class org.algernon.app.j2p.gui.J2PAdviceDialog
f_cardinality - Variable in class org.algernon.app.j2p.J2PSlot
f_classPanel - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_classTable - Variable in class org.algernon.app.Java2Protege
f_classTree - Variable in class org.algernon.app.Java2Protege
f_classTree - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_clause - Variable in class org.algernon.datatype.Clause
f_clientKey - Variable in class org.algernon.kb.agent.google.GoogleKB
f_columnNames - Variable in class org.algernon.app.j2p.AdviceTable
f_component - Variable in class org.algernon.kb.okbc.protege.plugins.action.ClearAction
f_convertPanel - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_currentResultDisplay - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_currentRow - Variable in class org.algernon.app.j2p.SlotTableIterator
f_defaultProject - Variable in class org.algernon.test.BackwardTest
f_deleteAdviceButton - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_description - Variable in class org.algernon.app.j2p.error.J2PError
f_direction - Variable in class org.algernon.kb.okbc.protege.plugins.action.ShowResultAction
f_displayNameRelation - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeKB
f_displayNameRelationName - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeKB
f_domain - Variable in class org.algernon.app.j2p.J2PSlot
f_domain - Variable in class org.algernon.app.j2p.error.J2PSlotWithSameNameAsClassError
f_domain - Variable in class org.algernon.app.j2p.error.J2PUnknownDomainError
f_domain - Variable in class org.algernon.app.j2p.error.J2PUnknownRangeError
f_drugkb - Variable in class org.algernon.test.PharmGKBTest2
f_enabled - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_error - Variable in class org.algernon.app.j2p.J2PFrame
f_errorMessage - Variable in class org.algernon.app.j2p.error.J2PConversionError
f_errorMessage - Static variable in class org.algernon.app.j2p.error.J2PDuplicateFrameNameError
f_errorMessage - Static variable in class org.algernon.app.j2p.error.J2PSlotWithSameNameAsClassError
f_errorMessage - Static variable in class org.algernon.app.j2p.error.J2PUnknownDomainError
f_errorMessage - Static variable in class org.algernon.app.j2p.error.J2PUnknownRangeError
f_errors - Variable in class org.algernon.app.Java2Protege
f_errors - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_frame - Variable in class org.algernon.app.j2p.error.J2PError
f_globalClassCapitalize - Variable in class org.algernon.app.j2p.Advice
f_globalClassLowercase - Variable in class org.algernon.app.j2p.Advice
f_globalClassPrefix - Variable in class org.algernon.app.j2p.Advice
f_globalClassSuffix - Variable in class org.algernon.app.j2p.Advice
f_globalClassUppercase - Variable in class org.algernon.app.j2p.Advice
f_globalSlotCapitalize - Variable in class org.algernon.app.j2p.Advice
f_globalSlotLowercase - Variable in class org.algernon.app.j2p.Advice
f_globalSlotPrefix - Variable in class org.algernon.app.j2p.Advice
f_globalSlotSuffix - Variable in class org.algernon.app.j2p.Advice
f_globalSlotUppercase - Variable in class org.algernon.app.j2p.Advice
f_handlers - Variable in class org.algernon.server.AlgernonServer
f_hasSpecialArguments - Variable in class org.algernon.datatype.Command: This tells the compiler to do something special.
f_helpPanel - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_id - Variable in class org.algernon.datatype.Closure
f_ignoreEnumerations - Variable in class org.algernon.app.Java2Protege
f_initialized - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_input - Variable in class org.algernon.server.AlgernonServer.SocketConnectionHandler
f_inputArea - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_inputClearButton - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_inputCounter - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_inputPanel - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_inputPanelScroller - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_inputStack - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_intValue - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
f_isIgnored - Variable in class org.algernon.app.j2p.J2PFrame
f_isObsolete - Variable in class org.algernon.datatype.Command: This tells the compiler to do something special.
f_isPathUnrestricted - Variable in class org.algernon.datatype.Command: This tells the compiler to do something special.
f_isRunning - Variable in class org.algernon.server.AlgernonServer.SocketConnectionHandler
f_isRunning - Variable in class org.algernon.server.AlgernonServer
f_javaAddMethod - Variable in class org.algernon.app.j2p.J2PSlot
f_javaGetMethod - Variable in class org.algernon.app.j2p.J2PSlot
f_javaSetMethod - Variable in class org.algernon.app.j2p.J2PSlot
f_javaType - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
f_kb - Variable in class org.algernon.app.Java2Protege
f_kb - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeKB
f_kb - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_kb - Variable in class org.algernon.test.BackwardTest
f_kb - Variable in class org.algernon.test.BasicTest
f_kb - Variable in class org.algernon.test.SimpleAlgernonExample
f_kbField - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_kbFile - Variable in class org.algernon.app.Java2Protege
f_key - Variable in class org.algernon.datatype.Closure
f_lastPackageName - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_lisp - Variable in class org.algernon.aam.Processor
f_lisp - Variable in class org.algernon.aam.Tracer
f_lisp - Variable in class org.algernon.aam.compile.AlgernonCompiler
f_lisp - Variable in class org.algernon.aam.register.GeneralRegister
f_lisp - Variable in class org.algernon.aam.register.RegisterSet
f_lisp - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_lisp - Variable in class org.algernon.test.BasicTest
f_lisp - Variable in class org.algernon.test.PharmGKBTest2
f_lookupVars - Variable in class org.algernon.datatype.Closure
f_mainLabel - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_mainPanel - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_menuBarInitialized - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_meshkb - Variable in class org.algernon.test.PharmGKBTest2
f_messageArea - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_messageClearButton - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_messagePanel - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_messagePanelScroller - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_model - Variable in class org.algernon.app.j2p.FrameTree
f_nValues - Static variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
f_name - Variable in class org.algernon.app.j2p.J2PFrame
f_nameSymbol - Variable in class org.algernon.datatype.Command
f_nameTable - Variable in class org.algernon.app.j2p.FrameTree
f_nextButton - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_obsoleteMessage - Variable in class org.algernon.datatype.Command: If this command is obsolete, this is the message the user receives.
f_opcode - Variable in class org.algernon.datatype.Command: This is the opcode corresponding to this comand.
f_opcodeSet - Variable in class org.algernon.aam.compile.AlgernonCompiler
f_originalName - Variable in class org.algernon.app.j2p.J2PFrame
f_outputFile - Variable in class org.algernon.app.Java2Protege
f_outputNumberLabel - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_outputPanel - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_outputPanelScroller - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_outputTable - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_owner - Variable in class org.algernon.app.j2p.gui.J2PAdviceDialog
f_package - Variable in class org.algernon.app.Java2Protege
f_packageField - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_parent - Variable in class org.algernon.kb.okbc.protege.plugins.gui.LoadRulesDialog
f_parentMap - Variable in class org.algernon.util.SimpleTree
f_pathBuilderPanel - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_pharmgkb - Variable in class org.algernon.test.PharmGKBTest2
f_pharmgkbProject - Variable in class org.algernon.test.PharmGKBTest2
f_portNumber - Variable in class org.algernon.server.AlgernonServer
f_prevButton - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_processor - Variable in class org.algernon.aam.OpcodeSet
f_processor - Variable in class org.algernon.aam.compile.AlgernonCompiler
f_processor - Variable in class org.algernon.aam.register.GeneralRegister
f_processor - Variable in class org.algernon.aam.register.RegisterSet
f_projectFile - Variable in class org.algernon.test.SimpleAlgernonExample
f_projectURI - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeKB
f_range - Variable in class org.algernon.app.j2p.J2PSlot
f_range - Variable in class org.algernon.app.j2p.error.J2PUnknownRangeError
f_registers - Variable in class org.algernon.datatype.Activation
f_result - Variable in class org.algernon.app.j2p.gui.J2PAdviceDialog
f_resultStack - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_reviewPanel - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_root - Variable in class org.algernon.app.j2p.FrameTree
f_rootField - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_rule - Variable in class org.algernon.datatype.Closure
f_ruleClasses - Variable in class org.algernon.kb.okbc.protege.plugins.gui.LoadRulesDialog
f_runConversionButton - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_saveAdviceButton - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_saveButton - Variable in class org.algernon.app.j2p.gui.J2PAdviceDialog
f_saveInAlgernonField - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_saveInAlgernonFile - Variable in class org.algernon.app.Java2Protege
f_savePanel - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_savedAdviceDirectory - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_savedAlgernonDirectory - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_savedDirectory - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_savedKBDirectory - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_selectAdviceFileButton - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_selectKBFileButton - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_server - Variable in class org.algernon.Algernon
f_server - Variable in class org.algernon.server.AlgernonServer.SocketConnectionHandler
f_slotPanel - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_slotTable - Variable in class org.algernon.app.Java2Protege
f_slotTable - Variable in class org.algernon.app.j2p.SlotTableIterator
f_slotTable - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_slotTableColumnNames - Static variable in class org.algernon.app.Java2Protege
f_socket - Variable in class org.algernon.server.AlgernonServer.SocketConnectionHandler
f_socket - Variable in class org.algernon.server.AlgernonServer
f_stepMode - Variable in class org.algernon.aam.Tracer
f_string - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
f_subClasses - Variable in class org.algernon.app.j2p.J2PClass
f_superClasses - Variable in class org.algernon.app.j2p.J2PClass
f_tab - Variable in class org.algernon.kb.okbc.protege.plugins.action.AlgernonTabAction
f_tabPane - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_tableSorter - Variable in class org.algernon.app.j2p.gui.J2PWindow
f_tellButton - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_testFile - Variable in class org.algernon.test.BackwardTest
f_testFile - Variable in class org.algernon.test.PharmGKBTest2
f_topRoot - Variable in class org.algernon.app.Java2Protege
f_values - Static variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
f_versionLabel - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
f_window - Variable in class org.algernon.app.Java2Protege
failIsGood - Variable in class org.algernon.aam.compile.AlgernonCompilerState: Sometimes (as in the macro :FAIL or :UNP) processing should continue if the command fails.
findBCRuleCode(Processor, AlgernonKBSet, BindingList) - Method in class org.algernon.rule.Rule: Returns the compiled code that is appropriate for the set of bound variables passed in.
findIllegalSNPPositions() - Method in class org.algernon.test.PharmGKBTest1
findIllegalSequences() - Method in class org.algernon.test.PharmGKBTest1
findMethod(Method[], String) - Static method in class org.algernon.util.ReflectionUtil: Finds a method with the given name from the set of methods.
findMethodName(Method[], String) - Static method in class org.algernon.util.ReflectionUtil: Finds a method with the given name from the set of methods.
findName(Processor, LispValue) - Method in class org.algernon.datatype.Path: Given a variable name, searches for a clause of the form ( variable string) and returns the string as a symbol.
findOpcodeForMacro(LispValue) - Method in class org.algernon.aam.compile.AlgernonCompiler: Send in a macro name (that is, a keyword).
findPackageLocation(String) - Static method in class org.algernon.util.ReflectionUtil: If the package is not found, returns null.
findSubmittedGenesNotOnWatchlist() - Method in class org.algernon.test.PharmGKBTest1
first(Collection) - Static method in class org.algernon.util.CollectionUtil: Returns the first element in a collection.
firstClause() - Method in class org.algernon.datatype.Path: Returns the first clause in the path.
frameName - Variable in class org.algernon.app.j2p.gui.J2PAdviceDialog
frameSearch(String, String, int) - Method in interface org.algernon.kb.AlgernonKB: Performs a string search within the KB for frames whose name contains the given string.
frameSearch(String) - Method in interface org.algernon.kb.AlgernonKB: Performs a string search within the KB for frames whose name contains the given string.
frameSearch(String, String) - Method in interface org.algernon.kb.AlgernonKB: Performs a string search within the KB for frames whose name contains the given string.
frameSearch(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Performs a string search within the KB for frames whose name contains the given string.
frameSearch(String, String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Performs a string search within the KB for frames whose name contains the given string.
frameSearch(String, String, int) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Performs a string search within the KB for frames whose name contains the given string.

