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## A

absolute(int) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedResult
AbsoluteEuclideanClassifier - class uk.ac.ic.doc.automed.matching.modules.AbsoluteEuclideanClassifier.
AbsoluteEuclideanClassifier(Cluster[], double) - Constructor for class uk.ac.ic.doc.automed.matching.modules.AbsoluteEuclideanClassifier
AbstractModule - class uk.ac.ic.doc.automed.matching.modules.AbstractModule.
AbstractModule() - Constructor for class uk.ac.ic.doc.automed.matching.modules.AbstractModule
AccessMethod - class uk.ac.ic.doc.automed.reps.AccessMethod.
  The AccessMethod class describes how a particular database presented by a `Schema` can be accessed by an AutoMed application, using a particular `Protocol`.
Accessories - class uk.ac.ic.doc.automed.templates.gui.Accessories.
Accessories() - Constructor for class uk.ac.ic.doc.automed.templates.gui.Accessories
action - Variable in class uk.ac.ic.doc.automed.editor.UserActionClass
ACTION_ADD - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
  Transformation action "add"
ACTION_ADD_STR - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
ACTION_CONTRACT - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
  Transformation action "contract"
ACTION_CONTRACT_STR - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
ACTION_DELETE - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
  Transformation action "delete"
ACTION_DELETE_STR - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
ACTION_EXTEND - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
  Transformation action "extend"
ACTION_EXTEND_STR - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
ACTION_IDENT - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
  Transformation action "ident"
ACTION_IDENT_STR - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
ACTION_MAXIMUM - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
ACTION_MINIMUM - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
action_obj - Variable in class uk.ac.bbk.dcs.automed.qproc.EnvParser
  Instance of action encapsulation class.
action_obj - Variable in class uk.ac.bbk.dcs.automed.qproc.QParser
  Instance of action encapsulation class.
ACTION_RENAME - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
  Transformation action "rename"
ACTION_RENAME_STR - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
action_table() - Method in class uk.ac.bbk.dcs.automed.qproc.EnvParser
  Access to parse-action table.
action_table() - Method in class uk.ac.bbk.dcs.automed.qproc.QParser
  Access to parse-action table.
actionARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
actionARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
actionARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
actionName - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
actionName - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
actionName - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.editor.PathwayOptimiserTool
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.editor.ReportException
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.editor.UserAction
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.gui.SchemaTool
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.gui.LoadDialog
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.gui.IntegrateDialog
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.gui.ArgumentsDialog
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.gui.ArgPane
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaFrame
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.templates.gui.LoadDialog
add - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
ADD - Static variable in class uk.ac.ic.doc.automed.IntegrityException
  Exception caused by an operation doing some sort of addition to the repository.
add(AutoMedFloat) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedFloat
  Return the sum of two AutoMedFloats.
add(AutoMedInteger) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedInteger
  Return the sum of two AutoMedIntegers.
add(BidirectionalDegree) - Method in class uk.ac.ic.doc.automed.matching.BidirectionalDegree
ADD(Construct, Object[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
ADD(Construct, Object[], TemplateCompilerSimulator.CONSTRAINTS) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
ADD(Construct, Object[], TemplateCompilerSimulator.CONSTRAINTS, TemplateCompilerSimulator.FUNCTION) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
ADD(Construct, Object[], TemplateCompilerSimulator.FUNCTION) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
ADD(Construct, Object[], TemplateCompilerSimulator.FUNCTION, TemplateCompilerSimulator.CONSTRAINTS) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
add(int, ModelingStatement) - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Inserts the specified statement at the specified position(program counter) in this program.
add(ModelingStatement) - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Appends the specified statement to the end of this ModelingProgram.
addArgument(Schema) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList
addArgument(SchemaObject) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList
addArgument(SchemaObject[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList
addArgument(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList
addArgument(String[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList
addArrayToList(Object[], List) - Static method in class uk.ac.ic.doc.automed.Util
  Adds in order all elements in the source array to the destination List and returns the destination list so that the method can be used as an argument to a method call.
addAutoMedTuple(AutoMedTuple) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedResult
  Assert that a certain row number exists in a result
addAuxiliaryModule(AbstractModule) - Method in class uk.ac.ic.doc.automed.matching.Aggregator
addChild(TreeNode) - Method in class uk.ac.bbk.dcs.automed.graph.TreeNode
  Adds a node to the set of children of the node
addCommand(String, Class, String) - Static method in class uk.ac.ic.doc.automed.DSR
  Looks for a public method with the signature doCommand(String[] args) in the class methodClass and adds it to the commands that can be invoked from the CLI.
addConstraint(HDMConstraint) - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
addConstraintScheme() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Constraint schemes can only be added to constructs of type Nodal, Link-Nodal, Link or Constraint Defaults to isKey = true, 1..1
addConstraintScheme(boolean) - Method in class uk.ac.ic.doc.automed.reps.Construct
addConstraintScheme(int, int) - Method in class uk.ac.ic.doc.automed.reps.Construct
addConstraintScheme(int, int, boolean) - Method in class uk.ac.ic.doc.automed.reps.Construct
addEdge(Edge) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Takes an `Edge` struture and stores this in the database.
addEdgeNameScheme() - Method in class uk.ac.ic.doc.automed.reps.Construct
  EdgeName schemes can only be added to LINK and LINK-NODAL construct types.
addEdgeNameScheme(boolean) - Method in class uk.ac.ic.doc.automed.reps.Construct
addElement(ElementVectorRepresentation) - Method in class uk.ac.ic.doc.automed.matching.modules.Clusterer
addElement(ElementVectorRepresentation) - Method in class uk.ac.ic.doc.automed.matching.modules.Cluster
addElement(HDMElement) - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
addElements(ElementVectorRepresentation[]) - Method in class uk.ac.ic.doc.automed.matching.modules.Clusterer
addFoldFunction(FoldFunction) - Method in class uk.ac.bbk.dcs.automed.qproc.optimise.FoldFunctionTable
addFunction(String, BuiltInFunction) - Method in class uk.ac.bbk.dcs.automed.qproc.FunctionTable
  Adds a string and function pair to the table.
addGenericRoot(Document, String) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Method that adds a generic root named newRootName on top of the old root and returns the new document.
addGraphNode(DirectedGraphNode) - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraph
  Adds a node in the graph.