G

GeneralRegister - class org.algernon.aam.register.GeneralRegister.: This class represents a RegisterSet in the AAM.
GeneralRegister(Processor, String, RegisterSet) - Constructor for class org.algernon.aam.register.GeneralRegister: Creates a new general-purpose AAM register.
GenericLoader - class org.algernon.test.GenericLoader.: Tests miscellaneous functionality of Algernon.
GenericLoader(String[]) - Constructor for class org.algernon.test.GenericLoader
GenericUnixShellEvaluator - class org.algernon.lang.shell.GenericUnixShellEvaluator.: Evaluator for java method calls and expressions.
GenericUnixShellEvaluator() - Constructor for class org.algernon.lang.shell.GenericUnixShellEvaluator
GoogleKB - class org.algernon.kb.agent.google.GoogleKB.: Implements a Google pseudo-KB for Algernon.
GoogleKB(Algernon, String, Collection, Collection, String) - Constructor for class org.algernon.kb.agent.google.GoogleKB: Opens the Google API for access.
generalIsa(String, String) - Method in class org.algernon.Algernon: Returns true if the first argument is an instance or subclass of the second argument.
generalIsa(String, String, AlgernonKB) - Method in class org.algernon.Algernon: Returns true if the first argument is an instance or subclass of the second argument.
generalIsa(String, String, AlgernonKBSet) - Method in class org.algernon.Algernon: Returns true if the first argument is an instance or subclass of the second argument.
generalIsa(String, String) - Method in interface org.algernon.kb.AlgernonKB: Returns true if the first argument is an instance or subclass of the second argument in this KB.
generalIsa(String, String) - Method in class org.algernon.kb.AlgernonKBSet: Returns true if the first argument is an instance or subclass of the second argument.
generalIsa(String, String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns true if the first argument is an instance or subclass of the second argument in this KB.
generalNotIsa(String, String) - Method in class org.algernon.Algernon: Returns true if the first argument is not an instance or subclass of the second argument.
generalNotIsa(String, String, AlgernonKB) - Method in class org.algernon.Algernon: Returns true if the first argument is not an instance or subclass of the second argument.
generalNotIsa(String, String, AlgernonKBSet) - Method in class org.algernon.Algernon: Returns true if the first argument is not an instance or subclass of the second argument.
generalNotIsa(String, String) - Method in interface org.algernon.kb.AlgernonKB: Returns true if the first argument is not an instance or subclass of the second argument this KB.
generalNotIsa(String, String) - Method in class org.algernon.kb.AlgernonKBSet: Returns true if the first argument is not an instance or subclass of the second argument.
generalNotIsa(String, String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns true if the first argument is not an instance or subclass of the second argument this KB.
generateID() - Static method in class org.algernon.datatype.Closure
generateRuleCode(Rule, AlgernonKBSet, int, Path, Path, int, Rule, BindingList, Map, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: Generates the actual code for the rule.
generateRuleName(Rule, BindingList) - Method in class org.algernon.aam.compile.AlgernonCompiler: Generates a fake rule name based on the set of bound variables.
generateVariableSets(Clause) - Method in class org.algernon.aam.compile.AlgernonCompiler: When a backward chaining rule is activated, some number of variables in the key will be bound.
get(String) - Method in class org.algernon.app.j2p.FrameTree: Returns a Collection of the entries in this table with the given name.
get(String) - Method in class org.algernon.app.j2p.SlotTable: Returns a Collection of the slots with the given name.
get(Object) - Method in class org.algernon.datatype.BindingList: Returns a value of a variable in the binding list.
getActivateBCClause() - Method in class org.algernon.datatype.Activation: Returns the value of ActivateBCClause.
getActivateFCClause() - Method in class org.algernon.datatype.Activation: Returns the value of ActivateFCClause.
getActivatedRules(AlgernonFrame, int, int) - Method in class org.algernon.Algernon: Returns a list of activatable rules that match the given criteria.
getActivatedRules(AlgernonFrame, int, int) - Method in class org.algernon.aam.Processor: Returns a list of activatable rules that match the given criteria.
getAdvice() - Method in class org.algernon.app.Java2Protege
getAdvice() - Method in class org.algernon.app.j2p.AdviceTable
getAdviceColumnNames() - Method in class org.algernon.app.Java2Protege
getAdviceFile() - Method in class org.algernon.app.Java2Protege
getAdviceString() - Method in class org.algernon.app.j2p.Advice: Dumps all the advice into a string.
getAlgernon() - Method in class org.algernon.aam.Processor: Returns the value of Algernon.
getAlgernon() - Method in class org.algernon.datatype.Clause: Returns the instance of Algernon that this Clause belongs to.
getAlgernon() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeObject
getAlgernon() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab: Returns the Algernon object associated with this tab.
getAlgernonBinding(String, BindingList) - Method in class org.algernon.Algernon: Returns the binding of a variable from a result.
getAlgernonMetaTaxonomy() - Method in class org.algernon.app.Java2Protege
getAlgernonValueType(Object) - Method in interface org.algernon.kb.AlgernonValueType: returns the AlgernonValueType associated with the java object
getAlgernonValueType(Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
getAllCode() - Method in class org.algernon.rule.Rule
getAllFrames() - Method in interface org.algernon.kb.AlgernonKB: Returns a collection of all frames in the KB.
getAllFrames() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns a collection of all frames in the KB.
getAllRules() - Method in class org.algernon.rule.RuleManager: Returns a Collection of all rules.
getAllowsChildren() - Method in class org.algernon.app.j2p.J2PClass: Returns true if this node is allowed to have children.
getAllowsChildren() - Method in class org.algernon.app.j2p.J2PFrame: Returns true if this node is allowed to have children.
getAntecedent() - Method in class org.algernon.rule.Rule: Returns the direction of the rule.
getApplication() - Method in class org.algernon.app.j2p.gui.J2PWindow
getArgs(LispValue) - Static method in class org.algernon.Algernon: Returns the relation of the clause, which is the first element of the list.
getArgumentTypes() - Method in interface org.algernon.kb.AlgernonRelation: Returns a list of the argument types for this relation.
getArgumentTypes() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: Returns a list of the argument types for this relation.
getArguments(Clause) - Static method in class org.algernon.Algernon: Returns the relation of the clause.
getArguments() - Method in class org.algernon.datatype.Clause: Returns the arguments of the clause (all elements except the first).
getAssociatedFrame() - Method in class org.algernon.datatype.Closure: Returns the frame the rule in this closure is associated with.
getBinding(String, BindingList) - Method in class org.algernon.Algernon: Returns the binding of a variable from a result.
getBinding(Object) - Method in class org.algernon.datatype.BindingList: Retrieves the binding for a variable.
getBindings() - Method in class org.algernon.datatype.Activation: Returns the value of Bindings.
getBindings() - Method in class org.algernon.datatype.Closure
getCardinality() - Method in class org.algernon.app.j2p.J2PSlot
getChildAt(int) - Method in class org.algernon.app.j2p.J2PClass: Returns the child at the specified index in this node's child array.
getChildAt(int) - Method in class org.algernon.app.j2p.J2PFrame: Returns the child at the specified index in this node's child array.
getChildCount() - Method in class org.algernon.app.j2p.J2PClass: Returns the number of children of this node.
getChildCount() - Method in class org.algernon.app.j2p.J2PFrame: Returns the number of children of this node.
getChildren(Object) - Method in class org.algernon.util.SimpleTree: Returns a collection of the children in the tree.
getClassMappingInfo(J2PFrame, FrameTree) - Method in class org.algernon.app.Java2Protege: Returns a TELL statement that creates a mapping frame that stores the mapping between a Java name (Class or field) and a Protege Class.
getClassPrefix(String) - Method in class org.algernon.app.j2p.Advice
getClassReplacement(String) - Method in class org.algernon.app.j2p.Advice
getClassSuffix(String) - Method in class org.algernon.app.j2p.Advice
getClassTable() - Method in class org.algernon.app.Java2Protege
getClassesFromDirectory(String, File) - Static method in class org.algernon.util.ReflectionUtil: Given a directory that is the root of a class hierarchy, and a package name, retrieves the Java Classes from the package in the jar file.
getClassesFromJar(String, URL) - Static method in class org.algernon.util.ReflectionUtil: Given a URL specifying a jar file and a package name, retrieves the Java Classes from the package in the jar file.
getClassesOfPackage(String) - Static method in class org.algernon.util.ReflectionUtil: Returns all Java Classes in the given package.
getClassesOfPackages(Collection) - Static method in class org.algernon.util.ReflectionUtil: Returns all of the Java Classes in all of the packages presented.
getClause() - Method in class org.algernon.datatype.Activation: Returns the value of Clause.
getClause() - Method in class org.algernon.datatype.Clause
getClientKey() - Method in class org.algernon.kb.agent.google.GoogleKB
getCode() - Method in class org.algernon.datatype.Activation: Returns the value of Code.
getCode() - Method in class org.algernon.rule.Rule: Returns the code for a forward chaining rule, or for a backward chaining rule with no bound variables.
getCode(Processor, AlgernonKBSet, BindingList) - Method in class org.algernon.rule.Rule: Returns the code for a forward chaining rule, or for a backward chaining rule with no bound variables.
getColumnClass(int) - Method in class org.algernon.app.j2p.TableMap
getColumnCount() - Method in class org.algernon.app.j2p.TableMap
getColumnName(int) - Method in class org.algernon.app.j2p.TableMap
getCommand(LispValue) - Method in class org.algernon.Algernon: Retrieves a command by its name (a LispSymbol).
getCommand() - Method in class org.algernon.app.j2p.gui.J2PAdviceDialog: Returns either SUFFIX, PREFIX, CAPITALIZE, UPPERCASE, LOWERCASE or REPLACE.
getCompiler() - Method in class org.algernon.Algernon: Returns the current compiler used by Algernon.
getCompiler() - Method in class org.algernon.aam.Processor: Returns the current compiler used by Algernon.
getConjunctiveID() - Method in class org.algernon.datatype.Activation: Returns the value of ConjunctiveID.
getConsequent() - Method in class org.algernon.rule.Rule
getCurrentTime() - Static method in class org.algernon.test.DBTest: Returns the current time in milliseconds.
getCurrentTime() - Static method in class org.algernon.test.DeleteTest: Returns the current time in milliseconds.
getCurrentTime() - Static method in class org.algernon.test.MiscellanyTest: Returns the current time in milliseconds.
getCurrentTime() - Static method in class org.algernon.test.PharmGKBTest1: Returns the current time in milliseconds.
getCurrentTime() - Static method in class org.algernon.test.SpecialTest: Returns the current time in milliseconds.
getCurrentTime() - Static method in class org.algernon.test.TaxonomyTest: Returns the current time in milliseconds.
getCurrentTime() - Static method in class org.algernon.test.TypeTest: Returns the current time in milliseconds.
getDescription() - Method in class org.algernon.app.j2p.gui.ProtegeProjectFileFilter
getDirectInstances() - Method in interface org.algernon.kb.AlgernonClass
getDirectInstances() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass
getDirectSubclasses() - Method in interface org.algernon.kb.AlgernonClass
getDirectSubclasses() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass
getDirectSuperclasses() - Method in interface org.algernon.kb.AlgernonClass
getDirectSuperclasses() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass
getDirection() - Method in class org.algernon.rule.Rule
getDisplayName() - Method in interface org.algernon.kb.AlgernonFrame: Returns the display name of this Frame, or the name if the display name relation is not defined.
getDisplayName() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Returns the name of this Frame.
getDisplayName(Object) - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
getDisplayNameRelation() - Method in interface org.algernon.kb.AlgernonKB: Get the actual DisplayName slot.
getDisplayNameRelation() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Get the actual DisplayName slot.
getDisplayNameRelationName() - Method in interface org.algernon.kb.AlgernonKB: Get the name of the DisplayName relation (slot).
getDisplayNameRelationName() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Get the name of the DisplayName slot.
getDomain() - Method in class org.algernon.app.j2p.J2PSlot: Gets the domain.
getElapsedTime(long) - Static method in class org.algernon.test.DBTest: Returns the elapsed time since the startTime in milliseconds.
getElapsedTime(long) - Static method in class org.algernon.test.DeleteTest: Returns the elapsed time since the startTime in milliseconds.
getElapsedTime(long) - Static method in class org.algernon.test.MiscellanyTest: Returns the elapsed time since the startTime in milliseconds.
getElapsedTime(long) - Static method in class org.algernon.test.PharmGKBTest1: Returns the elapsed time since the startTime in milliseconds.
getElapsedTime(long) - Static method in class org.algernon.test.SpecialTest: Returns the elapsed time since the startTime in milliseconds.
getElapsedTime(long) - Static method in class org.algernon.test.TaxonomyTest: Returns the elapsed time since the startTime in milliseconds.
getElapsedTime(long) - Static method in class org.algernon.test.TypeTest: Returns the elapsed time since the startTime in milliseconds.
getEntry(int) - Method in class org.algernon.aam.register.BindingsRegister: Return the nth BindingSet in this register, where the topmost item is entry number zero.
getEntry(int) - Method in class org.algernon.aam.register.GeneralRegister: Return the nth entry in the given register, where the topmost item is entry number zero.
getEntry(int) - Method in interface org.algernon.aam.register.Register: Return the nth entry in the given register, where the topmost item is entry number zero.
getEntry(int) - Method in class org.algernon.datatype.BindingSet: Return the nth BindingList in the given register, where the topmost item is entry number zero.
getError() - Method in class org.algernon.app.j2p.J2PFrame: Returns the error.
getErrorString() - Method in class org.algernon.app.j2p.FrameTree: Returns a string containing any errors found in the frames.
getErrors() - Method in class org.algernon.util.ErrorSet: Returns a collection of errors, which are Strings.
getEvaluator(String) - Method in class org.algernon.Algernon: Returns a language evaluator for the given language.
getExecutionOrder() - Method in class org.algernon.Algernon: Returns the value of ExecutionOrder.
getFacet(Slot, String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass
getFrame(LispValue) - Static method in class org.algernon.Algernon: Returns the frame of the clause, which is the second element of the list.
getFrame(Clause) - Static method in class org.algernon.Algernon: Returns the frame of the clause.
getFrame() - Method in class org.algernon.app.j2p.error.J2PError
getFrame() - Method in class org.algernon.datatype.Clause: Returns the frame of the clause (the element in the second position).
getFrame(String) - Method in interface org.algernon.kb.AlgernonKB: Returns a frame with the given name, if any exists.
getFrame() - Method in interface org.algernon.kb.event.KnowledgeBaseEvent
getFrame(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns a frame with the given name, if any exists.
getFrameName() - Method in class org.algernon.app.j2p.gui.J2PAdviceDialog: Returns either "ALL" or a frame name
getFromCache(Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Retrieves a Algernon-level frame or other value given a KBMS-level object as the key.
getFromDisplayNameCache(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Retrieves an Algernon frame from its display name.
getID() - Method in class org.algernon.datatype.Activation: Returns the unique ID of this object.
getId() - Method in class org.algernon.datatype.Closure
getImplementation() - Method in interface org.algernon.kb.AlgernonFrame: Returns the KBMS-specific object implementing this interface.
getImplementation() - Method in interface org.algernon.kb.AlgernonKB: Returns the KBMS-specific object implementing this interface.
getImplementation() - Method in interface org.algernon.kb.AlgernonValueType: returns the low level type associated with this class.
getImplementation() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Returns the KBMS-specific object implementing this interface.
getImplementation() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns the KBMS-specific object implementing this interface.
getImplementation() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
getImportantSupersetSlotName() - Method in class org.algernon.Algernon: Returns the name of the slot that represents the relation between a class and a superclass for inheritance purposes.
getImportantSupersetSlotName() - Method in class org.algernon.kb.AlgernonKBSet: Returns the name of the slot that represents the relation between a class and a superclass for inheritance purposes.
getIndex(TreeNode) - Method in class org.algernon.app.j2p.J2PClass: Returns the index of the specified child in this node's child array.
getIndex(TreeNode) - Method in class org.algernon.app.j2p.J2PFrame: Returns the index of the specified child in this node's child array.
getIndex() - Method in class org.algernon.datatype.Activation: Returns the value of Index.
getIndex() - Method in class org.algernon.rule.Rule
getInstances() - Method in interface org.algernon.kb.AlgernonClass
getInstances() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass
getIntValue() - Method in interface org.algernon.kb.AlgernonValueType: returns the int value associated with this valuetype
getIntValue() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
getIterator() - Method in class org.algernon.app.j2p.FrameTree: Returns an iterator over the keys in this FrameTree.
getIterator() - Method in class org.algernon.app.j2p.SlotTable
getJavaAddMethod() - Method in class org.algernon.app.j2p.J2PSlot: Stores the original method name so other programs can know the mapping from method to slot name.
getJavaGetMethod() - Method in class org.algernon.app.j2p.J2PSlot: Stores the original method name so other programs can know the mapping from method to slot name.
getJavaSetMethod() - Method in class org.algernon.app.j2p.J2PSlot: Stores the original method name so other programs can know the mapping from method to slot name.
getJavaType() - Method in interface org.algernon.kb.AlgernonValueType: returns the java class associated with this valuetype
getJavaType() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
getKB() - Method in interface org.algernon.kb.AlgernonFrame: Returns the KB this Frame belongs to.
getKB(String) - Method in class org.algernon.kb.AlgernonKBSet: returns a KB by its name.
getKB() - Method in class org.algernon.kb.AlgernonKBSet: Returns the first KB in the list.
getKB() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Returns the KB this Frame belongs to.
getKBFile() - Method in class org.algernon.app.Java2Protege
getKBRoot() - Method in class org.algernon.app.Java2Protege
getKBSet() - Method in class org.algernon.Algernon: Returns the set of KBs with the default AlgernonKBSet name.
getKBSet(String) - Method in class org.algernon.Algernon: Returns the set of KBs with the given name.
getKb() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB
getKey() - Method in class org.algernon.datatype.Activation: Returns the value of Key.
getKey() - Method in class org.algernon.datatype.Closure
getKey() - Method in class org.algernon.rule.Rule
getKeyIterator() - Method in class org.algernon.app.j2p.FrameTree: Returns an iterator over the keys in this FrameTree.
getKnowledgeBase() - Method in interface org.algernon.kb.event.KnowledgeBaseEvent
getLastCommand() - Method in class org.algernon.aam.Processor: Returns the value of LastCommand.
getLeafSubclasses() - Method in interface org.algernon.kb.AlgernonClass: Returns a collection of subclasses of this class that are leaves.
getLeafSubclasses() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Returns a collection of subclasses of this class that are leaves.
getLisp() - Method in class org.algernon.Algernon
getLisp() - Method in class org.algernon.aam.Processor
getLispParser() - Method in class org.algernon.Algernon: Returns a LISP parser.
getLookupVars() - Method in class org.algernon.datatype.Closure
getMappingInfo(FrameTree, SlotTable) - Method in class org.algernon.app.Java2Protege: Returns the mapping info to convert from Protege names to Java names.
getMaximumCardinality() - Method in interface org.algernon.kb.AlgernonRelation: Returns the maximum cardinality of this relation.
getMaximumCardinality() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: Returns the maximum cardinality of this relation.
getMinimumCardinality() - Method in interface org.algernon.kb.AlgernonRelation: Returns the minimum cardinality of this relation.
getMinimumCardinality() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: Returns the minimum cardinality of this relation.
getModel() - Method in class org.algernon.app.j2p.FrameTree: Returns the model defined by this.
getModel() - Method in class org.algernon.app.j2p.TableMap
getName() - Method in class org.algernon.aam.Opcode: Returns the value of Name.
getName() - Method in class org.algernon.aam.register.GeneralRegister
getName() - Method in interface org.algernon.aam.register.Register: Returns the name of this Register.
getName() - Method in class org.algernon.app.AlgernonApplication: Returns the program name, e.g.
getName() - Method in class org.algernon.app.j2p.J2PFrame: Returns the name
getName() - Method in interface org.algernon.kb.AlgernonFrame: Returns the name of this Frame.
getName() - Method in interface org.algernon.kb.AlgernonKB: Return the name of this KB.
getName() - Method in class org.algernon.kb.AlgernonKBSet
getName() - Method in interface org.algernon.kb.AlgernonObject
getName() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Returns the name of this Frame.
getName() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns the name of this KB as a string.
getName() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeObject
getName() - Method in class org.algernon.rule.Rule
getNameFormat() - Static method in class org.algernon.rule.Rule
getNameSymbol() - Method in class org.algernon.datatype.Command
getNewConjunctionID() - Method in class org.algernon.aam.compile.AlgernonCompiler: Generate a new label.
getNewLabel() - Method in class org.algernon.aam.compile.AlgernonCompiler: Generate a new label.
getNewRelationValue() - Method in interface org.algernon.kb.event.KnowledgeBaseEvent
getNewVariable() - Method in class org.algernon.aam.compile.AlgernonCompiler: Generate a new variable.
getNodes() - Method in class org.algernon.util.SimpleTree: Returns a collection of all of the nodes in the tree.
getNumberOfArguments() - Method in class org.algernon.aam.Opcode: Returns the value of NumberOfArguments.
getNumberOfStepsForward(int) - Method in class org.algernon.aam.Processor: When in (:TRACE :STEP) mode, this method reads in an integer number of steps to step forward.
getObsoleteMessage() - Method in class org.algernon.datatype.Command
getOldRelationValue() - Method in interface org.algernon.kb.event.KnowledgeBaseEvent
getOpcode() - Method in class org.algernon.datatype.Command
getOpcodeSet() - Method in class org.algernon.Algernon
getOpcodeSet() - Method in class org.algernon.aam.Processor
getOriginalName() - Method in class org.algernon.app.j2p.J2PFrame
getOwnRelationValues(AlgernonRelation) - Method in interface org.algernon.kb.AlgernonFrame: Returns a collection of the values in the given slot.
getOwnRelationValues(AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Returns a collection of the values in the given slot.
getPackage() - Method in class org.algernon.app.Java2Protege
getPackageName(Class) - Static method in class org.algernon.util.ReflectionUtil: Returns the name of the package of the class.
getParent() - Method in class org.algernon.app.j2p.J2PClass: Returns this node's parent or null if this node has no parent.
getParent() - Method in class org.algernon.app.j2p.J2PFrame: Returns this node's parent or null if this node has no parent.
getParent(Object) - Method in class org.algernon.util.SimpleTree: Returns the parent of a node.
getParents() - Method in interface org.algernon.kb.AlgernonFrame: Returns a List of the parents of this frame.
getParents() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Returns a List of the parents of this frame.
getParents(AlgernonFrame) - Method in class org.algernon.rule.RuleManager: Returns a list of the parents of a frame.
getPath() - Method in class org.algernon.datatype.Path: Returns the LispValue containing the list of clauses in the path.
getPortNumber() - Method in class org.algernon.server.AlgernonServer: Returns the current port number.
getPossibleRelationValues(AlgernonRelation) - Method in interface org.algernon.kb.AlgernonFrame: Returns the list of existing instances that could fill the given relation on this frame.
getPossibleRelationValues(AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Returns the list of existing instances that could fill the given relation on this frame.
getProcessor() - Method in class org.algernon.Algernon
getRandomBindingList() - Method in class org.algernon.datatype.BindingSet: Returns a random binding list from the set.
getRange() - Method in class org.algernon.app.j2p.J2PSlot: Returns the range.
getRegister(LispValue) - Method in class org.algernon.aam.register.RegisterSet: Returns the Register with the given name.
getRegisterEntry(LispValue, int) - Method in class org.algernon.aam.Processor: Return the nth entry in the given register, where the topmost item is entry number zero.
getRegisterEntry(LispValue, int) - Method in class org.algernon.aam.register.RegisterSet: Return the nth entry in the given register, where the topmost item is entry number zero.
getRegisterSet() - Method in class org.algernon.aam.register.GeneralRegister
getRegisterSet() - Method in interface org.algernon.aam.register.Register: Returns the RegisterSet this Register belongs to.
getRegisterSize(LispValue) - Method in class org.algernon.aam.Processor: Return the current size of the given register.
getRegisterSize(LispValue) - Method in class org.algernon.aam.register.RegisterSet: Return the size of (number of entries in) the given register.
getRegisterValue(LispValue) - Method in class org.algernon.aam.Processor: Return the value of the given register.
getRegisterValue(LispValue) - Method in class org.algernon.aam.register.RegisterSet: Return the value of the given register.
getRegisters() - Method in class org.algernon.Algernon
getRegisters() - Method in class org.algernon.aam.Processor: Returns the RegisterSet used by this processor.
getRelation(LispValue) - Static method in class org.algernon.Algernon: Returns the relation of the clause, which is the first element of the list.
getRelation(Clause) - Static method in class org.algernon.Algernon: Returns the relation of the clause.
getRelation() - Method in class org.algernon.datatype.Clause: Returns the relation of the clause (the element in the first position).
getRelation() - Method in interface org.algernon.kb.event.KnowledgeBaseEvent
getRelationArgumentTypes(AlgernonRelation) - Method in interface org.algernon.kb.AlgernonClass: Gets the argument types of a relation as defined for that class.
getRelationArgumentTypes(AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Gets the argument types of a relation as defined for that class.
getRelationValues(AlgernonRelation) - Method in interface org.algernon.kb.AlgernonFrame: Returns the relation values.
getRelationValues(AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Returns the relation values.
getReplacement() - Method in class org.algernon.app.j2p.gui.J2PAdviceDialog: Returns a string containing the replacement value, or null
getResultVariables() - Method in class org.algernon.datatype.Result: Returns a LISP list of the variables in the Result.
getRoot() - Method in class org.algernon.app.j2p.FrameTree: Note that the root is not a J2PFrame.
getRoot() - Method in class org.algernon.rule.Rule
getRootClass() - Method in interface org.algernon.kb.AlgernonKB: Returns a the "first" root class in the KB.
getRootClass() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns a the "first" root class in the KB.
getRootClasses() - Method in interface org.algernon.kb.AlgernonFrame: Returns a collection of root classes of this class.
getRootClasses() - Method in interface org.algernon.kb.AlgernonKB: Returns a LISP list of the root classes of the KB.
getRootClasses() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Returns a collection of root classes of this class.
getRootClasses() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns a Collection of the root classes of the KB.
getRootFrame(Component) - Static method in class org.algernon.util.WindowUtil: Returns the root Frame of the given component.
getRoots() - Method in class org.algernon.util.SimpleTree: Returns a collection of the roots of the tree - those that have no parents.
getRowCount() - Method in class org.algernon.app.j2p.TableMap
getRule(String) - Method in class org.algernon.Algernon: Returns the rule with the given name.
getRule(String) - Method in class org.algernon.aam.Processor: Retrieves a rule by name.
getRule() - Method in class org.algernon.datatype.Activation: Returns the value of Rule.
getRule() - Method in class org.algernon.datatype.Closure: Returns the rule this Closure encloses.
getRule(String) - Method in class org.algernon.rule.RuleManager: Looks up a rule by its name.
getRules(String) - Method in class org.algernon.Algernon: Returns all rules with the given string in their names.
getRules(AlgernonFrame, int, int) - Method in class org.algernon.rule.RuleManager: Retrieves a collection of Closures that are associated with the given frame.
getSaveInAlgernonFile() - Method in class org.algernon.app.Java2Protege: Returns the name of the file in which to save Algernon files.
getServerPortNumber() - Method in class org.algernon.Algernon: Returns the port number the server is running on.
getShortName(Class) - Static method in class org.algernon.util.ReflectionUtil: Returns the short name of a Java class (without the package name).
getSlot() - Method in class org.algernon.datatype.Clause: Returns the slot of the clause, which is the first element if performing the traditional mapping from predicates to frames.
getSlotMappingInfo(J2PSlot) - Method in class org.algernon.app.Java2Protege: Returns a TELL statement that creates a mapping frame that stores the mapping between a Java name (Class or field) and a Protege Slot.
getSlotPrefix(String) - Method in class org.algernon.app.j2p.Advice
getSlotReplacement(String) - Method in class org.algernon.app.j2p.Advice
getSlotSuffix(String) - Method in class org.algernon.app.j2p.Advice
getSlotTable() - Method in class org.algernon.app.Java2Protege
getStepMode() - Method in class org.algernon.aam.Processor: Returns true if the tracer is in Step mode.
getStepMode() - Method in class org.algernon.aam.Tracer: Returns true if the tracer is in Step mode.
getSubClasses() - Method in class org.algernon.app.j2p.J2PClass: Returns the subclasses of this class.
getSubclasses() - Method in interface org.algernon.kb.AlgernonClass
getSubclasses() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass
getSuperClasses() - Method in class org.algernon.app.j2p.J2PClass: Returns the superclass(es) of this class.
getSuperclasses() - Method in interface org.algernon.kb.AlgernonFrame: Returns the superclass(es) of a class or the class(es) of an instance.
getSuperclasses() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Returns the direct superclass(es) of a class or the direct class(es) of an instance.
getTemplateRelations() - Method in interface org.algernon.kb.AlgernonClass: Returns the relations that are templates on this class.
getTemplateRelations() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Returns the relations that are templates on this class.
getToolTipText(String) - Method in class org.algernon.app.Java2Protege
getToolTipText(MouseEvent) - Method in class org.algernon.app.j2p.gui.J2PFrameRenderer: Returns the string to be used as the tooltip for event.
getTraceLevel() - Method in class org.algernon.Algernon: Returns the relation of the clause.
getTraceLevel() - Method in class org.algernon.aam.Processor: Returns the value of trace level.
getTraceLevelAsString() - Method in class org.algernon.aam.Processor: Returns the current trace level as a symbol such as :NORMAL, :SILENT :VERBOSE, :DETAIL, :DEBUG or :ALWAYS.
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.algernon.app.j2p.gui.J2PFrameRenderer
getType() - Method in class org.algernon.app.j2p.gui.J2PAdviceDialog: Returns either "CLASS" or "SLOT"
getType() - Method in class org.algernon.rule.Rule
getUserName() - Method in interface org.algernon.kb.AlgernonKB: Returns a String containing the name of the current user of this KB.
getUserName() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns a String containing the name of the current user of this KB.
getValue() - Method in class org.algernon.aam.register.BindingsRegister: Return the value of the given register.
getValue() - Method in class org.algernon.aam.register.GeneralRegister: Return the value of the given register.
getValue() - Method in interface org.algernon.aam.register.Register: Return the value of the given register.
getValueAt(int) - Method in class org.algernon.app.j2p.AdviceTable: Returns an attribute Vector for the cell at row.
getValueAt(int, int) - Method in class org.algernon.app.j2p.TableMap
getValueAt(int, int) - Method in class org.algernon.app.j2p.TableSorter
getValueType(Object) - Method in class org.algernon.Algernon: Get the data type of the Java object passed in; we expect this to be Integer, Float, Boolean, Cls, or Instance
getValueType(Object) - Method in interface org.algernon.kb.AlgernonKB: Get the data type of the Java object passed in; we expect this to be Integer, Float, Boolean, Frame, etc., etc
getValueType(Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Get the data type of the Java object passed in; we expect this to be Integer, Float, Boolean, Frame, etc., etc
getValueType(Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType: Get the data type of the Java object passed in; we expect this to be Integer, Float, Boolean, Cls, or Instance
getValueTypes() - Method in class org.algernon.Algernon
getValueTypes() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns a collection of AlgernonValueTypes, listing all the value types the kb knows about
getValueTypes() - Static method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
getValues() - Method in class org.algernon.datatype.Clause: Returns the values of the clause, which is all but the first two elements if performing the traditional mapping from predicates to frames.
getValues() - Method in interface org.algernon.kb.AlgernonValueType
getValues() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
getVariableArguments() - Method in class org.algernon.datatype.Clause: Returns a BindingList of the arguments in the clause that are variables.
getVariableArguments() - Method in class org.algernon.datatype.Path: Returns a BindingList of the arguments in the path that are variables.
getVariables() - Method in class org.algernon.datatype.BindingList: Returns the variables in the binding list as a LISP list.
getVersionDate() - Method in class org.algernon.app.AlgernonApplication: Returns the date of this version as a string: "nn MONTH yyyy".
getVersionMajor() - Method in class org.algernon.app.AlgernonApplication: Returns the major version number, that is, 1 in version 1.2.3.
getVersionMicro() - Method in class org.algernon.app.AlgernonApplication: Returns the micro version number, that is, 3 in version 1.2.3.
getVersionMinor() - Method in class org.algernon.app.AlgernonApplication: Returns the minor version number, that is, 2 in version 1.2.3.
getVersionString() - Method in class org.algernon.app.AlgernonApplication: Returns the entire version string.
getVersionType() - Method in class org.algernon.app.AlgernonApplication: Returns the type of release: "production", "beta" or "alpha".
getVersionURL() - Method in class org.algernon.app.AlgernonApplication: Returns a URL where you can find info about Application.
getWarnings() - Method in class org.algernon.util.ErrorSet: Returns a collection of warnings, which are Strings.

H

HELP_TAB_INDEX - Static variable in class org.algernon.app.j2p.gui.J2PWindow
HELP_URL - Static variable in class org.algernon.app.Java2Protege
HaltException - exception org.algernon.aam.HaltException.: This exception is thrown when the processor executes a HALT opcode.
HaltException(String) - Constructor for class org.algernon.aam.HaltException: Creates a new HaltException.
hasDirectInstance(AlgernonInstance) - Method in interface org.algernon.kb.AlgernonClass: Returns true if this class includes instance as one of its direct instances.
hasDirectInstance(AlgernonInstance) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Returns true if this class includes instance as one of its direct instances.
hasDirectSuperclass(AlgernonClass) - Method in interface org.algernon.kb.AlgernonClass: Returns true if this class includes superclass as one of its direct superclasses.
hasDirectSuperclass(AlgernonClass) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Returns true if this class includes superclass as one of its direct superclasses.
hasError() - Method in class org.algernon.app.j2p.J2PFrame: gets the hasError flag.
hasInstance(AlgernonInstance) - Method in interface org.algernon.kb.AlgernonClass: Returns true if this class includes instance as one of its direct instances, or as a direct instance of one of its subclasses.
hasInstance(AlgernonInstance) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Returns true if this class includes instance as one of its direct instances, or as a direct instance of one of its subclasses.
hasInvalidArgumentCount(LispValue, int, int) - Method in class org.algernon.aam.compile.AlgernonCompiler: Checks the argument count against the requirements.
hasLeafSubclass(AlgernonClass) - Method in interface org.algernon.kb.AlgernonClass: Returns true if leaf is a leaf subclass of this class.
hasLeafSubclass(AlgernonClass) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Returns true if leaf is a leaf subclass of this class.
hasNext() - Method in class org.algernon.app.j2p.SlotTableIterator: Returns true if the iteration has more elements.
hasNoBindings - Variable in class org.algernon.aam.compile.AlgernonCompilerState: When a :SUBR is being compiled we don't want to push bindings onto the BINDINGS register.
hasParent(AlgernonFrame) - Method in interface org.algernon.kb.AlgernonFrame: Returns true if the argument is a parent of this frame.
hasParent(AlgernonFrame) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Returns true if the argument is a parent of this frame.
hasRootClass(AlgernonClass) - Method in interface org.algernon.kb.AlgernonFrame: Returns true if root is a root class of this class.
hasRootClass(AlgernonClass) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Returns true if root is a root class of this class.
hasSameVariables(BindingList) - Method in class org.algernon.datatype.BindingList: Returns true if the input binding list contains the exact same set of variables as this binding list.
hasSingleBinding(LispValue) - Method in class org.algernon.datatype.BindingSet: Returns true if the given variable has one and only one binding in this binding set.
hasSpecialArguments() - Method in class org.algernon.datatype.Command
hasSuperclass(AlgernonClass) - Method in interface org.algernon.kb.AlgernonFrame: Returns true if this class includes superclass as one of its superclasses, direct or indirect.
hasSuperclass(AlgernonClass) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Returns true if this class includes superclass as one of its superclasses, direct or indirect.
hasTemplateRelation(AlgernonRelation) - Method in interface org.algernon.kb.AlgernonClass: Returns true if the given relation is a template relation of this class.
hasTemplateRelation(AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Returns true if the given relation is a template relation of this class.
hashCode() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType: Forwards the hashcode method to the Protege object so that hash tables of Protege objects will not store duplicate frames.

I

ID - Variable in class org.algernon.aam.register.RegisterSet: The ID of the activation being processed.
ID_FORMAT - Static variable in class org.algernon.datatype.Closure
ID_NAME - Static variable in class org.algernon.datatype.Closure
INCLUSIVE - Variable in class org.algernon.Algernon: Used in structure-traversing commands like :CHILD.
INDEX - Variable in class org.algernon.aam.register.RegisterSet: Number of the clause being processed.
INITIAL_LIST_SIZE - Static variable in class org.algernon.rule.RuleManager
INPUT_AREA_TAB_SIZE - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
INPUT_COLUMNS - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
INPUT_PANEL_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
INPUT_ROWS - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
INSTANCE - Variable in class org.algernon.aam.OpcodeSet
INSTANCE_TYPE - Variable in class org.algernon.Algernon
INTEGER - Static variable in interface org.algernon.kb.AlgernonValueType
INTEGER - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
INTEGER_TYPE - Variable in class org.algernon.Algernon
INVERSE - Variable in class org.algernon.Algernon: Used when defining a relation.
IS_CLASS - Variable in class org.algernon.aam.OpcodeSet
IS_FACET - Variable in class org.algernon.aam.OpcodeSet
IS_FRAME - Variable in class org.algernon.aam.OpcodeSet
IS_INSTANCE - Variable in class org.algernon.aam.OpcodeSet
IS_RELATION - Variable in class org.algernon.aam.OpcodeSet
InitializeAlgernonTwice - class org.algernon.test.InitializeAlgernonTwice.: Tests whether Algernon works correctly when initialized twice from the same program.
InitializeAlgernonTwice() - Constructor for class org.algernon.test.InitializeAlgernonTwice
Instance - class org.algernon.aam.opcode.Instance.: This class implements the Instance Opcode in the AAM.
Instance(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Instance: Create a new AAM Opcode.
IsClass - class org.algernon.aam.opcode.IsClass.: This opcode confirms a class in the KB.
IsClass(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.IsClass
IsFacet - class org.algernon.aam.opcode.IsFacet.: This opcode confirms a facet in the KB.
IsFacet(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.IsFacet
IsFrame - class org.algernon.aam.opcode.IsFrame.: This opcode confirms a frame in the KB.
IsFrame(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.IsFrame
IsInstance - class org.algernon.aam.opcode.IsInstance.: This opcode confirms an instance in the KB.
IsInstance(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.IsInstance
IsRelation - class org.algernon.aam.opcode.IsRelation.: This opcode confirms a relation in the KB.
IsRelation(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.IsRelation
illegalSequence(LispString) - Method in class org.algernon.test.PharmGKBTest1
illegalSequence(String) - Method in class org.algernon.test.PharmGKBTest1
implicitTypeRestrict(AlgernonKBSet, Clause, Map, AlgernonCompilerState, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: Added 29 Sep 1999 (mh) Added type restriction - if the path contains an ISA or MEMBER clause, this information is used to restrict the type to a new type, eliminating some unnecessary warning messages The clause should NOT be negated.
indexes - Variable in class org.algernon.app.j2p.TableSorter
init(String[]) - Method in class org.algernon.app.Java2Protege: Initializes variables from the command-line arguments.
init() - Method in class org.algernon.app.j2p.gui.J2PAdviceDialog
init() - Method in class org.algernon.app.j2p.gui.J2PWindow
init() - Method in class org.algernon.test.BackwardTest: Reads in the parameters and tries to open the KB.
init() - Method in class org.algernon.test.BasicTest: Reads in the parameters and tries to open the KB.
init() - Method in class org.algernon.test.DBTest: Reads in the parameters and tries to open the KB.
init() - Method in class org.algernon.test.DeleteTest: Reads in the parameters and tries to open the KB.
init() - Method in class org.algernon.test.ForwardTest: Reads in the parameters and tries to open the KB.
init() - Method in class org.algernon.test.GenericLoader: Reads in the parameters and tries to open the KB.
init() - Method in class org.algernon.test.MiscellanyTest: Reads in the parameters and tries to open the KB.
init() - Method in class org.algernon.test.PharmGKBTest1: Reads in the parameters and tries to open the KB.
init() - Method in class org.algernon.test.PharmGKBTest2: Reads in the parameters and tries to open the KB.
init() - Method in class org.algernon.test.SimpleAlgernonExample: Opens the KB and initializes Algernon.
init() - Method in class org.algernon.test.SpecialTest: Reads in the parameters and tries to open the KB.
init() - Method in class org.algernon.test.StructureTest: Reads in the parameters and tries to open the KB.
init() - Method in class org.algernon.test.TaxonomyTest: Reads in the parameters and tries to open the KB.
init() - Method in class org.algernon.test.TestAll: Reads in the parameters and tries to open the KB.
init() - Method in class org.algernon.test.TypeTest: Reads in the parameters and tries to open the KB.
initAlgernon() - Method in class org.algernon.test.InitializeAlgernonTwice
initialize() - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
initializeArgumentTypes(AlgernonKBSet, Map, Path, AlgernonCompilerState, ErrorSet, boolean) - Method in class org.algernon.aam.compile.AlgernonCompiler: The compiler type-checks each clause.
initializeConstants() - Method in class org.algernon.aam.compile.AlgernonCompiler: variable initializer for this class.
initializeInstance(AlgernonInstance) - Method in class org.algernon.kb.agent.google.GoogleKB: Initialize an instance after creating it.
initializeOpcodes() - Method in class org.algernon.aam.OpcodeSet
initializeRegisters() - Method in class org.algernon.aam.register.RegisterSet: Initializes the register contents to NIL.
initializeValues() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
insertDepthFirst(LispValue, LispValue) - Method in class org.algernon.Algernon: This is the default actionQueueInsertionFunction.
instantiate(LispValue, LispValue) - Method in class org.algernon.Algernon
invalidPosition(LispInteger, LispInteger, LispInteger) - Method in class org.algernon.test.PharmGKBTest1
invalidPosition(long, long, long) - Method in class org.algernon.test.PharmGKBTest1
isBackwardChaining() - Method in class org.algernon.rule.Rule: Returns true if this rule is a backward-chaining rule.
isBuiltinRange(String) - Method in class org.algernon.app.Java2Protege: returns true if the string represents an atomic slot range such as :INTEGER.
isCellEditable(int, int) - Method in class org.algernon.app.j2p.AdviceTable
isCellEditable(int, int) - Method in class org.algernon.app.j2p.SlotTable
isCellEditable(int, int) - Method in class org.algernon.app.j2p.TableMap
isClass(String) - Method in interface org.algernon.kb.AlgernonKB: Returns true if the String is the name of a frame that is a class in the KB.
isClass(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns the Class if the String is the name of a frame that is a class in the KB.
isClassToInstanceRelation(String) - Method in class org.algernon.Algernon: Returns true if the given string is the name of the relation/slot linking an instance to its class in any KB of the default AlgernonKBSet.
isClassToInstanceRelation(String, AlgernonKBSet) - Method in class org.algernon.Algernon: Returns true if the given string is the name of the relation/slot linking an instance to its class in any KB of the given AlgernonKBSet.
isClassToInstanceRelation(String, AlgernonKB) - Method in class org.algernon.Algernon: Returns true if the given string is the name of the relation/slot linking an instance to its class in the given KB.
isClassToInstanceRelation(String) - Method in interface org.algernon.kb.AlgernonKB: Returns true if the given string is the name of the relation/slot linking a class to its instance in this KB.
isClassToInstanceRelation(String) - Method in class org.algernon.kb.AlgernonKBSet: Returns true if the given string is the name of the relation/slot linking a class to its instance in any KB of this AlgernonKBSet.
isClassToInstanceRelation(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns true if the given string is the name of the relation/slot linking a class to its instance in this KB.
isContinuable(Clause) - Method in class org.algernon.aam.compile.AlgernonCompiler: Returns true if continuations should be created for the given operation.
isDisjointRelation(String) - Method in class org.algernon.Algernon: Returns true if the given string is the name of a relation specifying that two classes are disjoint
isDisjointRelation(String, AlgernonKB) - Method in class org.algernon.Algernon: Returns true if the given string is the name of a relation specifying that two classes are disjoint in the given KB.
isDisjointRelation(String, AlgernonKBSet) - Method in class org.algernon.Algernon: Returns true if the given string is the name of a relation specifying that two classes are disjoint in any KB of the given AlgernonKBSet.
isDisjointRelation(String) - Method in interface org.algernon.kb.AlgernonKB: Returns true if the given string is the name of a relation specifying that two classes are disjoint
isDisjointRelation(String) - Method in class org.algernon.kb.AlgernonKBSet: Returns true if the given string is the name of a relation specifying that two classes are disjoint
isDisjointRelation(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Always returns false - Protege has no default disjoint relation.
isEmpty() - Method in class org.algernon.datatype.BindingSet: Returns true if this binding set contains no bindings.
isEmpty(String) - Static method in class org.algernon.util.StringUtil: Returns true if the string is null or empty.
isEnabled() - Method in class org.algernon.aam.Profiler: Returns the value of Enabled.
isEnumeration(String) - Method in class org.algernon.app.Java2Protege
isFacet(String) - Method in interface org.algernon.kb.AlgernonKB: Returns true if the String is the name of a frame in the KB.
isFacet(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns true if the String is the name of a frame that is a facet in the KB.
isForwardChaining() - Method in class org.algernon.rule.Rule: Returns true if this rule is a forward-chaining rule.
isFrame(String) - Method in class org.algernon.Algernon: Returns true if the given string is the name of a frame in any KB.
isFrame(String, AlgernonKB) - Method in class org.algernon.Algernon: Returns true if the given string is the name of a frame in the given KB.
isFrame(String, AlgernonKBSet) - Method in class org.algernon.Algernon: Returns true if the given string is the name of a frame in any KB in the given AlgernonKBSet.
isFrame(String) - Method in interface org.algernon.kb.AlgernonKB: Returns true if the String is the name of a frame in the KB.
isFrame(String) - Method in class org.algernon.kb.AlgernonKBSet: Returns true if the given string is the name of a frame in any KB of this AlgernonKBSet.
isFrame(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns the Frame if the String is the name of a frame in the KB.
isFrameType(Set) - Method in class org.algernon.aam.compile.AlgernonCompiler
isGround() - Method in class org.algernon.datatype.Clause: Returns true if the clause contains no variables.
isGround() - Method in class org.algernon.datatype.Path: Returns true if the path contains no unground clauses.
isGroundClause(Clause) - Static method in class org.algernon.Algernon: Returns true if the given clause is ground (contains no variables).
isGroundPath(Path) - Static method in class org.algernon.Algernon: Returns true if the given clause is ground (contains no variables).
isHistoricalQuery(Clause) - Method in class org.algernon.aam.Processor: Returns true if the clause or a generalization of it has been made before.
isIgnored() - Method in class org.algernon.app.j2p.J2PFrame: returns true if the user doesn't want to export this one.
isInstance(LispValue, LispValue) - Method in class org.algernon.Algernon: Determines whether clause is an instance of pattern, returning true or false.
isInstance(Clause, Clause) - Method in class org.algernon.Algernon: Determines whether clause is an instance of pattern, returning true or false.
isInstance(Clause, Clause, BindingList, BindingList) - Method in class org.algernon.Algernon: Determines whether clause is an instance of pattern, returning true or false.
isInstance(LispValue, LispValue, BindingList, BindingList) - Method in class org.algernon.Algernon: Determines whether clause is an instance of pattern, returning true or false.
isInstance(LispValue, LispValue) - Method in class org.algernon.aam.Processor: Determines whether clause is an instance of pattern, returning true or false.
isInstance(String) - Method in interface org.algernon.kb.AlgernonKB: Returns true if the String is the name of a frame that is an instance in the KB.
isInstance(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns the Instance if the String is the name of a frame that is an instance in the KB.
isInstanceToClassRelation(String) - Method in class org.algernon.Algernon: Returns true if the given string is the name of the relation/slot linking an instance to its class in any KB of the default AlgernonKBSet.
isInstanceToClassRelation(String, AlgernonKBSet) - Method in class org.algernon.Algernon: Returns true if the given string is the name of the relation/slot linking an instance to its class in any KB of the given AlgernonKBSet.
isInstanceToClassRelation(String, AlgernonKB) - Method in class org.algernon.Algernon: Returns true if the given string is the name of the relation/slot linking an instance to its class in the given KB.
isInstanceToClassRelation(String) - Method in interface org.algernon.kb.AlgernonKB: Returns true if the given string is the name of the relation/slot linking an instance to its class in this KB.
isInstanceToClassRelation(String) - Method in class org.algernon.kb.AlgernonKBSet: Returns true if the given string is the name of the relation/slot linking an instance to its class in any KB of this AlgernonKBSet.
isInstanceToClassRelation(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns true if the given string is the name of the relation/slot linking an instance to its class in this KB.
isLastClause - Variable in class org.algernon.aam.compile.AlgernonCompilerState: True if we are compiling the last clause of a path.
isLeaf() - Method in class org.algernon.app.j2p.J2PClass: Returns true if this node has no children.
isLeaf() - Method in class org.algernon.app.j2p.J2PFrame: Returns true if this node has no children.
isLeafClass() - Method in class org.algernon.app.j2p.J2PClass: Returns true if this is a leaf class.
isLeafClass() - Method in interface org.algernon.kb.AlgernonClass: Returns true if this is one of the leaf classes of the KB.
isLeafClass() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Returns true if this is one of the leaf classes of the KB.
isMacro(LispValue) - Method in class org.algernon.aam.compile.AlgernonCompiler: Returns true if the given symbol is an Algernon special form.
isNameRelation(String) - Method in class org.algernon.Algernon: Returns true if the given string is the name of the relation/attribute linking a frame to its name in any KB.
isNameRelation(String, AlgernonKB) - Method in class org.algernon.Algernon: Returns true if the given string is the name of the relation/slot linking a frame to its name in the given KB.
isNameRelation(String, AlgernonKBSet) - Method in class org.algernon.Algernon: Returns true if the given string is the name of the relation/slot linking a frame to its name in any KB in the given AlgernonKBSet.
isNameRelation(String) - Method in interface org.algernon.kb.AlgernonKB: Returns true if the given relation is the name relation in this KB.
isNameRelation(String) - Method in class org.algernon.kb.AlgernonKBSet: Returns true if the given string is the name of the name relation (or attribute) in any KB of this AlgernonKBSet.
isNameRelation(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns true if the string is the name of a NAME relation in this KB.
isNegated() - Method in class org.algernon.datatype.Clause: Returns true if the clause is negated, that is, if it has the form (NOT [clause]).
isObsolete() - Method in class org.algernon.datatype.Command
isOfSimpleType(LispValue, Set) - Method in class org.algernon.aam.compile.AlgernonCompiler: Returns true if the argument satisfies the simple type.
isPathUnrestricted(LispValue) - Method in class org.algernon.aam.compile.AlgernonCompiler: Returns true if the given symbol is not required to follow the Algernon path restrictions.
isPathUnrestricted() - Method in class org.algernon.datatype.Command
isRelation(String) - Method in class org.algernon.Algernon: Returns true if the given string is the name of a relation in any KB.
isRelation(String, AlgernonKB) - Method in class org.algernon.Algernon: Returns true if the given string is the name of a relation in the given KB.
isRelation(String, AlgernonKBSet) - Method in class org.algernon.Algernon: Returns true if the given string is the name of a frame in any KB in the given AlgernonKBSet.
isRelation(String) - Method in interface org.algernon.kb.AlgernonKB: Returns true if the String is the name of a frame that is a relation in the KB.
isRelation(String) - Method in class org.algernon.kb.AlgernonKBSet: Returns true if the given string is the name of a relation in any KB in the given AlgernonKBSet.
isRelation(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns the Relation if the String is the name of a frame that is a relation in the KB.
isRootClass() - Method in interface org.algernon.kb.AlgernonClass: Returns true if this is one of the root classes of the KB.
isRootClass() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Returns true if this is one of the root classes of the KB.
isRootClassOfItsPackage(Class) - Static method in class org.algernon.util.ReflectionUtil: Returns true if the given class does not have a superclass in the given package.
isRuleTraced(Rule) - Method in class org.algernon.aam.Tracer: Returns true if the given rule is currently traced.
isRunning() - Method in class org.algernon.server.AlgernonServer: Returns true if the server is running.
isSimpleType(LispValue) - Method in class org.algernon.aam.compile.AlgernonCompiler: Returns true if the type is not a frame type.
isSimpleType(Set) - Method in class org.algernon.aam.compile.AlgernonCompiler: Returns true if the type set contains only simple types.
isSimpleType(AlgernonRelation) - Method in interface org.algernon.kb.AlgernonKB: Determines if this slot takes an atomic data type value
isSimpleType(AlgernonFrame, AlgernonRelation) - Method in interface org.algernon.kb.AlgernonKB: Determines if this slot at the class takes an atomic data type value
isSimpleType() - Method in interface org.algernon.kb.AlgernonValueType: Predicate that returns true if this AlgernonValueType is a BOOLEAN, NUMBER, FLOAT, STRING, or SYMBOL
isSimpleType(Slot) - Static method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB
isSimpleType(AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Determines if this slot takes an atomic data type value
isSimpleType(Frame, Slot) - Static method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Checks the ValueType of slot AT THE CLASS--returns true if it's simple
isSimpleType(AlgernonFrame, AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Determines if this slot takes an atomic data type value.
isSimpleType() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType: Predicate that returns true if this AlgernonValueType is a BOOLEAN, INTEGER, FLOAT, STRING, or SYMBOL
isSubclassToSuperclassRelation(String) - Method in class org.algernon.Algernon: Returns true if the given string is the name of the relation/attribute linking a class to its superclass in any KB.
isSubclassToSuperclassRelation(String, AlgernonKB) - Method in class org.algernon.Algernon: Returns true if the given string is the name of the relation/slot linking a frame to its name in the given KB.
isSubclassToSuperclassRelation(String, AlgernonKBSet) - Method in class org.algernon.Algernon: Returns true if the given string is the name of the relation/slot linking a frame to its name in any KB in the given AlgernonKBSet.
isSubclassToSuperclassRelation(String) - Method in interface org.algernon.kb.AlgernonKB: Returns true if the given string is the name of the relation/slot linking a frame to its name in this KB.
isSubclassToSuperclassRelation(String) - Method in class org.algernon.kb.AlgernonKBSet: Returns true if the given string is the name of the relation/slot linking a frame to its name in any KB in the given AlgernonKBSet.
isSubclassToSuperclassRelation(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns true if the given string is the name of the relation/slot linking a frame to its name in any KB in the given AlgernonKBSet.
isSuperclassToSubclassRelation(String) - Method in interface org.algernon.kb.AlgernonKB: Returns true if the given string is the name of the relation/slot linking a frame to its name in this KB.
isSuperclassToSubclassRelation(String) - Method in class org.algernon.kb.AlgernonKBSet: Returns true if the given string is the name of the relation/slot linking a frame to its name in any KB in the given AlgernonKBSet.
isSuperclassToSubclassRelation(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns true if the given string is the name of the relation/slot linking a frame to its name in any KB in the given AlgernonKBSet.
isSyntacticallyLegal() - Method in class org.algernon.datatype.Path: Returns true if the path is syntactically legal.
isValidPackage(String) - Method in class org.algernon.app.Java2Protege
isVariable(LispValue) - Static method in class org.algernon.Algernon: Returns true if the given value represents a variable in the system.
iterator() - Method in class org.algernon.datatype.BindingList: Returns an iterator over the BindingSet.
iterator() - Method in class org.algernon.datatype.BindingSet: Returns an iterator over the BindingSet.
iterator() - Method in class org.algernon.datatype.Path: Returns an iterator across the path.
iterator() - Method in class org.algernon.datatype.Result: Each element of the iteration is a BindingList.