addIncomingEdge(DirectedGraphNode) - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraphNode
  Adds a node in the set of incoming edges of the calling node.
addInstance(String) - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
addLabelScheme() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Label schemes are scheme arguments that have no corresponding HDM (except maybe through automatic HDM node and edge names if the label is defined as key for its construct) Defaults to isKey = true, 1..1
addLabelScheme(boolean) - Method in class uk.ac.ic.doc.automed.reps.Construct
addLabelScheme(int, int) - Method in class uk.ac.ic.doc.automed.reps.Construct
addLabelScheme(int, int, boolean) - Method in class uk.ac.ic.doc.automed.reps.Construct
addLayoutComponent(String, Component) - Method in class uk.ac.ic.doc.automed.editor.PinBoardLayout
addModule(AbstractModule) - Method in class uk.ac.ic.doc.automed.matching.Filter
addNetworkChangeListener(NetworkChangeListener) - Method in class uk.ac.ic.doc.automed.reps.Network
addNetworksListener(NetworksListener) - Static method in class uk.ac.ic.doc.automed.reps.Network
addNewInputItem(boolean, int) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
addNewInputItemAndRedisplay(boolean, int) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
addNode(String, String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Takes a node type and a value and adds to the database
addNodeNameScheme() - Method in class uk.ac.ic.doc.automed.reps.Construct
  NodeName schemes can only be added to NODAL and LINK-NODAL construct types.
addNodeNameScheme(boolean) - Method in class uk.ac.ic.doc.automed.reps.Construct
addNodeNameScheme(int, int) - Method in class uk.ac.ic.doc.automed.reps.Construct
addNodeNameScheme(int, int, boolean) - Method in class uk.ac.ic.doc.automed.reps.Construct
addNonAuxiliaryModule(AbstractModule) - Method in class uk.ac.ic.doc.automed.matching.Aggregator
addObject(DefaultMutableTreeNode, Object) - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree
addObject(DefaultMutableTreeNode, Object, boolean) - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree
addObject(DefaultMutableTreeNode, Object, int, boolean) - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree
addObject(Object) - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree
  Add child to the currently selected node.
addOutgoingEdge(DirectedGraphNode) - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraphNode
  Adds a node in the set of outgoing edges of the calling node.
addPrefix(String, String) - Static method in class uk.ac.ic.doc.automed.Util
  Adds the prefix to the beginning of each line in message
addQuerySchemaObjectsToConditions(ArrayList) - Method in class uk.ac.ic.doc.automed.tml.TML
addReferencedArgument(TTemplateInputArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
addReferenceScheme(Construct) - Method in class uk.ac.ic.doc.automed.reps.Construct
addReferenceScheme(Construct, boolean) - Method in class uk.ac.ic.doc.automed.reps.Construct
addReferenceScheme(Construct, int, int) - Method in class uk.ac.ic.doc.automed.reps.Construct
addReferenceScheme(Construct, int, int, boolean) - Method in class uk.ac.ic.doc.automed.reps.Construct
addReloadHook(Method) - Static method in class uk.ac.ic.doc.automed.DSR
addSchemaChangeListener(SchemaChangeListener) - Method in class uk.ac.ic.doc.automed.reps.Schema
addSchemasListener(SchemasListener) - Static method in class uk.ac.ic.doc.automed.reps.Schema
AddStatement - class uk.ac.ic.doc.automed.templates.wrapper.AddStatement.
AddStatement() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.AddStatement
addSubGraph(DirectedGraph) - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraph
  Adds a subGraph in the set of subGraphs.
addToNegPostString(String) - Method in class uk.ac.ic.doc.automed.tml.TML
addToNegPreString(String) - Method in class uk.ac.ic.doc.automed.tml.TML
addToPosPostString(String) - Method in class uk.ac.ic.doc.automed.tml.TML
addToPosPreString(String) - Method in class uk.ac.ic.doc.automed.tml.TML
addTree(TreeNode) - Method in class uk.ac.bbk.dcs.automed.graph.Forest
  Adds a tree to the forest.
addVertex(HDMElement) - Method in class uk.ac.ic.doc.automed.reps.HDMEdge
Aggregator - class uk.ac.ic.doc.automed.matching.Aggregator.
Aggregator(SchemaElementPair[]) - Constructor for class uk.ac.ic.doc.automed.matching.Aggregator
ALIAS - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
  Define an alias of a table.
ALIAS(TemplateCompilerSimulator.ITEM, String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
aliases - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
ALL - Static variable in class uk.ac.ic.doc.automed.editor.MatchingTool
allArguments - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
allArgumentsSet - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
alternation - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
am - Variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
AMQfromIQL(ASG) - Method in class uk.ac.bbk.dcs.automed.wrappers.Translator
AMQfromIQL(ASG) - Method in class uk.ac.bbk.dcs.automed.wrappers.SQLTranslator
And - class uk.ac.bbk.dcs.automed.qproc.functions.And.
AND - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
  SQL logical AND binary operator for use within WHERE expressions
And() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.And
ANY - Static variable in class uk.ac.ic.doc.automed.editor.CommandLineDriver
appearsInSchemeOf(SchemaObject) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Determines whether or not the schema object appears anywhere in the scheme of another schema object.
Append - class uk.ac.bbk.dcs.automed.qproc.functions.Append.
Append() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Append
apply - Static variable in class uk.ac.bbk.dcs.automed.qproc.Cell
apply(Cell) - Method in class uk.ac.bbk.dcs.automed.qproc.optimise.PatternRule
apply(Cell) - Method in interface uk.ac.bbk.dcs.automed.qproc.optimise.Rule
apply(Cell) - Method in class uk.ac.bbk.dcs.automed.qproc.optimise.FoldNilRule
applyAddTransformation(Construct, Object[], String, String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the `Schema` which is the result of applying an ADD transformation.
applyAddTransformation(Construct, Object[], String, String, String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the `Schema` which is the result of applying an ADD transformation.
applyAddTransformation(Construct, String, String, String) - Method in class uk.ac.ic.doc.automed.reps.Schema
applyContractTransformation(SchemaObject, String, String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the `Schema` which is the result of applying a CONTRACT transformation.
applyContractTransformation(SchemaObject, String, String, String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the `Schema` which is the result of applying a CONTRACT transformation.