J

J2PAdviceDialog - class org.algernon.app.j2p.gui.J2PAdviceDialog.: J2PAdviceDialog shows a dialog that lets the user enter a piece of advice for the Java2Protege program.
J2PAdviceDialog(J2PWindow) - Constructor for class org.algernon.app.j2p.gui.J2PAdviceDialog
J2PClass - class org.algernon.app.j2p.J2PClass.: J2PClass does...
J2PClass(String, String) - Constructor for class org.algernon.app.j2p.J2PClass
J2PConversionError - exception org.algernon.app.j2p.error.J2PConversionError.: J2PConversionError defines an error that occurs during Java to KB conversion.
J2PConversionError(String) - Constructor for class org.algernon.app.j2p.error.J2PConversionError
J2PDuplicateFrameNameError - exception org.algernon.app.j2p.error.J2PDuplicateFrameNameError.: J2PDuplicateFrameNameError defines an error when a class name is used more than once.
J2PDuplicateFrameNameError(J2PFrame) - Constructor for class org.algernon.app.j2p.error.J2PDuplicateFrameNameError
J2PError - exception org.algernon.app.j2p.error.J2PError.: J2PError is the base class for all errors detected by J2PError.
J2PError(String, J2PFrame) - Constructor for class org.algernon.app.j2p.error.J2PError
J2PFrame - class org.algernon.app.j2p.J2PFrame.: J2PFrame is an abstract base class for Java2Protege classes and slots.
J2PFrame(String, String) - Constructor for class org.algernon.app.j2p.J2PFrame
J2PFrameRenderer - class org.algernon.app.j2p.gui.J2PFrameRenderer.: J2PFrameRenderer displays a J2PFrame in a JTree.
J2PFrameRenderer(Java2Protege) - Constructor for class org.algernon.app.j2p.gui.J2PFrameRenderer
J2PSlot - class org.algernon.app.j2p.J2PSlot.: J2PSlot stores a slot definition for Java2Protege
J2PSlot(String, String) - Constructor for class org.algernon.app.j2p.J2PSlot
J2PSlotWithSameNameAsClassError - exception org.algernon.app.j2p.error.J2PSlotWithSameNameAsClassError.: J2PSlotWithSameNameAsClassError defines an error when a slot has the same name as a class.
J2PSlotWithSameNameAsClassError(J2PFrame, String) - Constructor for class org.algernon.app.j2p.error.J2PSlotWithSameNameAsClassError
J2PUnknownDomainError - exception org.algernon.app.j2p.error.J2PUnknownDomainError.: J2PDuplicateFrameNameError defines an error when a class name is used more than once.
J2PUnknownDomainError(J2PFrame, String) - Constructor for class org.algernon.app.j2p.error.J2PUnknownDomainError
J2PUnknownRangeError - exception org.algernon.app.j2p.error.J2PUnknownRangeError.: J2PDuplicateFrameNameError defines an error when a class name is used more than once.
J2PUnknownRangeError(J2PFrame, String, String) - Constructor for class org.algernon.app.j2p.error.J2PUnknownRangeError
J2PWindow - class org.algernon.app.j2p.gui.J2PWindow.: J2PWindow is the main window for Java2Protege.
J2PWindow(Java2Protege) - Constructor for class org.algernon.app.j2p.gui.J2PWindow: Pass in the Java2Protege instance.
JathaEvaluator - class org.algernon.lang.lisp.JathaEvaluator.: Evaluator for java method calls and expressions.
JathaEvaluator() - Constructor for class org.algernon.lang.lisp.JathaEvaluator
Java2Protege - class org.algernon.app.Java2Protege.: Java2Protege converts a Java package to a Protege ontology.
Java2Protege() - Constructor for class org.algernon.app.Java2Protege
Java2ProtegeAction - class org.algernon.app.j2p.action.Java2ProtegeAction.: Abstract base class used for AlgernonTab actions.
Java2ProtegeAction(J2PWindow, String, String, KeyStroke, Integer) - Constructor for class org.algernon.app.j2p.action.Java2ProtegeAction: Creates a new Action.
JavaEvaluator - class org.algernon.lang.java.JavaEvaluator.: Evaluator for java method calls and expressions.
JavaEvaluator() - Constructor for class org.algernon.lang.java.JavaEvaluator

K

KBModified(KnowledgeBaseEvent) - Method in interface org.algernon.kb.event.KnowledgeBaseListener: This method is called when anything in a knowledge base is modified.
KB_CREATE_EVENT - Static variable in interface org.algernon.kb.event.KnowledgeBaseEvent
KB_DELETE_EVENt - Static variable in interface org.algernon.kb.event.KnowledgeBaseEvent
KB_MODIFY_EVENT - Static variable in interface org.algernon.kb.event.KnowledgeBaseEvent
KEY - Variable in class org.algernon.aam.register.RegisterSet: Key clause of backward chaining rules.
KNOWN - Variable in class org.algernon.aam.Processor
KnowledgeBaseEvent - interface org.algernon.kb.event.KnowledgeBaseEvent.: User: hewett Date: May 28, 2003 Time: 3:44:49 PM
KnowledgeBaseListener - interface org.algernon.kb.event.KnowledgeBaseListener.: User: hewett Date: May 28, 2003 Time: 3:42:01 PM
kbSetRenamed(AlgernonKBSet, String, String) - Method in class org.algernon.Algernon: Call this when a AlgernonKBSet is renamed.
keySet() - Method in class org.algernon.datatype.BindingList: Returns a set of the variables in this BindingList.

L

LABEL - Variable in class org.algernon.aam.OpcodeSet
LABEL_COLOR - Variable in class org.algernon.app.j2p.gui.J2PWindow
LABEL_COLOR - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
LARGE_INITIAL_HASH_SIZE - Static variable in class org.algernon.rule.RuleManager
LARGE_NEWSPAPER - Static variable in class org.algernon.test.ProtegeTest
LEAF_CLASS - Variable in class org.algernon.aam.OpcodeSet
LEAST_COMMON_SUPERCLASS - Variable in class org.algernon.aam.OpcodeSet
LIMIT - Variable in class org.algernon.aam.OpcodeSet
LISP_TYPE_DOMAINS - Variable in class org.algernon.Algernon
LOAD_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
LOAD_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
LOAD_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
LOAD_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
Label - class org.algernon.aam.opcode.Label.: This class represents a Label Opcode in the AAM.
Label(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Label: Create a new AAM :LABEL Opcode.
LeafClass - class org.algernon.aam.opcode.LeafClass.: LeafClass expects a clause of the form (:LEAF-CLASS class ?var).
LeafClass(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.LeafClass
LeastCommonSuperclass - class org.algernon.aam.opcode.LeastCommonSuperclass.: This opcode finds the least common superclass of two frames..
LeastCommonSuperclass(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.LeastCommonSuperclass
Limit - class org.algernon.aam.opcode.Limit.: This class implements the LIMIT Opcode in the AAM.
Limit(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Limit: Create a new AAM Limit Opcode.
LoadAction - class org.algernon.kb.okbc.protege.plugins.action.LoadAction.: LoadAction performs the action of loading a file in the Algernon Tab.
LoadAction(AlgernonTab, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.LoadAction: Creates a new LoadAction.
LoadRulesDialog - class org.algernon.kb.okbc.protege.plugins.gui.LoadRulesDialog.: A dialog that allows the user to select one class from a list of classes, or to specify another class to load from.
LoadRulesDialog(JRootPane, List) - Constructor for class org.algernon.kb.okbc.protege.plugins.gui.LoadRulesDialog
leastCommonSuperclass(AlgernonFrame, AlgernonFrame) - Method in interface org.algernon.kb.AlgernonKB: Returns the most specialized common superclass of the two classes or instances.
leastCommonSuperclass(AlgernonFrame, AlgernonFrame) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns the most specialized common superclass of the two classes or instances.
leftJustify(String, int) - Static method in class org.algernon.util.StringUtil: Returns a new string with spaces on the right to make the string as wide as the given width.
limit_testFile - Variable in class org.algernon.test.MiscellanyTest
load(String) - Method in class org.algernon.Algernon: Loads and executes a file of Algernon forms.
load(String, int) - Method in class org.algernon.Algernon: Loads and executes a file of Algernon forms.
loadRulesFromKB(Collection) - Method in class org.algernon.Algernon: Loads rules that have been stored in a KB.
localCache - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeKB
localDisplayNameCache - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeKB
lookupArgumentType(LispValue, Map) - Method in class org.algernon.aam.compile.AlgernonCompiler: Returns a set of argument types for an argument.
lookupClass(String) - Method in class org.algernon.Algernon: Returns a class with the given name if it can find one in any of the KBs in the default KBSet.
lookupClass(String, AlgernonKB) - Method in class org.algernon.Algernon: Returns a class with the given name if it can find one in the given KB.
lookupClass(String, AlgernonKBSet) - Method in class org.algernon.Algernon: Returns a class with the given name if it can find one in any of the KBs in the given KBSet.
lookupClass(String) - Method in interface org.algernon.kb.AlgernonKB: Returns a class with the given name, if any.
lookupClass(String) - Method in class org.algernon.kb.AlgernonKBSet: Returns a class with the given name if it can find one in any of the KBs in this KBSet.
lookupClass(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns a class with the given name if it can find one in this KB.
lookupDirectInstances(AlgernonClass) - Method in class org.algernon.Algernon: Returns a list of all direct instances of the given class.
lookupDirectSubclasses(AlgernonClass) - Method in class org.algernon.Algernon: Returns a list of all subclasses, whether indirect or direct, of the given class.
lookupFacet(String) - Method in interface org.algernon.kb.AlgernonKB: Returns a facet with the given name, if any.
lookupFacet(String) - Method in class org.algernon.kb.AlgernonKBSet: Returns a facet with the given name if it can find one in any of the KBs in this KBSet.
lookupFacet(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns a frame with the given name if it can find one in this KB.
lookupFrame(String) - Method in class org.algernon.Algernon: Returns a frame with the given name if it can find one in any of the KBs in the default KBSet.
lookupFrame(String, AlgernonKB) - Method in class org.algernon.Algernon: Returns a frame with the given name if it can find one in the given KB.
lookupFrame(String, AlgernonKBSet) - Method in class org.algernon.Algernon: Returns a class with the given name if it can find one in any of the KBs in the given KBSet.
lookupFrame(String) - Method in interface org.algernon.kb.AlgernonKB: Returns a frame with the given name, if any.
lookupFrame(String) - Method in class org.algernon.kb.AlgernonKBSet: Returns a frame with the given name if it can find one in any of the KBs in this KBSet.
lookupFrame(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns a frame with the given name if it can find one in this KB.
lookupInstance(String) - Method in interface org.algernon.kb.AlgernonKB: Returns an instance with the given name, if any.
lookupInstance(String, String) - Method in interface org.algernon.kb.AlgernonKB: Returns a frame with the given name if it can find one in this KB.
lookupInstance(String, String, String) - Method in interface org.algernon.kb.AlgernonKB: Returns a frame with the given name if it can find one in this KB.
lookupInstance(String) - Method in class org.algernon.kb.AlgernonKBSet
lookupInstance(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns a frame with the given name if it can find one in this KB.
lookupInstance(String, String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns a frame with the given name if it can find one in this KB.
lookupInstance(String, String, String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns a frame with the given name if it can find one in this KB.
lookupInstances(AlgernonClass) - Method in class org.algernon.Algernon: Returns a list of all instances, whether indirect or direct, of the given class.
lookupRelation(String) - Method in class org.algernon.Algernon: Returns a relation with the given name if it can find one in any of the KBs in the default KBSet.
lookupRelation(String, AlgernonKB) - Method in class org.algernon.Algernon: Returns a relation with the given name if it can find one in the given KB.
lookupRelation(String, AlgernonKBSet) - Method in class org.algernon.Algernon: Returns a relation with the given name if it can find one in any of the KBs in the given KBSet.
lookupRelation(String) - Method in interface org.algernon.kb.AlgernonClass: Some KBMS support redefining relations (slots) at different classes.
lookupRelation(String) - Method in interface org.algernon.kb.AlgernonKB: Returns a relation with the given name, if any.
lookupRelation(String, Set) - Method in interface org.algernon.kb.AlgernonKB: Returns a relation with the given name, if any.
lookupRelation(String) - Method in class org.algernon.kb.AlgernonKBSet: Returns a relation with the given name if it can find one in the given KB.
lookupRelation(String, Set) - Method in class org.algernon.kb.AlgernonKBSet: Returns a relation with the given name if it can find one in the given KB.
lookupRelation(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass: Returns the definition of the slot that is visible on this class.
lookupRelation(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns a relation with the given name if it can find one in this KB.
lookupRelation(String, Set) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB
lookupSubclasses(AlgernonClass) - Method in class org.algernon.Algernon: Returns a list of all subclasses, whether indirect or direct, of the given class.

M

MAIN_LABEL_FONT_SIZE - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
MAIN_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
MAX_CARDINALITY - Variable in class org.algernon.Algernon: Used when defining a relation.
MAX_NAME_LENGTH - Variable in class org.algernon.app.j2p.J2PFrame
MENU_HEIGHT - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
MENU_TITLE_COLOR - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
MENU_TITLE_FONT_SIZE - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
MENU_WIDTH - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
MERGE_BINDINGS - Variable in class org.algernon.aam.OpcodeSet
MESSAGE_AREA_TAB_SIZE - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
MESSAGE_COLUMNS - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
MESSAGE_PANEL_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
MESSAGE_ROWS - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
MIN_CARDINALITY - Variable in class org.algernon.Algernon: Used when defining a relation.
MergeBindings - class org.algernon.aam.opcode.MergeBindings.: This class represents a MergeBindings Opcode in the AAM.
MergeBindings(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.MergeBindings: Create a new AAM :MERGEBINDINGS Opcode.
MiscellanyTest - class org.algernon.test.MiscellanyTest.: Tests miscellaneous functionality of Algernon.
MiscellanyTest() - Constructor for class org.algernon.test.MiscellanyTest
MultipleAlgernonObjTestCase - class org.algernon.test.MultipleAlgernonObjTestCase.: Tests whether Algernon works correctly when initialized several times from the same program.
MultipleAlgernonObjTestCase() - Constructor for class org.algernon.test.MultipleAlgernonObjTestCase
m_KBSets - Variable in class org.algernon.Algernon
m_PharmGKB_Beta - Variable in class org.algernon.test.BasicTest
m_PharmGKB_Beta - Static variable in class org.algernon.test.ProtegeTest
m_PharmGKB_Prod - Variable in class org.algernon.test.BasicTest
m_PharmGKB_Prod - Static variable in class org.algernon.test.ProtegeTest
m_activateBCclause - Variable in class org.algernon.datatype.Activation
m_activateFCclause - Variable in class org.algernon.datatype.Activation
m_algernon - Variable in class org.algernon.kb.AlgernonKBSet
m_algy - Variable in class org.algernon.test.DBTest
m_algy - Variable in class org.algernon.test.DeleteTest
m_algy - Variable in class org.algernon.test.ForwardTest
m_algy - Variable in class org.algernon.test.GenericLoader
m_algy - Variable in class org.algernon.test.MiscellanyTest
m_algy - Variable in class org.algernon.test.PharmGKBTest1
m_algy - Variable in class org.algernon.test.SpecialTest
m_algy - Variable in class org.algernon.test.StructureTest
m_algy - Variable in class org.algernon.test.TaxonomyTest
m_algy - Variable in class org.algernon.test.TestAll
m_algy - Variable in class org.algernon.test.TypeTest
m_allRules - Variable in class org.algernon.rule.RuleManager
m_antecedent - Variable in class org.algernon.rule.Rule
m_assert1 - Variable in class org.algernon.test.BasicTest
m_bindingSets - Variable in class org.algernon.aam.register.BindingsRegister
m_bindings - Variable in class org.algernon.datatype.Activation
m_bindings - Variable in class org.algernon.datatype.BindingList
m_clause - Variable in class org.algernon.datatype.Activation
m_code - Variable in class org.algernon.datatype.Activation
m_code - Variable in class org.algernon.rule.Rule
m_compileSettings - Variable in class org.algernon.Algernon
m_compiler - Variable in class org.algernon.Algernon
m_conjID - Variable in class org.algernon.datatype.Activation
m_conjunctionIDCounter - Static variable in class org.algernon.aam.compile.AlgernonCompiler
m_consequent - Variable in class org.algernon.rule.Rule
m_create1 - Variable in class org.algernon.test.BasicTest
m_create2 - Variable in class org.algernon.test.BasicTest
m_create3 - Variable in class org.algernon.test.BasicTest
m_create4 - Variable in class org.algernon.test.BasicTest
m_create5a - Variable in class org.algernon.test.BasicTest
m_create5b - Variable in class org.algernon.test.BasicTest
m_create6a - Variable in class org.algernon.test.BasicTest
m_create6b - Variable in class org.algernon.test.BasicTest
m_create7a - Variable in class org.algernon.test.BasicTest
m_create7b - Variable in class org.algernon.test.BasicTest
m_create7c - Variable in class org.algernon.test.BasicTest
m_create7d - Variable in class org.algernon.test.BasicTest
m_create7e - Variable in class org.algernon.test.BasicTest
m_dataColumn1 - Variable in class org.algernon.Algernon
m_dataColumn2 - Variable in class org.algernon.Algernon
m_dataColumn3 - Variable in class org.algernon.Algernon
m_defaultProject - Variable in class org.algernon.test.BasicTest
m_defaultProject - Variable in class org.algernon.test.DeleteTest
m_defaultProject - Variable in class org.algernon.test.ForwardTest
m_defaultProject - Variable in class org.algernon.test.MiscellanyTest
m_defaultProject - Variable in class org.algernon.test.PharmGKBTest1
m_defaultProject - Variable in class org.algernon.test.SpecialTest
m_defaultProject - Variable in class org.algernon.test.StructureTest
m_defaultProject - Variable in class org.algernon.test.TaxonomyTest
m_defaultProject - Variable in class org.algernon.test.TypeTest
m_direction - Variable in class org.algernon.rule.Rule
m_enabled - Variable in class org.algernon.aam.Profiler
m_errors - Variable in class org.algernon.util.ErrorSet
m_evaluators - Variable in class org.algernon.Algernon
m_executionOrder - Variable in class org.algernon.Algernon
m_files - Variable in class org.algernon.test.GenericLoader
m_files - Variable in class org.algernon.test.TestAll
m_frame - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame
m_frameBCRules - Variable in class org.algernon.rule.RuleManager
m_frameFCRules - Variable in class org.algernon.rule.RuleManager
m_frameParents - Variable in class org.algernon.rule.RuleManager
m_index - Variable in class org.algernon.datatype.Activation
m_index - Variable in class org.algernon.rule.Rule
m_isProfiling - Variable in class org.algernon.aam.Processor
m_kb - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame
m_kb - Variable in class org.algernon.test.DBTest
m_kb - Variable in class org.algernon.test.DeleteTest
m_kb - Variable in class org.algernon.test.ForwardTest
m_kb - Variable in class org.algernon.test.GenericLoader
m_kb - Variable in class org.algernon.test.MiscellanyTest
m_kb - Variable in class org.algernon.test.PharmGKBTest1
m_kb - Variable in class org.algernon.test.SpecialTest
m_kb - Variable in class org.algernon.test.StructureTest
m_kb - Variable in class org.algernon.test.TaxonomyTest
m_kb - Variable in class org.algernon.test.TestAll
m_kb - Variable in class org.algernon.test.TypeTest
m_kbset - Variable in class org.algernon.test.BasicTest
m_key - Variable in class org.algernon.datatype.Activation
m_key - Variable in class org.algernon.rule.Rule
m_labelCounter - Static variable in class org.algernon.aam.compile.AlgernonCompiler
m_labelFormat - Static variable in class org.algernon.aam.compile.AlgernonCompiler
m_labelName - Variable in class org.algernon.aam.opcode.Skip
m_lastCommand - Variable in class org.algernon.aam.Processor
m_lisp - Variable in class org.algernon.Algernon
m_lisp - Variable in class org.algernon.test.DeleteTest
m_lisp - Variable in class org.algernon.test.SpecialTest
m_name - Variable in class org.algernon.aam.Opcode
m_name - Variable in class org.algernon.aam.register.GeneralRegister
m_name - Variable in class org.algernon.kb.AlgernonKBSet
m_name - Variable in class org.algernon.rule.Rule
m_nameFormat - Static variable in class org.algernon.rule.Rule
m_numberOfArguments - Variable in class org.algernon.aam.Opcode
m_oldTraceLevel - Variable in class org.algernon.aam.Processor
m_opcodes - Variable in class org.algernon.aam.Processor
m_path - Variable in class org.algernon.datatype.Path
m_processSettings - Variable in class org.algernon.Algernon
m_processor - Variable in class org.algernon.Algernon
m_processor - Variable in class org.algernon.aam.Profiler
m_processor - Variable in class org.algernon.aam.QueryHistory
m_processor - Variable in class org.algernon.aam.Tracer
m_processor - Variable in class org.algernon.aam.register.GeneralRegister
m_profiler - Variable in class org.algernon.aam.Processor
m_query1 - Variable in class org.algernon.test.BasicTest
m_query2 - Variable in class org.algernon.test.BasicTest
m_query3 - Variable in class org.algernon.test.BasicTest
m_query4 - Variable in class org.algernon.test.BasicTest
m_query5 - Variable in class org.algernon.test.BasicTest
m_query6 - Variable in class org.algernon.test.BasicTest
m_queryHistory - Variable in class org.algernon.aam.Processor
m_registerMap - Variable in class org.algernon.aam.register.RegisterSet
m_registerSet - Variable in class org.algernon.aam.register.GeneralRegister
m_registers - Variable in class org.algernon.aam.Processor
m_root - Variable in class org.algernon.rule.Rule
m_rule - Variable in class org.algernon.datatype.Activation
m_rule1 - Variable in class org.algernon.test.BasicTest
m_rule2 - Variable in class org.algernon.test.BasicTest
m_rule3 - Variable in class org.algernon.test.BasicTest
m_ruleManager - Variable in class org.algernon.Algernon
m_rulesTraced - Variable in class org.algernon.aam.Tracer
m_slotBCRules - Variable in class org.algernon.rule.RuleManager
m_slotFCRules - Variable in class org.algernon.rule.RuleManager
m_testFile - Variable in class org.algernon.test.ForwardTest
m_traceLevel - Variable in class org.algernon.aam.Processor
m_tracer - Variable in class org.algernon.aam.Processor
m_type - Variable in class org.algernon.rule.Rule
m_value - Variable in class org.algernon.aam.register.GeneralRegister
m_variableCounter - Static variable in class org.algernon.aam.compile.AlgernonCompiler
m_warnings - Variable in class org.algernon.util.ErrorSet
main(String[]) - Static method in class org.algernon.Algernon: The command line arguments are files to be processed.
main(String[]) - Static method in class org.algernon.app.Java2Protege: java org.algernon.app.Java2Protege package Protege-project-file advice-file
main(String[]) - Static method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
main(String[]) - Static method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
main(String[]) - Static method in class org.algernon.test.BackwardTest
main(String[]) - Static method in class org.algernon.test.BasicTest
main(String[]) - Static method in class org.algernon.test.DBTest
main(String[]) - Static method in class org.algernon.test.DeleteTest
main(String[]) - Static method in class org.algernon.test.ForwardTest
main(String[]) - Static method in class org.algernon.test.GenericLoader
main(String[]) - Static method in class org.algernon.test.InitializeAlgernonTwice
main(String[]) - Static method in class org.algernon.test.MiscellanyTest
main(String[]) - Static method in class org.algernon.test.MultipleAlgernonObjTestCase
main(String[]) - Static method in class org.algernon.test.PharmGKBTest1
main(String[]) - Static method in class org.algernon.test.PharmGKBTest2
main(String[]) - Static method in class org.algernon.test.ProtegeTest
main(String[]) - Static method in class org.algernon.test.SimpleAlgernonExample
main(String[]) - Static method in class org.algernon.test.SpecialTest
main(String[]) - Static method in class org.algernon.test.StructureTest
main(String[]) - Static method in class org.algernon.test.SubclassInclusive
main(String[]) - Static method in class org.algernon.test.TaxonomyTest
main(String[]) - Static method in class org.algernon.test.TestAll
main(String[]) - Static method in class org.algernon.test.TypeTest
makeAlgernon(String) - Method in class org.algernon.test.MultipleAlgernonObjTestCase: Creates an instance that can be returned by the pool.
makeAlgernon(String) - Method in class org.algernon.test.SubclassInclusive: Creates an instance that can be returned by the pool.
makeString(int) - Static method in class org.algernon.util.StringUtil: Creates a blank string of the given length containing the given character (default blank).
makeString(int, char) - Static method in class org.algernon.util.StringUtil: Creates a string of the given length containing the given character (default blank).
makeTaxonomyCommands(AlgernonKBSet, LispValue, BindingList) - Method in class org.algernon.aam.compile.AlgernonCompiler: Converts pseudo-taxonomy commands into real taxonomy commands.
mappingOfSlot(J2PSlot) - Static method in class org.algernon.app.Java2Protege: Returns the name of the mapping object in the KB that corresponds to this slot.
mappingOfSlot(String, String) - Static method in class org.algernon.app.Java2Protege: Returns the name of the mapping object in the KB that corresponds to this slot.
merge(BindingSet) - Method in class org.algernon.datatype.BindingSet: Merges two binding sets and returns a new one.
miscTests() - Method in class org.algernon.test.BasicTest
model - Variable in class org.algernon.app.j2p.TableMap
mouseClicked(MouseEvent) - Method in class org.algernon.app.j2p.gui.J2PWindow: Invoked when the mouse button has been clicked (pressed and released) on a component.
mouseEntered(MouseEvent) - Method in class org.algernon.app.j2p.gui.J2PWindow: Invoked when the mouse enters a component.
mouseExited(MouseEvent) - Method in class org.algernon.app.j2p.gui.J2PWindow: Invoked when the mouse exits a component.
mousePressed(MouseEvent) - Method in class org.algernon.app.j2p.gui.J2PWindow: Invoked when a mouse button has been pressed on a component.
mouseReleased(MouseEvent) - Method in class org.algernon.app.j2p.gui.J2PWindow: Invoked when a mouse button has been released on a component.
myContains(Collection, LispValue) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Needed because ArrayList.contains calls Object.equals() for some bizarre reason rather than LispValue.equals.

N

NAME - Variable in class org.algernon.aam.OpcodeSet
NEGATED - Static variable in class org.algernon.Algernon: Used when processing clauses - stating that the clause is negated.
NEWLINE - Static variable in class org.algernon.aam.compile.AlgernonCompiler
NEWSPAPER_PROJECT - Static variable in class org.algernon.test.SimpleAlgernonExample
NEXT - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
NEXT_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
NEXT_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
NEXT_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
NEXT_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
NORMAL - Static variable in class org.algernon.aam.Tracer: Normal trace level.
NORMAL_MODE - Static variable in class org.algernon.aam.compile.AlgernonCompiler
NORMAL_STRING - Static variable in class org.algernon.aam.Tracer
NOT - Variable in class org.algernon.Algernon: This is used in the Algernon macro for adding a known false value to an object-relation.
NOTHING - Variable in class org.algernon.aam.Processor
NOT_EQUAL - Variable in class org.algernon.aam.OpcodeSet
NO_NEWLINE - Static variable in class org.algernon.aam.compile.AlgernonCompiler
NUMBER_OF_COLS - Static variable in class org.algernon.app.j2p.SlotTable
Name - class org.algernon.aam.opcode.Name.: This class implements the :NAME operation.
Name(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Name: Create a new AAM Opcode.
NotEqual - class org.algernon.aam.opcode.NotEqual.: This class represents a NEQ Opcode in the AAM.
NotEqual(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.NotEqual: Create a new AAM :TEST Opcode.
n2sort() - Method in class org.algernon.app.j2p.TableSorter
negateClause() - Method in class org.algernon.datatype.Clause: Returns a negated form of the clause.
neq_testFile - Variable in class org.algernon.test.MiscellanyTest
newKB(String) - Method in class org.algernon.app.Java2Protege: Creates a new KB for the system to use.
next() - Method in class org.algernon.app.j2p.SlotTableIterator: Returns the next element in the interation.
nextClause() - Method in class org.algernon.aam.Processor: Increments the index of the clause we are examining.

O

OP_A - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_ADD_CLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_ADD_FACET - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_ADD_INSTANCE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_ADD_RELATION - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_ADD_RELATION_RULE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_ADD_RULE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_ALL_PATHS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_ALL_PATHS_PART_1 - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_ALL_PATHS_PART_2 - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_ANY - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_ASK - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_ASSUME - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_BIND - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_BOUNDP - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_BRANCH - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_CHILD - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_CLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_CLEAR_RELATION - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_CLEAR_SLOT - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_COUNT - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_DATE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_DELETE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_DELETE_CLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_DELETE_FACET - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_DELETE_FRAME - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_DELETE_INSTANCE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_DELETE_RELATION - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_DIRECT_CLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_DIRECT_INSTANCE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_DIRECT_SUBCLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_DIRECT_SUPERCLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_EVAL - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_FAIL - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_FIRE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_FOR - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_FORC - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_FORC_CLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_FORC_INSTANCE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_INSTANCE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_IS_CLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_IS_FACET - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_IS_FRAME - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_IS_INSTANCE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_IS_RELATION - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_LEAF_CLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_LEAST_COMMON_SUPERCLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_LIMIT - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_NAME - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_NEQ - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_NO_COMPLETION - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_NO_CONTINUATION - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_OR - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_PARENT - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_PRINT - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_PRINTLN - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_RETRIEVE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_ROOT_CLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_RULES - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_SHOW - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_SHOW_CODE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_SLOT - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_SRULES - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_STOP - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_SUBCLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_SUPERCLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_TAXONOMY - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_TEMPLATE_RELATION - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_TEST - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_THE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_THE_CLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_THE_INSTANCE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_TRACE - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_UNBOUNDP - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_UNP - Variable in class org.algernon.aam.compile.AlgernonCompiler
OP_USE_KB - Variable in class org.algernon.aam.compile.AlgernonCompiler
OUTPUT_PANEL_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
OUTPUT_TABLE_HEIGHT - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
OUTPUT_TABLE_WIDTH - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
Opcode - class org.algernon.aam.Opcode.: This class represents an Opcode in the AAM.
Opcode(Algernon, String, int) - Constructor for class org.algernon.aam.Opcode: Create a new AAM Opcode.
OpcodeSet - class org.algernon.aam.OpcodeSet.: This class represents a OpcodeSet in the AAM.
OpcodeSet(Algernon, Processor) - Constructor for class org.algernon.aam.OpcodeSet: Create a new AAM OpcodeSet.
objectsToCollection(Object) - Static method in class org.algernon.util.CollectionUtil: Turns an object into a Collection containing just the object.
objectsToCollection(Object, Object) - Static method in class org.algernon.util.CollectionUtil: Turns two objects into a Collection containing just the objects.
objectsToCollection(Object, Object, Object) - Static method in class org.algernon.util.CollectionUtil: Turns three objects into a Collection containing just the objects.
objectsToCollection(Object, Object, Object, Object) - Static method in class org.algernon.util.CollectionUtil: Turns four objects into a Collection containing just the objects.
openKB(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB
or_testFile - Variable in class org.algernon.test.MiscellanyTest
org.algernon - package org.algernon
org.algernon.aam - package org.algernon.aam
org.algernon.aam.compile - package org.algernon.aam.compile
org.algernon.aam.opcode - package org.algernon.aam.opcode
org.algernon.aam.register - package org.algernon.aam.register
org.algernon.app - package org.algernon.app
org.algernon.app.j2p - package org.algernon.app.j2p
org.algernon.app.j2p.action - package org.algernon.app.j2p.action
org.algernon.app.j2p.error - package org.algernon.app.j2p.error
org.algernon.app.j2p.gui - package org.algernon.app.j2p.gui
org.algernon.datatype - package org.algernon.datatype
org.algernon.exception - package org.algernon.exception
org.algernon.io - package org.algernon.io
org.algernon.kb - package org.algernon.kb
org.algernon.kb.agent.google - package org.algernon.kb.agent.google
org.algernon.kb.event - package org.algernon.kb.event
org.algernon.kb.okbc.protege - package org.algernon.kb.okbc.protege
org.algernon.kb.okbc.protege.plugins - package org.algernon.kb.okbc.protege.plugins
org.algernon.kb.okbc.protege.plugins.action - package org.algernon.kb.okbc.protege.plugins.action
org.algernon.kb.okbc.protege.plugins.gui - package org.algernon.kb.okbc.protege.plugins.gui
org.algernon.lang - package org.algernon.lang
org.algernon.lang.java - package org.algernon.lang.java
org.algernon.lang.lisp - package org.algernon.lang.lisp
org.algernon.lang.shell - package org.algernon.lang.shell
org.algernon.rule - package org.algernon.rule
org.algernon.server - package org.algernon.server
org.algernon.test - package org.algernon.test
org.algernon.util - package org.algernon.util