applyDeleteTransformation(SchemaObject, String, String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the `Schema` which is the result of applying a DELETE transformation.
applyDeleteTransformation(SchemaObject, String, String, String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the `Schema` which is the result of applying a DELETE transformation.
applyExtendTransformation(Construct, Object[], String, String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the `Schema` which is the result of applying an EXTEND transformation.
applyExtendTransformation(Construct, Object[], String, String, String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the `Schema` which is the result of applying an EXTEND transformation.
applyExtendTransformation(Construct, String, String, String) - Method in class uk.ac.ic.doc.automed.reps.Schema
applyIdent(Object[]) - Static method in class uk.ac.ic.doc.automed.editor.Gui
applyRenameTransformation(SchemaObject, Object[]) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the `Schema` which is the result of applying a RENAME transformation.
applyRenameTransformation(SchemaObject, Object[], String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the `Schema` which is the result of applying a RENAME transformation.
applyRetract(Object[]) - Static method in class uk.ac.ic.doc.automed.editor.Gui
Arc - class uk.ac.ic.doc.automed.gui.Arc.
Arc() - Constructor for class uk.ac.ic.doc.automed.gui.Arc
areCompatible(SchemaElementPair) - Method in class uk.ac.ic.doc.automed.matching.Integrator
areCompatible(SchemaElementPair[]) - Method in class uk.ac.ic.doc.automed.matching.Integrator
areRelated(SchemaObject[], SchemaObject[], SemanticRelationship, boolean) - Method in class uk.ac.ic.doc.automed.matching.Integrator
areRelativesMaximal() - Method in class uk.ac.ic.doc.automed.reps.Network
areSchemasIntegrated() - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
ARG_ACTION_IN_PRIMITIVE - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for action
ARG_ARGSEQUENCES_IN_FOREACH - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the FOREACH_STATEMENT for argument sequence ID of the lists to iterate
ARG_ARGSINGLETONS_IN_FOREACH - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the FOREACH_STATEMENT for argument sequence ID of singleton arguments
ARG_ARGUMENTS_IN_INVOCATION - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the INVOCATION_STATEMENT for the argument sequnce ID
ARG_CID_IN_NEWOBJECT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the NEW_OBJECT_STATEMENT for CID(Construct ID)
ARG_CONCATENATIONOP_IN_DEFINE_STRING - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position int the DEFINE_STRING statement for concatenation operator of the list of string fragments.
ARG_CONSTRAINTS_IN_PRIMITIVE - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for constraints
ARG_FROMOBJ_IN_PRIMITIVE - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for FromObject OBID
ARG_FROMSCHEMA_IN_CONTRACT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the CONTRACT_STATEMENT for the initial schema ID
ARG_FROMSCHEMA_IN_PRIMITIVE - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for FromSchema SID
ARG_FUNCTION_IN_PRIMITIVE - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for function
ARG_INDEX_IN_INDEX_LIST - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
ARG_ISTEMP_IN_NEWOBJECT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the NEW_OBJECT_STATEMENT for IsTemp
ARG_LIST_IN_INDEX_LIST - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
ARG_LISTPOINTER_IN_CREATE_LIST - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
ARG_LISTPOINTER_IN_DEFINE_STRING - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the DEFINE_STRING statement for the (pointer to the) list of string fragments that will make up the resulting string when concatenated
ARG_OBID_IN_NEWOBJECT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the NEW_OBJECT_STATEMENT for OBID(Object ID)
ARG_OBID_IN_SCHEMELIST - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
ARG_OBJECT_IN_CONTRACT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the CONTRACT_STATEMENT for object ID
ARG_RESULT_IN_DEFINE_STRING - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the DEFINE_STRING statement for the resulting string
ARG_RESULT_IN_INDEX_LIST - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
ARG_RESULT_IN_SCHEMELIST - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
ARG_RETURNED_ARGS_START_IN_FOREACH - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the FOREACH_STATEMENT where the returned argument sequences start
ARG_SCHEMA_IN_CREATE_LIST - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
ARG_SCHEMA_IN_DEFINE_STRING - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position int the DEFINE_STRING statement for the initial and final schema.
ARG_SCHEMA_IN_FOREACH - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the FOREACH_STATEMENT for current schema SID
ARG_SCHEMA_IN_INDEX_LIST - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
ARG_SCHEMA_IN_SCHEMELIST - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
ARG_SCHEME_IN_NEWOBJECT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the NEW_OBJECT_STATEMENT for the argument sequence ID of the object's scheme
ARG_SCHEMEID_IN_EXTGENSCHEME - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the EXTGENSCHEME_STATEMENT for the argument sequence ID of the generalisation's scheme
ARG_SCHEMEPOS_IN_EXTGENSCHEME - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the EXTGENSCHEME_STATEMENT for the position in the scheme where to start extending
ARG_SID_IN_NEWOBJECT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the NEW_OBJECT_STATEMENT for SID(Schema ID)
ARG_SUBENTITIES_IN_EXTGENSCHEME - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the EXTGENSCHEME_STATEMENT for the argument sequence ID of the sub-entities
ARG_TOOBJ_IN_PRIMITIVE - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for ToObject OBID
ARG_TOSCHEMA_IN_CONTRACT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the CONTRACT_STATEMENT for the final schema ID
ARG_TOSCHEMA_IN_PRIMITIVE - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for ToSchema SID
ARG_TRANS_IN_FOREACH - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the FOREACH_STATEMENT for template transformation ID
ARG_TRANSFORMATION_IN_INVOCATION - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the INVOCATION_STATEMENT for the template transformation's ID
ARG_VALUE_IN_NEWOBJECT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Position in the NEW_OBJECT_STATEMENT for the object's value
ArgPane - class uk.ac.ic.doc.automed.gui.ArgPane.
  Panel for defining an argument sequence.
ArgPane(String[]) - Constructor for class uk.ac.ic.doc.automed.gui.ArgPane
  Creates a new ArgPane.
ArgumentsDialog - class uk.ac.ic.doc.automed.gui.ArgumentsDialog.
  A dialog that can be used for the argument assignment.
ArgumentsDialog(Frame, ActionListener, String, boolean, String[]) - Constructor for class uk.ac.ic.doc.automed.gui.ArgumentsDialog
  Creates a new ArgumentsDialog.