P

PARENT - Variable in class org.algernon.aam.OpcodeSet
PATH_BUILDER_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
POP - Variable in class org.algernon.aam.OpcodeSet
PREV - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
PREV_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
PREV_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
PREV_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
PREV_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
PRINT - Variable in class org.algernon.aam.OpcodeSet
PROGRAM_NAME - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
PUSH - Variable in class org.algernon.aam.OpcodeSet
Parent - class org.algernon.aam.opcode.Parent.: Parent expects a clause of the form (:PARENT child parent).
Parent(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Parent
Path - class org.algernon.datatype.Path.
Path(Algernon) - Constructor for class org.algernon.datatype.Path: Creates an empty path.
Path(Algernon, String) - Constructor for class org.algernon.datatype.Path: Creates a new Path.
Path(Algernon, LispValue) - Constructor for class org.algernon.datatype.Path: Creates a new Path.
PharmGKBTest() - Method in class org.algernon.test.BasicTest: This performs the same function as the misc.MHQuery1 program.
PharmGKBTest1 - class org.algernon.test.PharmGKBTest1.: Tests basic execution functionality of Algernon.
PharmGKBTest1() - Constructor for class org.algernon.test.PharmGKBTest1
PharmGKBTest2 - class org.algernon.test.PharmGKBTest2.: Tests basic execution functionality of Algernon.
PharmGKBTest2() - Constructor for class org.algernon.test.PharmGKBTest2
Pop - class org.algernon.aam.opcode.Pop.: This class represents a Test Opcode in the AAM.
Pop(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Pop: Create a new AAM :TEST Opcode.
Print - class org.algernon.aam.opcode.Print.: This class implements the Print and Println Opcode in the AAM.
Print(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Print: Create a new AAM Print Opcode.
Processor - class org.algernon.aam.Processor.: This class represents a Processor in the AAM.
Processor(Algernon) - Constructor for class org.algernon.aam.Processor: Create a new AAM Processor.
Profiler - class org.algernon.aam.Profiler.: Profiler provides methods for tracing execution in the AAM.
Profiler(Processor) - Constructor for class org.algernon.aam.Profiler: Creates a new Profiler object.
ProtegeProjectFileFilter - class org.algernon.app.j2p.gui.ProtegeProjectFileFilter.: ProtegeProjectFileFilter does...
ProtegeProjectFileFilter() - Constructor for class org.algernon.app.j2p.gui.ProtegeProjectFileFilter
ProtegeTest - class org.algernon.test.ProtegeTest.: Tests basic execution functionality of Algernon.
ProtegeTest() - Constructor for class org.algernon.test.ProtegeTest
Push - class org.algernon.aam.opcode.Push.: This class represents a Push Opcode in the AAM.
Push(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Push: Create a new AAM :PUSH opcode.
pathRestrictionWarning(Clause, Rule) - Method in class org.algernon.aam.compile.AlgernonCompiler: Returns a warning about path restriction.
performEnterAction(KeyEvent) - Method in class org.algernon.app.j2p.gui.J2PAdviceDialog
pop() - Method in class org.algernon.aam.register.BindingsRegister: Pops the register and returns the popped entry.
pop() - Method in class org.algernon.aam.register.GeneralRegister: Pops the register and returns the popped entry.
pop() - Method in interface org.algernon.aam.register.Register: Pops the register and returns the popped entry.
pop() - Method in class org.algernon.datatype.BindingSet: Removes the first BindingList and returns it.
pop(Clause) - Method in class org.algernon.datatype.Path: Pops a clause from the front of the path.
popRegisterValue(LispValue) - Method in class org.algernon.aam.Processor: Pops the register and returns the popped entry.
popRegisterValue(LispValue) - Method in class org.algernon.aam.register.RegisterSet: Pops the register and returns the popped entry.
preprocessClause(Clause) - Method in class org.algernon.aam.compile.AlgernonCompiler: Preprocesses a clause.
preprocessPath(Path) - Method in class org.algernon.aam.compile.AlgernonCompiler: Preprocesses a path
preprocessTaxonomy(AlgernonKBSet, LispValue) - Method in class org.algernon.aam.compile.AlgernonCompiler: preprocesses the :TAXONOMY form to turn it into a set of :THE-CLASS and :THE-INSTANCE commands.
printBindingList(int, int, PrintWriter, BindingList, LispValue) - Method in class org.algernon.Algernon: Prints a binding list to the given stream.
printBindingList(PrintWriter, BindingList) - Method in class org.algernon.Algernon: This method has the original Algernon output format.
printCode(LispValue) - Method in class org.algernon.aam.OpcodeSet: prints code to System.out.
printErrors(ErrorSet) - Static method in class org.algernon.Algernon: Prints an ErrorSet to System.err.
printErrorsToString(ErrorSet) - Static method in class org.algernon.Algernon: Prints an ErrorSet to a String.
printProfileStatistics() - Method in class org.algernon.kb.AlgernonKBSet
printResult(PrintWriter, String, LispValue, LispValue) - Method in class org.algernon.Algernon: Prints the results of Algernon execution in a nice format.
printResultToString(String, LispValue, LispValue) - Method in class org.algernon.Algernon: Prints the results of Algernon execution in a nice format to a string
printResultToString(String, LispValue) - Method in class org.algernon.Algernon: Prints the results of Algernon execution in a nice format to a string
printResultToTable(LispValue, LispValue) - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab: This defines a method that takes a result from Algernon and prints the results in a table.
printResults(PrintWriter, Result, LispValue) - Method in class org.algernon.Algernon: Prints the actual binding lists from the execution.
printRules() - Method in class org.algernon.test.BackwardTest
printRules() - Method in class org.algernon.test.PharmGKBTest2
printStatistics() - Method in class org.algernon.aam.Profiler: Prints or logs all current statistics.
printWarnings(ErrorSet) - Static method in class org.algernon.Algernon: Only prints warnings to System.err.
printWarningsToString(ErrorSet) - Static method in class org.algernon.Algernon: Prints only the warnings in an ErrorSet to a String.
process(LispValue, AlgernonKBSet, ErrorSet) - Method in class org.algernon.Algernon: Executes a set of AAM opcodes.
process(LispValue, AlgernonKB, ErrorSet) - Method in class org.algernon.aam.Processor: Process the given code.
process(LispValue, AlgernonKBSet, BindingSet, Rule, Process, ErrorSet) - Method in class org.algernon.aam.Processor: Process the given code.
processAdviceCommand(String, String, String, String) - Method in class org.algernon.app.j2p.Advice: Processes and stores the advice.
processDomainAndRange(Collection, ValueType, Collection) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: Helper function to turn a set of Domains and a Range into the form needed by the AlgernonCompiler.
processSNDQuery(String, String) - Method in class org.algernon.test.PharmGKBTest1
profile(String) - Method in class org.algernon.aam.Processor
profile(String) - Method in class org.algernon.aam.Profiler
push(LispValue) - Method in class org.algernon.aam.register.BindingsRegister: Pushes the given BindingSet onto the register.
push(LispValue) - Method in class org.algernon.aam.register.GeneralRegister: Pushes the given value onto the register.
push(LispValue) - Method in interface org.algernon.aam.register.Register: Pushes the given value onto the register.
push(BindingList) - Method in class org.algernon.datatype.BindingSet: Pushes the new BindingList onto the BindingSet.
push(Clause) - Method in class org.algernon.datatype.Path: Pushes a clause onto the front of the path.
pushRegisterValue(LispValue, LispValue) - Method in class org.algernon.aam.Processor: Pushes the given value onto the register.
pushRegisterValue(LispValue, LispValue) - Method in class org.algernon.aam.register.RegisterSet: Pushes the given value onto the register.
put(Object, LispValue) - Method in class org.algernon.datatype.BindingList: Stores a variable-value binding in the binding list.

Q

QUERY - Variable in class org.algernon.aam.OpcodeSet
QUERY_MODE - Static variable in class org.algernon.aam.compile.AlgernonCompiler
Query - class org.algernon.aam.opcode.Query.: This class represents a Query Opcode in the AAM.
Query(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Query: Create a new AAM :QUERY Opcode.
QueryHistory - class org.algernon.aam.QueryHistory.
QueryHistory(Processor) - Constructor for class org.algernon.aam.QueryHistory
query(Clause) - Method in interface org.algernon.kb.AlgernonKB: Returns all of the values that match the given clause.
query(Clause, AlgernonFacet) - Method in interface org.algernon.kb.AlgernonKB: See the simpler form with one argument.
query(Clause) - Method in class org.algernon.kb.AlgernonKBSet: Queries KBs until one of the queries is successful.
query(Clause) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns all of the values that match the given clause.
query(Clause, AlgernonFacet) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: See the simpler form getValues.
queueInsertionFunction(LispValue, LispValue) - Method in class org.algernon.Algernon: Default queue insertion function.

R

RANGE_POSITION - Static variable in class org.algernon.app.j2p.SlotTable
RELOAD_ALL_RULES_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
RELOAD_ALL_RULES_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
RELOAD_ALL_RULES_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
RELOAD_ALL_RULES_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
RELOAD_RULES_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
RELOAD_RULES_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
RELOAD_RULES_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
RELOAD_RULES_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
RESULTS - Variable in class org.algernon.aam.register.RegisterSet: Binding lists stored for return to user.
RETURN - Variable in class org.algernon.aam.OpcodeSet
REVIEW_TAB_INDEX - Static variable in class org.algernon.app.j2p.gui.J2PWindow
ROOT_CLASS - Variable in class org.algernon.aam.OpcodeSet
ROOT_NODE_LABEL - Static variable in class org.algernon.app.j2p.gui.J2PWindow
RULE - Variable in class org.algernon.aam.register.RegisterSet: The rule being processed.
R_ACTIONS - Variable in class org.algernon.aam.register.RegisterSet: Stack or queue of paths to be followed.
R_ACTIVATE_BC - Variable in class org.algernon.aam.register.RegisterSet: Activation clause for forward chaining rules.
R_ACTIVATE_FC - Variable in class org.algernon.aam.register.RegisterSet: Activation clause for backard chaining rules.
R_BINDINGS - Variable in class org.algernon.aam.register.RegisterSet: Stack of binding lists.
R_CLAUSE - Variable in class org.algernon.aam.register.RegisterSet: The clause currently being executed.
R_CODE - Variable in class org.algernon.aam.register.RegisterSet: Code register (like a Program Counter).
R_CONTEXT - Variable in class org.algernon.aam.register.RegisterSet: Stack of execution contexts.
R_ID - Variable in class org.algernon.aam.register.RegisterSet: The ID of the activation being processed.
R_INDEX - Variable in class org.algernon.aam.register.RegisterSet: Number of the clause being processed.
R_KEY - Variable in class org.algernon.aam.register.RegisterSet: Key clause of backward chaining rules.
R_RESULTS - Variable in class org.algernon.aam.register.RegisterSet: Binding lists stored for return to user.
R_RULE - Variable in class org.algernon.aam.register.RegisterSet: The rule being processed.
ReflectionUtil - class org.algernon.util.ReflectionUtil.: ReflectionUtil contains static methods that are useful when dealing with reflection and packages.
ReflectionUtil() - Constructor for class org.algernon.util.ReflectionUtil
Register - interface org.algernon.aam.register.Register.: This class prescribes the behavior of a register in the AAM processor.
RegisterSet - class org.algernon.aam.register.RegisterSet.: This class represents a RegisterSet in the AAM.
RegisterSet(Processor) - Constructor for class org.algernon.aam.register.RegisterSet: Create a new AAM RegisterSet.
ReloadAllRulesAction - class org.algernon.kb.okbc.protege.plugins.action.ReloadAllRulesAction.: User: hewett Date: Mar 7, 2003 Time: 11:50:02 AM
ReloadAllRulesAction(AlgernonTab, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.ReloadAllRulesAction: Calls back to Algernon to reload all rules.
ReloadRulesAction - class org.algernon.kb.okbc.protege.plugins.action.ReloadRulesAction.: User: hewett Date: Mar 7, 2003 Time: 11:50:02 AM
ReloadRulesAction(AlgernonTab, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.ReloadRulesAction: Calls back to Algernon to reload some rules.
Result - class org.algernon.datatype.Result.: This class contains a result from an Algernon ask or tell operation.
Result(Algernon, LispValue) - Constructor for class org.algernon.datatype.Result
Return - class org.algernon.aam.opcode.Return.: This class represents a Return Opcode in the AAM.
Return(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Return: Create a new AAM :RETURN Opcode.
RootClass - class org.algernon.aam.opcode.RootClass.: Superclass expects a clause of the form (:ROOT-CLASS class ?var).
RootClass(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.RootClass
Rule - class org.algernon.rule.Rule.: This class represents a Rule in the AAM.
Rule(Algernon, LispValue, int, Rule) - Constructor for class org.algernon.rule.Rule: Create a new Algernon Rule
Rule(Algernon, String, LispValue, int, Rule) - Constructor for class org.algernon.rule.Rule: Create a new Algernon Rule
Rule(Algernon, String, Path, int, Path, Clause, int, Rule) - Constructor for class org.algernon.rule.Rule: Create a new Algernon Rule
RuleManager - class org.algernon.rule.RuleManager.: The RuleManager manages rules in Algernon.
RuleManager(Algernon) - Constructor for class org.algernon.rule.RuleManager: Create a new Algernon Rule
RunConversionAction - class org.algernon.app.j2p.action.RunConversionAction.: RunConversionAction performs the action of selecting a KB.
RunConversionAction(J2PWindow, String, String, KeyStroke, Integer) - Constructor for class org.algernon.app.j2p.action.RunConversionAction: Creates a new SelectKBFileAction.
rangeIsSimpleType() - Method in interface org.algernon.kb.AlgernonRelation: Returns true if the range is a non-frame type.
rangeIsSimpleType() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: Returns true if the range is a simple, that is, non-frame, type.
readAdviceFile(String) - Method in class org.algernon.app.j2p.Advice: Reads advice from a file.
reallocateIndexes() - Method in class org.algernon.app.j2p.TableSorter
relationIsFull(AlgernonFrame, AlgernonRelation) - Method in class org.algernon.Algernon: Returns true if the frame/relation combination is full - that is, the number of values stored in the slot is equal to the slot's maximum cardinality.
relationIsFull(AlgernonFrame, AlgernonRelation) - Method in class org.algernon.aam.Processor: Returns true if the frame/relation combination is full - that is, the number of values stored in the slot is equal to the slot's maximum cardinality.
relationLengthMismatchError(int, Clause, LispValue) - Method in class org.algernon.aam.compile.AlgernonCompiler
remove() - Method in class org.algernon.app.j2p.SlotTableIterator: Removes from the underlying collection the last element returned by the iterator (optional operation).
removeBinding(Object) - Method in class org.algernon.datatype.BindingList: Removes a variable's entry in the list.
removeFromCache(Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Removes a frame from the cache.
removeFromDisplayNameCache(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Removes it from the display name cache.
removeKB(AlgernonKB) - Method in class org.algernon.Algernon: Removes a KB from the default KB Set.
removeKB(AlgernonKB, AlgernonKBSet) - Method in class org.algernon.Algernon: Removes a KB from the given KB Set.
removeSubClass(J2PClass) - Method in class org.algernon.app.j2p.J2PClass: Removes a subclass
removeSuperClass(J2PClass) - Method in class org.algernon.app.j2p.J2PClass: Removes a superclass
replacement - Variable in class org.algernon.app.j2p.gui.J2PAdviceDialog
reset() - Method in class org.algernon.aam.Profiler: Erases all statistics and turns off the profiler.
reset() - Method in interface org.algernon.kb.AlgernonKB: Resets a KB.
reset() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Resets a KB.
resetErrors() - Method in class org.algernon.app.j2p.FrameTree: Sets the error flag on all frames to false;
resetProfiler() - Method in class org.algernon.aam.Processor: Resets the statistics in the code profiler.
resetProfiler() - Method in class org.algernon.kb.AlgernonKBSet
resolveClassName(String) - Method in class org.algernon.lang.java.JavaEvaluator: Returns a fully-qualified Java class name.
resolveMethodName(String) - Method in class org.algernon.lang.java.JavaEvaluator
results - Variable in class org.algernon.datatype.Result
rightJustify(String, int) - Static method in class org.algernon.util.StringUtil: Returns a new string with spaces on the left to make the string as wide as the given width.
ruleCounter - Static variable in class org.algernon.rule.Rule
ruleNameIterator() - Method in class org.algernon.Algernon: An iterator that iterates over all Rules in the system.
ruleNameIterator() - Method in class org.algernon.rule.RuleManager: An iterator that iterates over the names of all the rules in the system.
run() - Method in class org.algernon.app.Java2Protege: Performs the operations.
run() - Method in class org.algernon.app.j2p.gui.J2PWindow
run() - Method in class org.algernon.server.AlgernonServer.SocketConnectionHandler
run() - Method in class org.algernon.server.AlgernonServer: Called by start().
runTest() - Method in class org.algernon.test.MultipleAlgernonObjTestCase
runTest() - Method in class org.algernon.test.SubclassInclusive