ArrowIcon - class uk.ac.ic.doc.automed.gui.ArrowIcon.
  An icon that's a picture of an arrow.
ArrowIcon(int) - Constructor for class uk.ac.ic.doc.automed.gui.ArrowIcon
ASG - class uk.ac.bbk.dcs.automed.qproc.ASG.
  Every IQL query is internally represented as an Abstract Syntax Graph (ASG).
ASG(Cell) - Constructor for class uk.ac.bbk.dcs.automed.qproc.ASG
ASG(File) - Constructor for class uk.ac.bbk.dcs.automed.qproc.ASG
ASG(String) - Constructor for class uk.ac.bbk.dcs.automed.qproc.ASG
askForConstraints(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForConstraintsList(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForConstraintsList(String, TemplateCompilerSimulator.LIST) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForFunction(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForFunctionList(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForFunctionList(String, TemplateCompilerSimulator.LIST) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForName(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForNameList(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForNameList(String, TemplateCompilerSimulator.LIST) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForObject(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForObject(String, Construct) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForObjectList(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForObjectList(String, Construct) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForObjectList(String, Construct, TemplateCompilerSimulator.LIST) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
askForObjectList(String, TemplateCompilerSimulator.LIST) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
assertProtocol(String) - Static method in class uk.ac.ic.doc.automed.reps.Protocol
  Returns the `Protocol` with a certain name, creating it if it does not already exist..
AT_LEAST_ONE - Static variable in class uk.ac.ic.doc.automed.editor.CommandLineDriver
at(int) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.ModifiedArray
atDebugLevel(int) - Static method in class uk.ac.ic.doc.automed.STR
  Return true if the debug level set by `STR.setDebugLevel(int)` is at least at a certain level.
atDebugLevel(int) - Static method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Determine is debug is at or above a certain level.
atSectionDebugLevel(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Tests whether the section of code has been set to at least the debug level specified.
attribute - Static variable in class uk.ac.bbk.dcs.automed.xml.XMLConstants
AUTOMED_SQL_MODEL_COLUMN - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
AUTOMED_SQL_MODEL_FOREIGN_KEY - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
AUTOMED_SQL_MODEL_INDEX - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
AUTOMED_SQL_MODEL_PRIMARY_KEY - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
AUTOMED_SQL_MODEL_TABLE - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
AutoMedBoolean - class uk.ac.ic.doc.automed.wrappers.AutoMedBoolean.
  Provides generic representation boolean values.
AutoMedBoolean() - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedBoolean
  Create a new AutoMedBoolean that is null in value.
AutoMedBoolean(boolean) - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedBoolean
  Create a new AutoMedBoolean
AutoMedBoolean(String) - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedBoolean
  Create a new AutoMedBoolean from a String value.
AutoMedException - exception uk.ac.ic.doc.automed.AutoMedException.
  The class root of all AutoMed generated exceptions.
AutoMedException(String) - Constructor for class uk.ac.ic.doc.automed.AutoMedException
  Creates an AutoMedException.
AutoMedFloat - class uk.ac.ic.doc.automed.wrappers.AutoMedFloat.
  Provides generic representation of floating values with abritrary precision.
AutoMedFloat() - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedFloat
  Create a new AutoMedFloat that is null in value
AutoMedFloat(BigDecimal) - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedFloat
  Create a new AutoMedFloat from a BigDecimal.
AutoMedFloat(double, int) - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedFloat
  Create a new AutoMedFloat from a 64 bit floating point value.
AutoMedFloat(float, int) - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedFloat
  Create a new AutoMedFloat from a 32 bit floating point value.
AutoMedID - Static variable in class uk.ac.bbk.dcs.automed.xml.XMLConstants
AutoMedInteger - class uk.ac.ic.doc.automed.wrappers.AutoMedInteger.
  Provides generic representation of integer values with up to 64 bit precision.
AutoMedInteger() - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedInteger
  Create a new AutoMedInteger that is a null value
AutoMedInteger(int, int) - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedInteger
  Create a new AutoMedInteger from a 32 bit integer value.
AutoMedInteger(long, int) - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedInteger
  Create a new AutoMedInteger
automedModelName - Variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
AutoMedQuery - class uk.ac.ic.doc.automed.wrappers.AutoMedQuery.
  A generic representation of query expressions as trees, where each AutoMedQuery has an operator type, and 0 or more fields that have a field type
AutoMedQuery(AutoMedQueryToken, Object[]) - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
AutoMedQueryToken - class uk.ac.ic.doc.automed.wrappers.AutoMedQueryToken.
  A generic representation of query langauge tokens
AutoMedResult - class uk.ac.ic.doc.automed.wrappers.AutoMedResult.
  Provides a representation of the data associated with a scheme in an AutoMed Schema.
AutoMedResult(int) - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedResult
  Create a new AutoMedResult with a fixed size of tuple in the resultCache
AutoMedString - class uk.ac.ic.doc.automed.wrappers.AutoMedString.
  Provides generic representation of string values of abritrary size.
AutoMedString(String) - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedString
  Create a new AutoMedString
AutoMedTime - class uk.ac.ic.doc.automed.wrappers.AutoMedTime.
  Provides generic representation of time values in GMT.
AutoMedTime() - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedTime
  Create a new AutoMedTime that is a null value
AutoMedTime(Date, int) - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedTime
  Create a new AutoMedTime
AutoMedTime(long, int) - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedTime
  Create a new AutoMedTime, measured as the number of milliseconds since 1st January 1970, 00:00:00 GMT
AutoMedTuple - class uk.ac.ic.doc.automed.wrappers.AutoMedTuple.
  A structure to hold one tuple of data, to be used by AutoMedResult as the basis for storing sets, lists or bags of tuples.
AutoMedTuple(AutoMedResult, int, int) - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedTuple
  Create a new tuple belonging to row i and with nc attributes
AutoMedType - class uk.ac.ic.doc.automed.wrappers.AutoMedType.
  Provides a base for the representation of basic types supported by AutoMed.
AutoMedType() - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedType
AutoMedWrapper - class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper.
  An AutoMedWrapper represents an open connection to a datasource.
AutoMedWrapper() - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
AutoMedWrapperFactory - class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory.
  An AutoMedWrapperFactory class able to produce AutoMedWrapper instances, together with any data that the wrapper requires to be present in the repository.
AutoMedWrapperFactory() - Constructor for class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
AutoRepException - exception uk.ac.ic.doc.automed.reps.AutoRepException.
  The class of exceptions generated by the uk.ac.ic.doc.automed.reps package.
AutoRepException(String) - Constructor for class uk.ac.ic.doc.automed.reps.AutoRepException
  Creates an AutoRepException.
AutoRepException(String, Exception) - Constructor for class uk.ac.ic.doc.automed.reps.AutoRepException
  Creates an AutoRepException.
Average - class uk.ac.bbk.dcs.automed.qproc.functions.Average.
Average() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Average
awf - Variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
awf - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator

## B

BadSchemaException - exception uk.ac.ic.doc.automed.reps.BadSchemaException.
  The class of exceptions generated when the contents of an intentional schema materialized via a particular transformation pathway are not the same as those of the same schema materialized via its default transformation pathway (path to the cloesest extensional schema).
BadSchemaException(String, Schema) - Constructor for class uk.ac.ic.doc.automed.reps.BadSchemaException
  Creates a BadSchemaException.
BagIntersect - class uk.ac.bbk.dcs.automed.qproc.functions.BagIntersect.
BagIntersect() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.BagIntersect
banner() - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Prints a line of 90 stars.
banner(int) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Prints a line of num stars.
Bar - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
baseName - Variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
BidirectionalDegree - class uk.ac.ic.doc.automed.matching.BidirectionalDegree.
BidirectionalDegree(double, double) - Constructor for class uk.ac.ic.doc.automed.matching.BidirectionalDegree
bidirectionalDegrees - Variable in class uk.ac.ic.doc.automed.matching.modules.AbstractModule
BidirectionalMap - class uk.ac.ic.doc.automed.matching.BidirectionalMap.
BidirectionalMap(double, double, double) - Constructor for class uk.ac.ic.doc.automed.matching.BidirectionalMap
BINARY_CLASS - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
blockStatements - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
BOOLEAN - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
BOOLEAN - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedType
  Type to represent a boolean true/false value.
BOOLEAN_TOKEN - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
booleanValue() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedBoolean
  Return a boolean representation of this AutoMedBoolean.
BoolToken - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
bounds - Variable in class uk.ac.ic.doc.automed.editor.DrawVertex
Box - class uk.ac.ic.doc.automed.gui.Box.
Box() - Constructor for class uk.ac.ic.doc.automed.gui.Box
BREAK_ICON - Static variable in class uk.ac.ic.doc.automed.templates.gui.Accessories
breakList() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
build(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapperFactory
buildTemplate() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
BuiltInFunction - interface uk.ac.bbk.dcs.automed.qproc.BuiltInFunction.
  Interface class for all functions.

## C

cacheWrapper() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Cache this `AutoMedWrapper` as being able to provide the implementation of an `AccessMethod` used to create the wrapper.
calcRectangleConnector(Rectangle, Rectangle) - Static method in class uk.ac.ic.doc.automed.editor.EditorPanel
  Compute three points, the first two of which represent a rectangle that forms a box `between' the supplied rectangles, and the third point represents the `sign' of the relationship between the rectangles.
callConfirmMessagePane(String) - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool
callErrorMessagePane(String) - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool
CallToWrapper - class uk.ac.bbk.dcs.automed.qproc.functions.CallToWrapper.
CallToWrapper() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.CallToWrapper
cancelButton - Variable in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
caseCommand(String) - Static method in class uk.ac.ic.doc.automed.Util
  converts the argument into lower case with the first letter in uppercase
Cell - class uk.ac.bbk.dcs.automed.qproc.Cell.
  Every node in an ASG is a Cell, so one has to use this class in order to perform any operations on an ASG
Cell(int, Object) - Constructor for class uk.ac.bbk.dcs.automed.qproc.Cell
Cell(int, Object, Object) - Constructor for class uk.ac.bbk.dcs.automed.qproc.Cell
Cell(int, Object, Object, Object) - Constructor for class uk.ac.bbk.dcs.automed.qproc.Cell
Cell(Object, Object) - Constructor for class uk.ac.bbk.dcs.automed.qproc.Cell
Cell(String) - Constructor for class uk.ac.bbk.dcs.automed.qproc.Cell
centre - Variable in class uk.ac.ic.doc.automed.editor.DrawVertex
characters(char[], int, int) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLDSSSAX
checkEditable() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Checks whether a schema is editable.
CheckExistenceModule - class uk.ac.ic.doc.automed.matching.modules.CheckExistenceModule.
CheckExistenceModule(ArrayList, ArrayList) - Constructor for class uk.ac.ic.doc.automed.matching.modules.CheckExistenceModule
chooseBackgroundColor(Object[]) - Static method in class uk.ac.ic.doc.automed.editor.Gui
chooseForegroundColor(Object[]) - Static method in class uk.ac.ic.doc.automed.editor.Gui
chooseTextColor(Object[]) - Static method in class uk.ac.ic.doc.automed.editor.Gui
cid - Variable in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
cidExists(int) - Static method in class uk.ac.ic.doc.automed.MDR
  Checks if a particular construct identifier (CID) exists in the MDR.
CLASS_ALTERNATION - Static variable in class uk.ac.ic.doc.automed.reps.Construct
  Class of construct which acts as a place holder for one of list of alternative constructs.
CLASS_CONSTRAINT - Static variable in class uk.ac.ic.doc.automed.reps.Construct
  Class of construct for constraints, i.e.
CLASS_LINK - Static variable in class uk.ac.ic.doc.automed.reps.Construct
  Class of construct for linking constructs, i.e.
CLASS_LINK_NODAL - Static variable in class uk.ac.ic.doc.automed.reps.Construct
  Class of construct for link-nodal constructs, i.e.
CLASS_MAXIMUM - Static variable in class uk.ac.ic.doc.automed.reps.Construct
CLASS_MINIMUM - Static variable in class uk.ac.ic.doc.automed.reps.Construct
CLASS_NODAL - Static variable in class uk.ac.ic.doc.automed.reps.Construct
  Class of construct for nodal constructs, i.e.
CLASS_SEQUENCE - Static variable in class uk.ac.ic.doc.automed.reps.Construct
  Class of construct which acts as a place holder for a list of constructs.