S

SAVE - Variable in class org.algernon.aam.OpcodeSet
SAVE_TAB_INDEX - Static variable in class org.algernon.app.j2p.gui.J2PWindow
SELECT - Variable in class org.algernon.aam.OpcodeSet
SELECT - Static variable in class org.algernon.datatype.Activation
SERVER_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
SERVER_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
SERVER_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
SERVER_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
SHOW - Variable in class org.algernon.aam.OpcodeSet
SHOW_CODE - Variable in class org.algernon.aam.OpcodeSet
SILENT - Static variable in class org.algernon.aam.Tracer: A trace level that is very quiet.
SILENT_STRING - Static variable in class org.algernon.aam.Tracer
SKIP - Variable in class org.algernon.aam.OpcodeSet
SLOT_CREATE_EVENt - Static variable in interface org.algernon.kb.event.KnowledgeBaseEvent
SLOT_DELETE_EVENT - Static variable in interface org.algernon.kb.event.KnowledgeBaseEvent
SLOT_MODIFY_EVENT - Static variable in interface org.algernon.kb.event.KnowledgeBaseEvent
SLOT_POSITION - Static variable in class org.algernon.app.j2p.SlotTable
SLOT_RULE - Static variable in class org.algernon.rule.RuleManager
SMALL_INITIAL_HASH_SIZE - Static variable in class org.algernon.rule.RuleManager
STANDARD_CODE_TAIL - Variable in class org.algernon.aam.compile.AlgernonCompiler
STANDARD_FOOTER - Variable in class org.algernon.app.j2p.gui.J2PWindow
STANDARD_FOOTER_FONT_SIZE - Variable in class org.algernon.app.j2p.gui.J2PWindow
STANDARD_HEADER - Variable in class org.algernon.app.j2p.gui.J2PWindow
STANDARD_HEADER_FONT_SIZE - Variable in class org.algernon.app.j2p.gui.J2PWindow
STANDARD_HORIZONTAL_GAP - Static variable in class org.algernon.app.j2p.gui.J2PWindow
STANDARD_RULE_CODE_TAIL - Variable in class org.algernon.aam.compile.AlgernonCompiler
STANDARD_VERTICAL_GAP - Static variable in class org.algernon.app.j2p.gui.J2PWindow
STOP - Variable in class org.algernon.aam.OpcodeSet
STRING - Static variable in interface org.algernon.kb.AlgernonValueType
STRING - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
STRING_TYPE - Variable in class org.algernon.Algernon
SUBCLASS - Variable in class org.algernon.aam.OpcodeSet
SUBROUTINE - Variable in class org.algernon.aam.OpcodeSet
SUBSTITUTE - Variable in class org.algernon.aam.OpcodeSet
SUBSTITUTE1 - Variable in class org.algernon.aam.OpcodeSet
SUCCEED_LABEL - Variable in class org.algernon.aam.compile.AlgernonCompiler
SUCCESS - Variable in class org.algernon.aam.Processor
SUPERCLASS - Variable in class org.algernon.aam.OpcodeSet
SYMBOL - Static variable in interface org.algernon.kb.AlgernonValueType
SYMBOL - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
SYMBOL_TYPE - Variable in class org.algernon.Algernon
Save - class org.algernon.aam.opcode.Save.: This class represents a Test Opcode in the AAM.
Save(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Save: Create a new AAM :TEST Opcode.
SaveAdviceFileAction - class org.algernon.app.j2p.action.SaveAdviceFileAction.: SaveAdviceFileAction performs the action of writing an advice file.
SaveAdviceFileAction(J2PWindow, String, String, KeyStroke, Integer) - Constructor for class org.algernon.app.j2p.action.SaveAdviceFileAction: Creates a new SaveAdviceFileAction.
Select - class org.algernon.aam.opcode.Select.: This class represents a Select Opcode in the AAM.
Select(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Select: Create a new AAM :SELECT Opcode.
SelectAdviceFileAction - class org.algernon.app.j2p.action.SelectAdviceFileAction.: SelectAdviceFileAction performs the action of loading a file in the Algernon Tab.
SelectAdviceFileAction(J2PWindow, String, String, KeyStroke, Integer) - Constructor for class org.algernon.app.j2p.action.SelectAdviceFileAction: Creates a new LoadAction.
SelectAlgernonFileAction - class org.algernon.app.j2p.action.SelectAlgernonFileAction.: SelectAdviceFileAction performs the action of selecting a file to write to.
SelectAlgernonFileAction(J2PWindow, String, String, KeyStroke, Integer) - Constructor for class org.algernon.app.j2p.action.SelectAlgernonFileAction: Creates a new SelectAdviceFileAction.
SelectKBFileAction - class org.algernon.app.j2p.action.SelectKBFileAction.: SelectKBFileAction performs the action of selecting a KB.
SelectKBFileAction(J2PWindow, String, String, KeyStroke, Integer) - Constructor for class org.algernon.app.j2p.action.SelectKBFileAction: Creates a new SelectKBFileAction.
Show - class org.algernon.aam.opcode.Show.: This class represents a Show Opcode in the AAM.
Show(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Show: Create a new AAM :SHOW Opcode.
ShowCode - class org.algernon.aam.opcode.ShowCode.: This class represents a Test Opcode in the AAM.
ShowCode(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.ShowCode: Create a new AAM :SHOW-CODE Opcode.
ShowResultAction - class org.algernon.kb.okbc.protege.plugins.action.ShowResultAction.: This action executes when the user selects "Previous Result" on the Algernon Tab.
ShowResultAction(AlgernonTab, String, String, KeyStroke, Integer, int) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.ShowResultAction: Creates a new AskAction.
SimpleAlgernonExample - class org.algernon.test.SimpleAlgernonExample.: Opens the Protege newspaper KB and makes some simple queries on it.
SimpleAlgernonExample() - Constructor for class org.algernon.test.SimpleAlgernonExample
SimpleAlgernonExample(String) - Constructor for class org.algernon.test.SimpleAlgernonExample
SimpleTree - class org.algernon.util.SimpleTree.: SimpleTree stores a tree whose nodes can contain multiple children.
SimpleTree() - Constructor for class org.algernon.util.SimpleTree
SimpleTree(int) - Constructor for class org.algernon.util.SimpleTree: Pass in the approximate number of nodes in the tree.
Skip - class org.algernon.aam.opcode.Skip.: This class represents a Skip Opcode in the AAM.
Skip(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Skip: Create a new AAM :TEST Opcode.
Skip(Algernon, LispValue) - Constructor for class org.algernon.aam.opcode.Skip: When called internally, use this creator.
SlotTable - class org.algernon.app.j2p.SlotTable.: SlotTable stores information about slots and serves as the Data Model for displaying them in a JTable.
SlotTable(Java2Protege, Object[]) - Constructor for class org.algernon.app.j2p.SlotTable
SlotTableIterator - class org.algernon.app.j2p.SlotTableIterator.: SlotTableIterator does...
SlotTableIterator(SlotTable) - Constructor for class org.algernon.app.j2p.SlotTableIterator: Returns an iterator that iterates through the Slots in the table.
SpecialTest - class org.algernon.test.SpecialTest.: Tests basic execution functionality of Algernon.
SpecialTest() - Constructor for class org.algernon.test.SpecialTest
Stop - class org.algernon.aam.opcode.Stop.: This class represents a Test Opcode in the AAM.
Stop(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Stop: Create a new AAM :TEST Opcode.
StringUtil - class org.algernon.util.StringUtil.: Contains various useful string utilities.
StringUtil() - Constructor for class org.algernon.util.StringUtil
StructureTest - class org.algernon.test.StructureTest.: Tests basic delete functionality of Algernon.
StructureTest() - Constructor for class org.algernon.test.StructureTest
Subclass - class org.algernon.aam.opcode.Subclass.: Subclass expects a clause of the form (:SUBCLASS class ?var).
Subclass(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Subclass
SubclassInclusive - class org.algernon.test.SubclassInclusive.: Tests whether Algernon works correctly when initialized several times from the same program.
SubclassInclusive() - Constructor for class org.algernon.test.SubclassInclusive
Subroutine - class org.algernon.aam.opcode.Subroutine.: This class represents a Test Opcode in the AAM.
Subroutine(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Subroutine: Create a new AAM :TEST Opcode.
SubstituteBindings - class org.algernon.aam.opcode.SubstituteBindings.: This opcode performs a substitute bindings of the clause in the Clause register.
SubstituteBindings(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.SubstituteBindings: Create a new AAM SubstituteBindings Opcode.
SubstituteBindings1 - class org.algernon.aam.opcode.SubstituteBindings1.: This class represents a Substitute1 Opcode in the AAM.
SubstituteBindings1(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.SubstituteBindings1: Create a new AAM :Substitute1 Opcode.
Superclass - class org.algernon.aam.opcode.Superclass.: Superclass expects a clause of the form (:SUPERCLASS class ?var).
Superclass(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Superclass
save(String) - Method in class org.algernon.app.j2p.Advice: Saves the advice to a file.
save() - Method in interface org.algernon.kb.AlgernonKB: Saves the KB to a file.
save() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Saves the kb to a file.
saveKB() - Method in class org.algernon.app.Java2Protege: Saves the kb.
searchForRules(String) - Method in class org.algernon.rule.RuleManager: Returns all rules with the given string in their names.
selectClass() - Method in class org.algernon.kb.okbc.protege.plugins.gui.LoadRulesDialog
serverIsRunning() - Method in class org.algernon.Algernon: Returns true if the server is running.
setActivateBCClause(LispValue) - Method in class org.algernon.datatype.Activation: Sets the value of ActivateBCClause.
setActivateFCClause(LispValue) - Method in class org.algernon.datatype.Activation: Sets the value of ActivateFCClause.
setAdviceFile(String) - Method in class org.algernon.app.j2p.AdviceTable
setAlgernon(Algernon) - Method in class org.algernon.aam.Processor: Sets the value of Algernon.
setAntecedent(Path) - Method in class org.algernon.rule.Rule
setAssociatedFrame(AlgernonFrame) - Method in class org.algernon.datatype.Closure
setBindings(BindingList) - Method in class org.algernon.datatype.Activation: Sets the value of Bindings.
setBindings(BindingList) - Method in class org.algernon.datatype.Closure
setCardinality(String) - Method in class org.algernon.app.j2p.J2PSlot
setClassRange() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: This is only called when the range is :CLASS.
setClause(Clause) - Method in class org.algernon.datatype.Activation: Sets the value of Clause.
setClause(LispValue) - Method in class org.algernon.datatype.Clause
setClientKey(String) - Method in class org.algernon.kb.agent.google.GoogleKB
setCode(LispValue) - Method in class org.algernon.datatype.Activation: Sets the value of Code.
setCode(Collection) - Method in class org.algernon.rule.Rule
setCompilerDebug(boolean) - Method in class org.algernon.Algernon: Use this to turn compiler debug mode on and off.
setConjunctiveID(LispValue) - Method in class org.algernon.datatype.Activation: Sets the value of ConjunctiveID.
setConsequent(Path) - Method in class org.algernon.rule.Rule
setDebug(boolean) - Method in class org.algernon.aam.compile.AlgernonCompiler: Set to true to turn on compiler debug mode.
setDefaultValue(Object) - Method in interface org.algernon.kb.AlgernonRelation: Sets the default value of a template slot.
setDefaultValue(Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: Sets the default value of a template slot.
setDirection(int) - Method in class org.algernon.rule.Rule
setDisplayName(String) - Method in interface org.algernon.kb.AlgernonFrame: Sets this frame's display name (that is, a pretty name) to the given string.
setDisplayName(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Sets this frame's display name (that is, a pretty name) to the given string.
setDisplayNameRelationName(String) - Method in interface org.algernon.kb.AlgernonKB: Sets the name of the relation (slot) used for "pretty names", "common names", "display names" or whatever you want to call it.
setDisplayNameRelationName(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Sets the name of the relation (slot) used for "pretty names", "common names", "display names" or whatever you want to call it.
setDomain(String) - Method in class org.algernon.app.j2p.J2PSlot: Sets the domain.
setDuplicateSlotNameErrorOnClasses(J2PSlot) - Method in class org.algernon.app.Java2Protege: Adds an error to classes if they have the same name as the given slot.
setEnabled(boolean) - Method in class org.algernon.aam.Profiler: Sets the value of Enabled.
setError(J2PError) - Method in class org.algernon.app.j2p.J2PFrame: sets the hasError flag.
setExecutionOrder(int) - Method in class org.algernon.Algernon: Sets the value of ExecutionOrder.
setHasSpecialArguments(boolean) - Method in class org.algernon.datatype.Command
setId(String) - Method in class org.algernon.datatype.Closure
setIndex(int) - Method in class org.algernon.datatype.Activation: Sets the value of Index.
setIndex(int) - Method in class org.algernon.rule.Rule
setInverseRelation(AlgernonRelation) - Method in interface org.algernon.kb.AlgernonRelation: Sets the inverse relation of this relation.
setInverseRelation(AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: Sets the inverse relation of this relation.
setIsIgnored(boolean) - Method in class org.algernon.app.j2p.J2PFrame: Sets the isIgnored flag.
setIsObsolete(boolean) - Method in class org.algernon.datatype.Command
setIsPathUnrestricted(boolean) - Method in class org.algernon.datatype.Command
setJavaAddMethod(String) - Method in class org.algernon.app.j2p.J2PSlot: Stores the original method name so other programs can know the mapping from method to slot name.
setJavaGetMethod(String) - Method in class org.algernon.app.j2p.J2PSlot: Stores the original method name so other programs can know the mapping from method to slot name.
setJavaSetMethod(String) - Method in class org.algernon.app.j2p.J2PSlot: Stores the original method name so other programs can know the mapping from method to slot name.
setKB(String) - Method in class org.algernon.app.Java2Protege: Sets the KB used with this program.
setKey(LispValue) - Method in class org.algernon.datatype.Activation: Sets the value of Key.
setKey(LispValue) - Method in class org.algernon.datatype.Closure
setKey(Clause) - Method in class org.algernon.rule.Rule
setLastCommand(LispValue) - Method in class org.algernon.aam.Processor: Sets the value of LastCommand.
setLookupVars(LispValue) - Method in class org.algernon.datatype.Closure
setMaxCardinality(Integer) - Method in interface org.algernon.kb.AlgernonRelation: Sets the maximum cardinality of the Relation.
setMaxCardinality(Integer) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: Sets the maximum cardinality of the Relation.
setMinCardinality(Integer) - Method in interface org.algernon.kb.AlgernonRelation: Sets the minimum cardinality of the Relation.
setMinCardinality(Integer) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: Sets the minimum cardinality of the Relation.
setModel(TableModel) - Method in class org.algernon.app.j2p.TableMap
setModel(TableModel) - Method in class org.algernon.app.j2p.TableSorter
setName(String) - Method in class org.algernon.aam.Opcode: Sets the value of Name.
setName(String) - Method in class org.algernon.aam.register.GeneralRegister
setName(String) - Method in interface org.algernon.aam.register.Register: Sets the name of this Register.
setName(String) - Method in class org.algernon.app.j2p.J2PFrame: Sets the name of this class.
setName(String) - Method in interface org.algernon.kb.AlgernonFrame: Sets the name (:NAME) of this frame.
setName(String) - Method in interface org.algernon.kb.AlgernonKB: Sets the name of the KB.
setName(String) - Method in class org.algernon.kb.AlgernonKBSet
setName(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame: Sets the name (:NAME) of this frame.
setName(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Sets the name of the KB.
setName(String) - Method in class org.algernon.rule.Rule
setNameFormat(DecimalFormat) - Static method in class org.algernon.rule.Rule
setNameSymbol(LispValue) - Method in class org.algernon.datatype.Command
setNumberOfArguments(int) - Method in class org.algernon.aam.Opcode: Sets the value of NumberOfArguments.
setObsoleteMessage(String) - Method in class org.algernon.datatype.Command
setOpcode(Opcode) - Method in class org.algernon.datatype.Command
setOpcodeSet(OpcodeSet) - Method in class org.algernon.aam.Processor
setOriginalName(String) - Method in class org.algernon.app.j2p.J2PFrame
setProfilerEnabled(boolean) - Method in class org.algernon.kb.AlgernonKBSet
setRange(String) - Method in class org.algernon.app.j2p.J2PSlot
setRange(LispValue) - Method in interface org.algernon.kb.AlgernonRelation: Sets the range of a relation when it is a value type such as :INTEGER, instead of a class.
setRange(AlgernonClass) - Method in interface org.algernon.kb.AlgernonRelation: Sets the range of the relation.
setRange(Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: Sets the range of a relation when it is a value type such as :INTEGER, instead of a class.
setRange(LispValue) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: Sets the range of a relation when it is a value type such as :INTEGER, instead of a class.
setRange(AlgernonClass) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeRelation: Sets the range of the relation.
setRegisterSet(RegisterSet) - Method in class org.algernon.aam.register.GeneralRegister
setRegisterSet(RegisterSet) - Method in interface org.algernon.aam.register.Register: Sets the RegisterSet this Register belongs to.
setRegisterValue(LispValue, LispValue) - Method in class org.algernon.aam.Processor: Sets the value of the given register.
setRegisterValue(LispValue, LispValue) - Method in class org.algernon.aam.register.RegisterSet: Sets the value of the given register.
setRelationDefaultValue(AlgernonRelation, Object) - Method in interface org.algernon.kb.AlgernonClass: Sets the default value of a relation as defined on this class.
setRelationDefaultValue(AlgernonRelation, Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass
setRelationInverseRelation(AlgernonRelation, AlgernonRelation) - Method in interface org.algernon.kb.AlgernonClass: Sets the inverse relation of a relation as defined on this class.
setRelationInverseRelation(AlgernonRelation, AlgernonRelation) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass
setRelationMaxCardinality(AlgernonRelation, Integer) - Method in interface org.algernon.kb.AlgernonClass: Sets the maximum cardinality of a relation as defined on this class.
setRelationMaxCardinality(AlgernonRelation, Integer) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass
setRelationMinCardinality(AlgernonRelation, Integer) - Method in interface org.algernon.kb.AlgernonClass: Sets the minimum cardinality of a relation as defined on this class.
setRelationMinCardinality(AlgernonRelation, Integer) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass
setRelationRange(AlgernonRelation, AlgernonClass) - Method in interface org.algernon.kb.AlgernonClass: Sets the range of a relation as defined on this class.
setRelationRange(AlgernonRelation, LispValue) - Method in interface org.algernon.kb.AlgernonClass: Sets the range of a relation as defined on this class.
setRelationRange(AlgernonRelation, AlgernonClass) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass
setRelationRange(AlgernonRelation, LispValue) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeClass
setRoot(Rule) - Method in class org.algernon.rule.Rule
setRule(Rule) - Method in class org.algernon.datatype.Activation: Sets the value of Rule.
setStepMode(boolean) - Method in class org.algernon.aam.Processor: Turns Step mode on or off.
setStepMode(boolean) - Method in class org.algernon.aam.Tracer: Turns Step mode on or off.
setTraceLevel(int) - Method in class org.algernon.Algernon
setTraceLevel(int) - Method in class org.algernon.aam.Processor: Sets the value of trace level
setTraceLevel(LispValue) - Method in class org.algernon.aam.Processor: Sets the value of trace level from a string such as ":NORMAL".
setType(int) - Method in class org.algernon.rule.Rule
setValue(LispValue) - Method in class org.algernon.aam.register.BindingsRegister: Sets the value of the given register.
setValue(LispValue) - Method in class org.algernon.aam.register.GeneralRegister: Sets the value of the given register.
setValue(LispValue) - Method in interface org.algernon.aam.register.Register: Sets the value of the given register.
setValueAt(Object, int, int) - Method in class org.algernon.app.j2p.SlotTable
setValueAt(Object, int, int) - Method in class org.algernon.app.j2p.TableMap
setValueAt(Object, int, int) - Method in class org.algernon.app.j2p.TableSorter
setup(WidgetDescriptor, Project) - Method in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
shouldIgnoreClass(String) - Method in class org.algernon.app.j2p.Advice: Returns true if the advice file said that this class should be ignored.
shouldIgnoreSlot(String) - Method in class org.algernon.app.j2p.Advice: Returns true if the advice file said that this slot should be ignored.
showDialog() - Method in class org.algernon.app.j2p.gui.J2PAdviceDialog
showMessage(String, String, int) - Method in class org.algernon.app.Java2Protege: Displays an error message, using the GUI if possible.
showPackageError(String) - Method in class org.algernon.app.j2p.gui.J2PWindow: shows an error when the package can't be found.
showRegisters() - Method in class org.algernon.aam.register.RegisterSet: Displays all of the registers.
shutdownServer() - Method in class org.algernon.Algernon: Shut down the Algernon server.
shuttlesort(int[], int[], int, int) - Method in class org.algernon.app.j2p.TableSorter
singularForm(String) - Method in class org.algernon.app.Java2Protege
size() - Method in class org.algernon.aam.register.BindingsRegister: Returns the number of values in this register.
size() - Method in class org.algernon.aam.register.GeneralRegister: Returns the number of values in this register.
size() - Method in interface org.algernon.aam.register.Register: Return the size of (number of entries in) the given register.
size() - Method in class org.algernon.datatype.BindingList: Returns the number of binding lists in this binding set.
size() - Method in class org.algernon.datatype.BindingSet: Returns the number of binding lists in this binding set.
size() - Method in class org.algernon.datatype.Clause: Returns the size of the clause.
size() - Method in class org.algernon.datatype.Path: Returns the size of the Path.
size() - Method in class org.algernon.datatype.Result: Returns the number of results in the Result.
size() - Method in class org.algernon.util.ErrorSet: Returns the number of errors plus the number of warnings.
skipLabel - Variable in class org.algernon.aam.compile.AlgernonCompilerState: This is the label the code should skip to if processing proceeds normally.
slotToAlgernonSlot(J2PSlot) - Method in class org.algernon.app.Java2Protege
slotsToAlgernon(SlotTable) - Method in class org.algernon.app.Java2Protege: Returns a set of TELL statements that use :ADD-RELATION to create new slots.
sort(Object) - Method in class org.algernon.app.j2p.TableSorter
sortByColumn(int) - Method in class org.algernon.app.j2p.TableSorter
sortByColumn(int, boolean) - Method in class org.algernon.app.j2p.TableSorter
sortingColumns - Variable in class org.algernon.app.j2p.TableSorter
start() - Method in class org.algernon.server.AlgernonServer.SocketConnectionHandler
start() - Method in class org.algernon.server.AlgernonServer: Starts the algernon server, it runs on a new thread.
start() - Method in class org.algernon.test.BackwardTest: Executes some small code snippets.
start() - Method in class org.algernon.test.BasicTest: Executes some small code snippets.
start() - Method in class org.algernon.test.DBTest: Executes some small code snippets.
start() - Method in class org.algernon.test.DeleteTest: Executes some small code snippets.
start() - Method in class org.algernon.test.ForwardTest: Executes some small code snippets.
start() - Method in class org.algernon.test.GenericLoader: Executes some small code snippets.
start() - Method in class org.algernon.test.MiscellanyTest: Executes some small code snippets.
start() - Method in class org.algernon.test.PharmGKBTest1: Executes some small code snippets.
start() - Method in class org.algernon.test.PharmGKBTest2: Executes some small code snippets.
start() - Method in class org.algernon.test.SimpleAlgernonExample
start() - Method in class org.algernon.test.SpecialTest: Executes some small code snippets.
start() - Method in class org.algernon.test.StructureTest: Executes some small code snippets.
start() - Method in class org.algernon.test.TaxonomyTest: Executes some small code snippets.
start() - Method in class org.algernon.test.TestAll: Executes some small code snippets.
start() - Method in class org.algernon.test.TypeTest: Executes some small code snippets.
startServer(int) - Method in class org.algernon.Algernon: Starts the Algernon server.
stop() - Method in class org.algernon.server.AlgernonServer.SocketConnectionHandler
stop() - Method in class org.algernon.server.AlgernonServer: Stops the algernon server thread.
stop() - Method in class org.algernon.test.BackwardTest: Halts the program nicely.
stop() - Method in class org.algernon.test.BasicTest: Halts the program nicely.
stop() - Method in class org.algernon.test.DBTest: Halts the program nicely.
stop() - Method in class org.algernon.test.DeleteTest: Halts the program nicely.
stop() - Method in class org.algernon.test.ForwardTest: Halts the program nicely.
stop() - Method in class org.algernon.test.GenericLoader: Halts the program nicely.
stop() - Method in class org.algernon.test.MiscellanyTest: Halts the program nicely.
stop() - Method in class org.algernon.test.PharmGKBTest1: Halts the program nicely.
stop() - Method in class org.algernon.test.PharmGKBTest2: Halts the program nicely.
stop() - Method in class org.algernon.test.SimpleAlgernonExample: Halts the program nicely.
stop() - Method in class org.algernon.test.SpecialTest: Halts the program nicely.
stop() - Method in class org.algernon.test.StructureTest: Halts the program nicely.
stop() - Method in class org.algernon.test.TaxonomyTest: Halts the program nicely.
stop() - Method in class org.algernon.test.TestAll: Halts the program nicely.
stop() - Method in class org.algernon.test.TypeTest: Halts the program nicely.
stopAlgernonServer() - Method in class org.algernon.server.AlgernonServer
store(Clause) - Method in interface org.algernon.kb.AlgernonKB: stores the given clause into the storage.
store(Clause, AlgernonFacet) - Method in interface org.algernon.kb.AlgernonKB: stores the given clause into the storage.
store(Clause) - Method in class org.algernon.kb.AlgernonKBSet: Stores the clause in the first KB that accepts it.
store(Clause) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Asserts the given clause into the storage.
store(Clause, AlgernonFacet) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Asserts the given clause into the storage.
stringSplit(String, String) - Static method in class org.algernon.util.StringUtil: Splits a string into a collection of strings.
stringToArray(String, String) - Static method in class org.algernon.util.StringUtil
stripHtml(String) - Method in class org.algernon.app.j2p.gui.J2PFrameRenderer: Strips any leading and trailing HTML from the string.
structure_testFile - Variable in class org.algernon.test.StructureTest
substituteBindings(LispValue) - Method in class org.algernon.datatype.BindingList: Replaces variables with values for each variable in the expression.
succeedIsGood - Variable in class org.algernon.aam.compile.AlgernonCompilerState: The normal state is that a command should succeed for processing to continue.
succeedLabel - Variable in class org.algernon.aam.compile.AlgernonCompilerState: This is the label the code should skip to if processing succeeds.
supportsNegatedClauses() - Method in interface org.algernon.kb.AlgernonKB: Returns true if this KB supports negated clauses.
supportsNegatedClauses() - Method in class org.algernon.kb.AlgernonKBSet: Returns true if any of the KBs in the set support negated clauses.
supportsNegatedClauses() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB
swap(int, int) - Method in class org.algernon.app.j2p.TableSorter