Classifier - interface uk.ac.ic.doc.automed.matching.modules.Classifier.
classify(ElementVectorRepresentation) - Method in class uk.ac.ic.doc.automed.matching.modules.RelativeEuclideanClassifier
classify(ElementVectorRepresentation) - Method in interface uk.ac.ic.doc.automed.matching.modules.Classifier
classify(ElementVectorRepresentation) - Method in class uk.ac.ic.doc.automed.matching.modules.AbsoluteEuclideanClassifier
CLAUSE_CLASS - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
clear() - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Removes all of the statements from this ModelingProgram.
clear() - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree
  Remove all nodes except the root node.
clearAccessMethods() - Static method in class uk.ac.ic.doc.automed.reps.AccessMethod
clearFeatures() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Clear all the features for this factory.
clearSchemas() - Static method in class uk.ac.ic.doc.automed.reps.Schema
  This method empties all the cached Schema, SchemaObject, Transformation, AccessMethods and Protocols that have been cached.
clone() - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Returns a deep copy of this `ModelingProgram` instance.
clone() - Method in class uk.ac.ic.doc.automed.matching.SchemaElementPairRelationship
close() - Method in class uk.ac.ic.doc.automed.editor.Gui
closeScheme - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
Cluster - class uk.ac.ic.doc.automed.matching.modules.Cluster.
Cluster() - Constructor for class uk.ac.ic.doc.automed.matching.modules.Cluster
Clusterer - class uk.ac.ic.doc.automed.matching.modules.Clusterer.
Clusterer() - Constructor for class uk.ac.ic.doc.automed.matching.modules.Clusterer
ClustererClassifier - class uk.ac.ic.doc.automed.matching.modules.ClustererClassifier.
ClustererClassifier() - Constructor for class uk.ac.ic.doc.automed.matching.modules.ClustererClassifier
clusters - Variable in class uk.ac.ic.doc.automed.matching.modules.Clusterer
COLLECTING - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
COLLECTS(TemplateCompilerSimulator.ITEM) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
colon - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
Colon - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
Colon - Static variable in class uk.ac.bbk.dcs.automed.qproc.FSym
COLUMN_POSITION - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  A feature option to model the position of a column in a table as part of a column in any `Schema` the factory generates
columns - Variable in class uk.ac.ic.doc.automed.matching.SQLRelationshipExtractor
combineRelationships(SemanticRelationship, SemanticRelationship) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
comma - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
Comma - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
Comma - Static variable in class uk.ac.bbk.dcs.automed.qproc.FSym
CommandLineDriver - class uk.ac.ic.doc.automed.editor.CommandLineDriver.
CommandLineDriver() - Constructor for class uk.ac.ic.doc.automed.editor.CommandLineDriver
CommandLineException - exception uk.ac.ic.doc.automed.editor.CommandLineException.
CommandLineException(String) - Constructor for class uk.ac.ic.doc.automed.editor.CommandLineException
commit() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
ComparableExact - interface uk.ac.ic.doc.automed.matching.modules.ComparableExact.
compare(Object, Object) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
compare(Object, Object) - Method in class uk.ac.ic.doc.automed.reps.Construct
compare(Object, Object) - Method in class uk.ac.ic.doc.automed.matching.Instance
compareNodes(Cell, Cell) - Static method in class uk.ac.bbk.dcs.automed.qproc.functions.Comparisons
comparePrecision(SchemaElement, SchemaElement) - Static method in class uk.ac.ic.doc.automed.matching.modules.PrecisionModule
compareRange(ComparableExact, ComparableExact, ComparableExact, ComparableExact) - Static method in class uk.ac.ic.doc.automed.matching.modules.PrecisionModule
compareTo(Object) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
compareTo(Object) - Method in class uk.ac.ic.doc.automed.reps.Transformation
compareTo(Object) - Method in interface uk.ac.ic.doc.automed.matching.modules.ComparableExact
Comparisons - class uk.ac.bbk.dcs.automed.qproc.functions.Comparisons.
Comparisons() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Comparisons
compositeDescription - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
compositeName - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
CompositeTransformation - class uk.ac.ic.doc.automed.templates.CompositeTransformation.
  The CompositeTransformation class.
CompositeTransformation(String, String, boolean) - Constructor for class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Constructs a new CompositeTransformation without any argument definitions nor program.
CompositeTransformationRecord - class uk.ac.ic.doc.automed.templates.CompositeTransformationRecord.
CompositeTransformationRecord() - Constructor for class uk.ac.ic.doc.automed.templates.CompositeTransformationRecord
CompositeTransformationRecord(Schema, Vector) - Constructor for class uk.ac.ic.doc.automed.templates.CompositeTransformationRecord
Comprehension - class uk.ac.bbk.dcs.automed.qproc.functions.Comprehension.
Comprehension() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Comprehension
concat(Object[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
concat(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
concat(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
ConfigException - exception uk.ac.ic.doc.automed.editor.ConfigException.
ConfigException(String) - Constructor for class uk.ac.ic.doc.automed.editor.ConfigException
ConfigException(String, int, String) - Constructor for class uk.ac.ic.doc.automed.editor.ConfigException
confirmOptimise(TML, TML, String) - Method in class uk.ac.ic.doc.automed.editor.PathwayOptimiserTool
connect() - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapper
  Connect to a JDBC database in the standard way.
connect() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Use the connection details held with this wrapper to connect to the data source.
connect() - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
  Connect to a semistructured textfile --- i.e.
connect() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
connect() - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapper
connect() - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  If connecting to the HDM store without a schema being passed assume same data source as for the MDR
connect(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Connect to the database using the access method for the named schema.
connect(String, String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Connect to the database using the access method for the named schema using the access method in the repository for the schema and the password supplied.
constant - Static variable in class uk.ac.bbk.dcs.automed.qproc.Cell
Constants - interface uk.ac.ic.doc.automed.Constants.
  Deprecated. use constants in individual classes instead, such as Construct .CLASS_MINIMUM instead of CONSTRUCT_CLASS_MINIMUM
constrain(Component, int, int, int, int) - Method in class uk.ac.ic.doc.automed.editor.GUITool
constrain(Component, int, int, int, int, int, int, double, double) - Method in class uk.ac.ic.doc.automed.editor.GUITool
constrain(Component, int, int, int, int, int, int, double, double, int, int, int, int) - Method in class uk.ac.ic.doc.automed.editor.GUITool
constraint - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
CONSTRAINTS - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TConstants
constraintsARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
constraintsARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
construct - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
construct - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
Construct - class uk.ac.ic.doc.automed.reps.Construct.
  The Construct class
CONSTRUCT - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
CONSTRUCT - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TConstants
CONSTRUCT_CLASS_CONSTRAINT - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Class of construct for constraints
CONSTRUCT_CLASS_LINK - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Class of construct for linking constructs
CONSTRUCT_CLASS_LINK_NODAL - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Class of construct for link-nodal constructs
CONSTRUCT_CLASS_MAXIMUM - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated.
CONSTRUCT_CLASS_MINIMUM - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated.
CONSTRUCT_CLASS_NODAL - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Class of construct for nodal constructs
CONSTRUCT_TYPE_ANY - Static variable in class uk.ac.ic.doc.automed.reps.Construct
CONSTRUCT_TYPE_ARRAY - Static variable in class uk.ac.ic.doc.automed.reps.Construct
CONSTRUCT_TYPE_REFERENCE - Static variable in class uk.ac.ic.doc.automed.reps.Construct
Construct(Model, int, String, int, boolean) - Constructor for class uk.ac.ic.doc.automed.reps.Construct
  Instantiates a `Construct`, which is assumed to already exist in the `STR`.
ConstructAny - Static variable in class uk.ac.ic.doc.automed.reps.Construct
constructARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
ConstructArray - Static variable in class uk.ac.ic.doc.automed.reps.Construct
constructor - Static variable in class uk.ac.bbk.dcs.automed.qproc.Cell
ConstructReference - Static variable in class uk.ac.ic.doc.automed.reps.Construct
ConstructScheme - class uk.ac.ic.doc.automed.reps.ConstructScheme.
  The ConstructScheme class
ConstructScheme(int, int, int, Construct, boolean, int, int, int) - Constructor for class uk.ac.ic.doc.automed.reps.ConstructScheme
  Instantiates a new ConstructScheme object.
ConstructSchemeSyntaxException - exception uk.ac.ic.doc.automed.reps.ConstructSchemeSyntaxException.
ConstructSchemeSyntaxException(String) - Constructor for class uk.ac.ic.doc.automed.reps.ConstructSchemeSyntaxException
ConstructWithModelingProgram - class uk.ac.ic.doc.automed.reps.ConstructWithModelingProgram.
  The class describing Construct objects together with their graphical representations/ModelingProgram objects
ConstructWithModelingProgram(Model, int, String, int, boolean) - Constructor for class uk.ac.ic.doc.automed.reps.ConstructWithModelingProgram
  Creates a new Construct.
ConstToken - Static variable in class uk.ac.bbk.dcs.automed.qproc.FSym
contains(Node) - Method in class uk.ac.ic.doc.automed.reps.Network
  Returns whether or not the network contains the supplied node.
contains(Point) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
contains(Point) - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
contains(Point) - Method in class uk.ac.ic.doc.automed.gui.Arc
contains(Schema) - Method in class uk.ac.ic.doc.automed.reps.Network
  Returns whether or not the network contains the supplied schema
contains(SchemaElementPair[], SchemaElement[], int) - Static method in class uk.ac.ic.doc.automed.matching.Integrator
contains(SchemaElementPair[], SchemaElementPair[]) - Static method in class uk.ac.ic.doc.automed.matching.Integrator
contains(String) - Method in class uk.ac.ic.doc.automed.reps.Network
  Returns whether or not the network contains the named schema
containsInstance(String) - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
containsRelationship(SemanticRelationship[], SemanticRelationship) - Static method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
containsSchemaObject(String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Determine if the `SchemaObject` that has the supplied name exists in this `Schema`
contract - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
CONTRACT_STATEMENT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Statement to contract an object
CONTRACT() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT
CONTRACT(TemplateCompilerSimulator.CONSTRAINTS) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT
CONTRACT(TemplateCompilerSimulator.FUNCTION) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT
CONTRACT(TemplateCompilerSimulator.FUNCTION, TemplateCompilerSimulator.CONSTRAINTS) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT
CONTRACT(TemplateCompilerSimulator.OBJECT) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
CONTRACT(TemplateCompilerSimulator.OBJECT, TemplateCompilerSimulator.CONSTRAINTS) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
CONTRACT(TemplateCompilerSimulator.OBJECT, TemplateCompilerSimulator.CONSTRAINTS, TemplateCompilerSimulator.FUNCTION) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
CONTRACT(TemplateCompilerSimulator.OBJECT, TemplateCompilerSimulator.FUNCTION) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
CONTRACT(TemplateCompilerSimulator.OBJECT, TemplateCompilerSimulator.FUNCTION, TemplateCompilerSimulator.CONSTRAINTS) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
ContractStatement - class uk.ac.ic.doc.automed.templates.wrapper.ContractStatement.
ContractStatement() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.ContractStatement
copyOfASG() - Method in class uk.ac.bbk.dcs.automed.qproc.ASG
  Creates and returns an exact copy of the ASG.
copyOfGraph() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns an exact copy of the ASG
Count - class uk.ac.bbk.dcs.automed.qproc.functions.Count.
count() - Method in class uk.ac.ic.doc.automed.matching.modules.Vectors
Count() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Count
countAppearances(String, char) - Static method in class uk.ac.ic.doc.automed.matching.Util
CREATE_LIST_STATEMENT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
CREATE_LIST(TemplateCompilerSimulator.ITEM[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
createAccessMethod(int, String, int, String, String, String, String, int) - Static method in class uk.ac.ic.doc.automed.STR
  Add the access methods of a schema to the STR.