T

TAX_CLASS - Variable in class org.algernon.aam.compile.AlgernonCompiler
TAX_COMPLETE - Variable in class org.algernon.aam.compile.AlgernonCompiler
TAX_INSTANCE - Variable in class org.algernon.aam.compile.AlgernonCompiler
TELL - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
TELL_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
TELL_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
TELL_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
TELL_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
TEMPLATE_RELATION - Variable in class org.algernon.aam.OpcodeSet
TEST_BOUND - Variable in class org.algernon.aam.OpcodeSet
TEST_FAIL - Variable in class org.algernon.aam.OpcodeSet
TEST_KNOWN - Variable in class org.algernon.aam.OpcodeSet
TEST_SUCCEED - Variable in class org.algernon.aam.OpcodeSet
TEST_TRUE - Variable in class org.algernon.aam.OpcodeSet
TEST_UNBOUND - Variable in class org.algernon.aam.OpcodeSet
TEST_UNIQUE - Variable in class org.algernon.aam.OpcodeSet
TOO_FEW_ARGS - Static variable in class org.algernon.aam.compile.AlgernonCompiler
TOO_MANY_ARGS - Static variable in class org.algernon.aam.compile.AlgernonCompiler
TRACE - Variable in class org.algernon.aam.OpcodeSet
TRACE_RULES_ACCELERATOR - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
TRACE_RULES_MNEMONIC - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
TRACE_RULES_TITLE - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
TRACE_RULES_TOOLTIP - Variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
TRUE - Variable in class org.algernon.Algernon: Boolean true = :TRUE.
TableMap - class org.algernon.app.j2p.TableMap.: In a chain of data manipulators some behaviour is common.
TableMap() - Constructor for class org.algernon.app.j2p.TableMap
TableSorter - class org.algernon.app.j2p.TableSorter.
TableSorter() - Constructor for class org.algernon.app.j2p.TableSorter
TableSorter(TableModel) - Constructor for class org.algernon.app.j2p.TableSorter
TaxonomyTest - class org.algernon.test.TaxonomyTest.: Tests basic delete functionality of Algernon.
TaxonomyTest() - Constructor for class org.algernon.test.TaxonomyTest
TellAction - class org.algernon.kb.okbc.protege.plugins.action.TellAction.: The action performed from a menu or button when the user performs a TELL operation.
TellAction(AlgernonTab, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.TellAction: Creates a new TellAction.
TemplateRelation - class org.algernon.aam.opcode.TemplateRelation.: This class implements the TemplateRelation Opcode in the AAM.
TemplateRelation(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.TemplateRelation: Create a new AAM Opcode.
TestAll - class org.algernon.test.TestAll.: Tests miscellaneous functionality of Algernon.
TestAll(String[]) - Constructor for class org.algernon.test.TestAll
TestBound - class org.algernon.aam.opcode.TestBound.: This class represents a Boundp Opcode in the AAM.
TestBound(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.TestBound: Create a new AAM :BOUNDP Opcode.
TestFail - class org.algernon.aam.opcode.TestFail.: This class represents a FAIL Opcode in the AAM.
TestFail(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.TestFail: Create a new AAM :FAIL Opcode.
TestKnown - class org.algernon.aam.opcode.TestKnown.: This class represents a Test Opcode in the AAM.
TestKnown(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.TestKnown: Create a new AAM :TEST Opcode.
TestSucceed - class org.algernon.aam.opcode.TestSucceed.: This class represents a Test Opcode in the AAM.
TestSucceed(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.TestSucceed: Create a new AAM :TEST Opcode.
TestTrue - class org.algernon.aam.opcode.TestTrue.: This class represents a Test Opcode in the AAM.
TestTrue(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.TestTrue: Create a new AAM :TEST Opcode.
TestUnbound - class org.algernon.aam.opcode.TestUnbound.: This class represents a Test Opcode in the AAM.
TestUnbound(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.TestUnbound: Create a new AAM :TEST Opcode.
TestUnique - class org.algernon.aam.opcode.TestUnique.: This class represents a Test Opcode in the AAM.
TestUnique(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.TestUnique: Create a new AAM :TEST Opcode.
Trace - class org.algernon.aam.opcode.Trace.: This class implements the Trace Opcode in the AAM.
Trace(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Trace: Create a new AAM Trace Opcode.
TraceRulesAction - class org.algernon.kb.okbc.protege.plugins.action.TraceRulesAction.: User: hewett Date: Mar 7, 2003 Time: 11:50:02 AM
TraceRulesAction(AlgernonTab, String, String, KeyStroke, Integer) - Constructor for class org.algernon.kb.okbc.protege.plugins.action.TraceRulesAction: Calls back to Algernon to pop up the rule trace dialog.
Tracer - class org.algernon.aam.Tracer.: Tracer provides methods for tracing execution in the AAM.
Tracer(Processor) - Constructor for class org.algernon.aam.Tracer: Creates a new Tracer object.
TypeTest - class org.algernon.test.TypeTest.: Tests basic delete functionality of Algernon.
TypeTest() - Constructor for class org.algernon.test.TypeTest
tableChanged(TableModelEvent) - Method in class org.algernon.app.j2p.TableMap
tableChanged(TableModelEvent) - Method in class org.algernon.app.j2p.TableSorter
tail() - Method in class org.algernon.datatype.Path: Returns a path containing all of the clauses in the given path after the first.
tell(String) - Method in class org.algernon.Algernon: Processes the path in ASSERT mode.
tell(String, AlgernonKB) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
tell(String, ErrorSet) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
tell(String, AlgernonKB, ErrorSet) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
tell(String, AlgernonKBSet) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
tell(String, AlgernonKBSet, String) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
tell(String, AlgernonKBSet, String, ErrorSet) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
tell(String, AlgernonKBSet, String, ErrorSet, AlgernonSettings) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
tell(Path, AlgernonKBSet, String, ErrorSet, AlgernonSettings) - Method in class org.algernon.Algernon: See the single-parameter version for documentation.
tell(String) - Method in class org.algernon.server.AlgernonServer
test() - Method in class org.algernon.test.InitializeAlgernonTwice
test(String, String) - Method in class org.algernon.test.MiscellanyTest
testAsk() - Method in class org.algernon.test.BasicTest: Tests the Algernon "ask" command.
testBad() - Method in class org.algernon.test.SpecialTest: Tests bad forms of the :TEST operator.
testCompile() - Method in class org.algernon.test.BasicTest
testCompile2() - Method in class org.algernon.test.BasicTest
testCompile3() - Method in class org.algernon.test.BasicTest
testCreate() - Method in class org.algernon.test.BasicTest
testDrugVocabulary() - Method in class org.algernon.test.PharmGKBTest2
testEval() - Method in class org.algernon.test.SpecialTest
testFail() - Method in class org.algernon.test.SpecialTest
testFunction0() - Static method in class org.algernon.test.SpecialTest
testFunction1(String) - Static method in class org.algernon.test.SpecialTest
testFunction1WithPrint() - Static method in class org.algernon.test.SpecialTest
testFunction2(Long, Long) - Static method in class org.algernon.test.SpecialTest
testFunction2WithPrint() - Static method in class org.algernon.test.SpecialTest
testFunction3(Long, Long, Long) - Static method in class org.algernon.test.SpecialTest
testGetClass(KnowledgeBase, String) - Static method in class org.algernon.test.ProtegeTest: Tests frame retrieval.
testGetFrame(KnowledgeBase, String) - Static method in class org.algernon.test.ProtegeTest: Tests frame retrieval.
testGetSlot(KnowledgeBase, String) - Static method in class org.algernon.test.ProtegeTest: Tests frame retrieval.
testInstance() - Method in class org.algernon.test.SpecialTest
testJavaEval() - Method in class org.algernon.test.SpecialTest
testJavaTest() - Method in class org.algernon.test.SpecialTest
testKB(String) - Static method in class org.algernon.test.ProtegeTest
testLispEval() - Method in class org.algernon.test.SpecialTest
testLispTest() - Method in class org.algernon.test.SpecialTest
testLookup() - Method in class org.algernon.test.BasicTest
testMeSH() - Method in class org.algernon.test.PharmGKBTest2
testNoCompile() - Method in class org.algernon.test.BasicTest
testPharmGKB() - Method in class org.algernon.test.PharmGKBTest2
testRuleCompile1() - Method in class org.algernon.test.BasicTest
testRuleCompile2() - Method in class org.algernon.test.BasicTest
testShellEval() - Method in class org.algernon.test.SpecialTest
testShellTest() - Method in class org.algernon.test.SpecialTest
testStructure() - Method in class org.algernon.test.StructureTest
testTell() - Method in class org.algernon.test.BasicTest: Tests the Algernon "tell" command.
testTest() - Method in class org.algernon.test.SpecialTest
testTrace() - Method in class org.algernon.test.SpecialTest
theStateVariable - Variable in class org.algernon.aam.compile.AlgernonCompilerState: Holds the variable being used in a :THE macro.
toArray() - Method in class org.algernon.app.j2p.J2PSlot: Returns an array of information about the slot.
toBoolean(Object, Algernon) - Method in interface org.algernon.lang.ExternalLanguageEvaluator: This method must return a Java Boolean value for any type of Object returned by the evaluateExpression method.
toBoolean(Object, Algernon) - Method in class org.algernon.lang.java.JavaEvaluator: This method must return a Java Boolean value for any type of Object returned by the evaluateExpression method.
toBoolean(Object, Algernon) - Method in class org.algernon.lang.lisp.JathaEvaluator: This method must return a Java Boolean value for any type of Object returned by the evaluateExpression method.
toBoolean(Object, Algernon) - Method in class org.algernon.lang.shell.GenericUnixShellEvaluator: This method must return a Java Boolean value for any type of Object returned by the evaluateExpression method.
toInt(LispValue) - Static method in class org.algernon.aam.Tracer: Returns the given trace level as an int.
toString() - Method in class org.algernon.aam.Opcode
toString(int) - Static method in class org.algernon.aam.Tracer: Returns the given trace level as a LISP symbol.
toString() - Method in class org.algernon.aam.compile.AlgernonCompilerState
toString() - Method in class org.algernon.aam.register.BindingsRegister: Displays the register name and its contents.
toString() - Method in class org.algernon.aam.register.GeneralRegister: Displays the register name and its contents.
toString() - Method in class org.algernon.app.j2p.J2PFrame
toString() - Method in class org.algernon.app.j2p.error.J2PConversionError
toString() - Method in class org.algernon.app.j2p.error.J2PDuplicateFrameNameError
toString() - Method in class org.algernon.app.j2p.error.J2PSlotWithSameNameAsClassError
toString() - Method in class org.algernon.app.j2p.error.J2PUnknownDomainError
toString() - Method in class org.algernon.app.j2p.error.J2PUnknownRangeError
toString() - Method in class org.algernon.datatype.Activation
toString() - Method in class org.algernon.datatype.BindingList
toString() - Method in class org.algernon.datatype.BindingSet
toString() - Method in class org.algernon.datatype.Clause: Returns a string representation of the clause.
toString() - Method in class org.algernon.datatype.Closure
toString() - Method in class org.algernon.datatype.Command
toString() - Method in class org.algernon.datatype.Path: Returns a string representation of the clause.
toString() - Method in class org.algernon.datatype.Result: Returns a printed representation
toString() - Method in interface org.algernon.kb.AlgernonValueType: returns the string label, such as "CLS" associated with this valuetype
toString() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeFrame
toString() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeObject
toString() - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
toString() - Method in class org.algernon.rule.Rule
toString() - Method in class org.algernon.util.ErrorSet
toValueType(Object) - Method in class org.algernon.Algernon: Converts an object like ":INTEGER" to an official type.
toValueType(Object) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Range should be one of the ranges specified in the Algernon class, such as BOOLEAN_TYPE, STRING_TYPE, etc.
toVectors() - Method in class org.algernon.app.j2p.Advice: Returns a vector of vectors containing the advice information
trace(int, String) - Method in class org.algernon.Algernon: Prints a trace message, dependent on the current level of tracing.
trace(int, String, boolean) - Method in class org.algernon.Algernon: Prints a trace message, dependent on the current level of tracing.
trace(int, String) - Method in class org.algernon.aam.Processor: Prints or logs the message if the current system trace level is greater than or equal to the given trace level.
trace(int, String, boolean) - Method in class org.algernon.aam.Processor: Prints or logs the message if the current system trace level is greater than or equal to the given trace level.
trace(String, boolean) - Method in class org.algernon.aam.Tracer
trace(String) - Method in class org.algernon.aam.compile.AlgernonCompiler
transformClassName(String) - Method in class org.algernon.app.j2p.Advice: Transforms a class name into the canonical form, given advice.
transformSlotName(String) - Method in class org.algernon.app.j2p.Advice: Transforms a slot name into the canonical form, given advice.
treeBranchToTaxonomy(J2PFrame, FrameTree, String) - Method in class org.algernon.app.Java2Protege
tryToInstantiate(Closure, Clause) - Method in class org.algernon.aam.Processor: Returns a closure if the rule can be instantiated from the clause.
typeEQ(AlgernonKBSet, LispValue, Set, Map, Clause, AlgernonCompilerState, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: Checks for equality and stores the type, if not previously known.
typeList - Variable in class org.algernon.app.j2p.gui.J2PAdviceDialog
typeSubsumedBy(AlgernonKBSet, LispValue, Set) - Method in class org.algernon.aam.compile.AlgernonCompiler: Returns true if one frame type is a subclass or equal to any of a set of frame types.
type_testFile - Variable in class org.algernon.test.TaxonomyTest
type_testFile - Variable in class org.algernon.test.TypeTest
typesIntersect(AlgernonKBSet, Set, Set) - Method in class org.algernon.aam.compile.AlgernonCompiler: Returns true if the two Sets of types intersect.

U

UNNAMED - Static variable in class org.algernon.kb.AlgernonKBSet
UNTYPED_VAR - Variable in class org.algernon.aam.compile.AlgernonCompiler
USE_KB - Variable in class org.algernon.aam.OpcodeSet
UseKB - class org.algernon.aam.opcode.UseKB.: This class implements the USE-KB Opcode in the AAM.
UseKB(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.UseKB: Create a new AAM UseKB Opcode.
undefinedRelationError(Clause, LispValue) - Method in class org.algernon.aam.compile.AlgernonCompiler
undeterminedDomainWarning(Clause, LispValue, Set) - Method in class org.algernon.aam.compile.AlgernonCompiler
unify(LispValue, LispValue) - Method in class org.algernon.datatype.BindingSet: Unifies the unbound clause with the bound clauses (data) and returns a binding list containing the bindings derived from unification.
unifyAux(LispValue, LispValue, LispValue, LispValue) - Method in class org.algernon.datatype.BindingSet
unmerge(LispValue) - Method in class org.algernon.datatype.BindingSet: Takes a merged binding set and undoes the combinatorial merge, returning a binding set which represents the previous version of the input set before the merge.
unpMode - Variable in class org.algernon.aam.compile.AlgernonCompilerState: The mode when doing a recursive call to UNP.
unrecognizedOperatorError(Clause, LispValue) - Method in class org.algernon.aam.compile.AlgernonCompiler: Returns an error string about an unrecognized command used in an Algernon clause.

V

VALUETYP - Static variable in interface org.algernon.kb.AlgernonValueType
VALUETYPE - Variable in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
VARIABLE_START_CHAR - Static variable in class org.algernon.Algernon
VERBOSE - Static variable in class org.algernon.aam.Tracer: A little more detail than normal.
VERBOSE_STRING - Static variable in class org.algernon.aam.Tracer
VERIFY - Variable in class org.algernon.aam.OpcodeSet
VERIFY_MODE - Static variable in class org.algernon.aam.compile.AlgernonCompiler
VERSION_DATE - Variable in class org.algernon.app.AlgernonApplication
VERSION_LABEL_FONT_SIZE - Static variable in class org.algernon.kb.okbc.protege.plugins.AlgernonTab
VERSION_MAJOR - Variable in class org.algernon.app.AlgernonApplication
VERSION_MICRO - Variable in class org.algernon.app.AlgernonApplication
VERSION_MINOR - Variable in class org.algernon.app.AlgernonApplication
VERSION_NAME - Variable in class org.algernon.app.AlgernonApplication
VERSION_TYPE - Variable in class org.algernon.app.AlgernonApplication
VERSION_URL - Variable in class org.algernon.app.AlgernonApplication
Verify - class org.algernon.aam.opcode.Verify.: This class represents a Verify Opcode in the AAM.
Verify(Algernon, String, int) - Constructor for class org.algernon.aam.opcode.Verify: Create a new AAM :VERIFY Opcode.
validateArgumentTypes(Clause, AlgernonKBSet, Map, AlgernonCompilerState, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: validates that arguments are of the correct type.
validateMacroArgumentTypes(Clause, AlgernonKBSet, Map, AlgernonCompilerState, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: Validates argument types for macros like :INSTANCE, :CLASS, and so on.
validateSpecialFormArgumentTypes(Clause, AlgernonKBSet, Map, AlgernonCompilerState, ErrorSet) - Method in class org.algernon.aam.compile.AlgernonCompiler: Validates argument types for macros like :THE, :A and :FORC, which have different forms of arguments.
valueOf(LispValue) - Method in interface org.algernon.kb.AlgernonKB: Returns the Protege value type for the given named type
valueOf(LispValue) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Returns the Protege value type for the given named type
valueOf(String) - Static method in class org.algernon.kb.okbc.protege.AlgernonProtegeValueType
valueSearch(String, Collection, Collection, int) - Method in interface org.algernon.kb.AlgernonKB: Performs a string search within the KB for slot values that contain the given string.
valueSearch(String, Collection, Collection) - Method in interface org.algernon.kb.AlgernonKB: Performs a string search within the KB for slot values that contain the given string.
valueSearch(String) - Method in interface org.algernon.kb.AlgernonKB: Performs a string search within the KB for slot values that contain the given string.
valueSearch(String) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Performs a string search within the KB for slot values that contain the given string.
valueSearch(String, Collection, Collection) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Performs a string search within the KB for slot values that contain the given string.
valueSearch(String, Collection, Collection, int) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Performs a string search within the KB for slot values that contain the given string.
verify(Clause) - Method in interface org.algernon.kb.AlgernonKB: Verifies that the clause is in the KB.
verify(Clause) - Method in class org.algernon.kb.AlgernonKBSet: Verifies against all of the KBs in the KBSet.
verify(Clause) - Method in class org.algernon.kb.okbc.protege.AlgernonProtegeKB: Verifies that the clause is in the KB.

W

WindowUtil - class org.algernon.util.WindowUtil.: WindowUtil has utility routines for GUIs.
WindowUtil() - Constructor for class org.algernon.util.WindowUtil
WriteAlgernonFileAction - class org.algernon.app.j2p.action.WriteAlgernonFileAction.: WriteAlgernonFileAction performs the action of writing a file.
WriteAlgernonFileAction(J2PWindow, String, String, KeyStroke, Integer) - Constructor for class org.algernon.app.j2p.action.WriteAlgernonFileAction: Creates a new WriteAlgernonFileAction.
willBeGround(BindingList) - Method in class org.algernon.datatype.Clause: Returns true if the clause will be ground if the given set of variables is bound at runtime.

Z

ZERO_OR_MORE - Static variable in class org.algernon.aam.compile.AlgernonCompiler

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