  Precondition: The schema whose access methods are being added must already exist in the schemas table.
createAccessMethod(Schema, String, Protocol, String, String) - Static method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Used to created an AccessMethod where no password is required to access the data source.
createAccessMethod(Schema, String, Protocol, String, String, String, String, int) - Static method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Creates a new access method.
createAddTransformation(Schema, Construct, Object[], String, String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates a new ADD transformation.
createAddTransformation(Schema, Construct, Object[], String, String, String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates an ADD transformation.
createArc() - Static method in class uk.ac.ic.doc.automed.gui.SchemaManager
createArgument(int, int) - Method in class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
  Constructs a new TemplateArgument and adds it to this TemplateArgumentSequence.
createArgument(int, int, int, int, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Adds a new argument to a sequence of arguments
createArgument(int, int, String) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Adds a new argument to a sequence of arguments
createArgument(int, String) - Method in class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
  Constructs a new TemplateArgument and adds it to this TemplateArgumentSequence.
createArgument(int, String) - Method in class uk.ac.ic.doc.automed.templates.RuntimeArgumentSequence
  Constructs a new RuntimeArgument and adds it to this RuntimeArgumentSequence.
createArgument(int, TemplateArgument) - Method in class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
  Constructs a new TemplateArgument and adds it to this TemplateArgumentSequence.
createArgument(int, TemplateArgumentSequence, int) - Method in class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
  Constructs a new TemplateArgument and adds it to this TemplateArgumentSequence.
createArgumentDefinition(int, String, boolean) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Defines an argument for this CompositeTransformation.
createArgumentDefinition(int, String, boolean, int, int, int, int) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Defines an argument for this CompositeTransformation.
createArgumentDefinition(int, String, String, String) - Method in class uk.ac.ic.doc.automed.templates.Statement
  Defines an argument for this Statement.
createArgumentDefinition(int, String, String, String, boolean) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Defines an argument for this CompositeTransformation.
createArgumentInRepository() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
createArgumentSequence(Vector) - Method in class uk.ac.ic.doc.automed.gui.SchemaTool
createArgumentSequence(Vector) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList
createAutoMedModel() - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  Define a relational modelling language for the SQL standard which is an "AutoMed" oriented modelling language..
createAutoMedSchema(AutoMedWrapper, String) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Create an AutoMed oriented schema from the source oriented schema.
createAutoMedSchema(AutoMedWrapper, String) - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
createAutoMedSchema(AutoMedWrapper, String) - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapperFactory
  Create an AutoMed oriented schema from the source oriented schema.
createAutoMedSchema(AutoMedWrapper, String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapperFactory
createAutoMedSchema(AutoMedWrapper, String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapperFactory
createBox() - Static method in class uk.ac.ic.doc.automed.gui.SchemaManager
createClusters() - Method in class uk.ac.ic.doc.automed.matching.modules.MapDisplay
createClusters() - Method in class uk.ac.ic.doc.automed.matching.modules.JSomClusterer
createClusters() - Method in class uk.ac.ic.doc.automed.matching.modules.Clusterer
createCompositeArgument(CompositeTransformation) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
createCompositeTransformation(String, String, boolean) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Adds a new composite transformation to the TTR.
createCompositeTransformationDefinition(int, int, String, boolean, int, int, int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
createCompositeTransformationDefinition(int, int, String, String, String, boolean) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Adds a new argument to the composite transformation's definition of arguments.
createCompositeTransformationExecution(int, int, int, int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Adds a statement to the composite transformation's execution
createCompositeTransformationInvocation(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Creates a composite transformation's invocation
createCompositeTransformationProgram(int, int, int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Adds a new statement to a composite transformation's program
createCompositeTransformationReturnedValuesDefinition(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Defines where the transformation's returned values are stored.
createConstruct(int, String, int, boolean) - Static method in class uk.ac.ic.doc.automed.MDR
  Creates a new construct for a modelling language
createConstruct(String, int, boolean) - Method in class uk.ac.ic.doc.automed.reps.Model
  Creates a new construct and add to the model.
createConstructModeling(int, int, String) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Adds a new method invocation to a construct's modeling program
createConstructScheme(int, Construct, boolean, int, int, int) - Method in class uk.ac.ic.doc.automed.reps.Construct
  Semi-deprecated! See the various addXxxScheme() methods.
createConstructScheme(int, int, int, boolean, int, int, int) - Static method in class uk.ac.ic.doc.automed.MDR
  Creates a new constructScheme argument for a construct
createContractTransformation(Schema, SchemaObject, String, String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates an CONTRACT transformation.
createContractTransformation(Schema, SchemaObject, String, String, String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates an CONTRACT transformation.
createDBtables() - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
createDBtables(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Check to see if the repository tables are in place on the HDM store data source.
createDeleteTransformation(Schema, SchemaObject, String, String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates a DELETE transformation.
createDeleteTransformation(Schema, SchemaObject, String, String, String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates a DELETE transformation.
createdObject - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
createExecutionStatement(int, CompositeTransformation) - Method in class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement
createExecutionStatement(int, CompositeTransformation) - Method in class uk.ac.ic.doc.automed.templates.wrapper.SchemeListStatement
createExecutionStatement(int, CompositeTransformation) - Method in class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement
createExecutionStatement(int, CompositeTransformation) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatement
createExecutionStatement(int, CompositeTransformation) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
createExecutionStatement(int, CompositeTransformation) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
createExecutionStatement(int, CompositeTransformation) - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
createExecutionStatement(int, CompositeTransformation) - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
createExecutionStatement(int, CompositeTransformation) - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
createExtendTransformation(Schema, Construct, Object[], String, String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates an EXTEND transformation.
createExtendTransformation(Schema, Construct, Object[], String, String, String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates an EXTEND transformation.
createFields() - Method in class uk.ac.ic.doc.automed.editor.PathwayOptimiserTool
createFields() - Method in class uk.ac.ic.doc.automed.editor.GUITool
createFields() - Method in class uk.ac.ic.doc.automed.editor.ReportException
createFields() - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
createFirstArgument(int, int, int, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Creates a new sequence of arguments and adds a new argument to the sequence
createFirstArgument(int, String) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Creates a new sequence of arguments and adds a new argument to the sequence
createFirstArgument(int, String, Vector) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Creates a new sequence of arguments and adds a new argument to the sequence
createFollowingSchemaName() - Method in class uk.ac.ic.doc.automed.reps.Schema
createFollowingSchemaName(String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Generate a name of a schema that "appears" to be following the name used for this Schema, and which has not already been used as a Schema name
createHdmStore(String, String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Create a logical HDM store for the given schema.
createIdentTransformation(Schema, Schema, String, String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates an IDENT transformation.
createIdentTransformations(Schema, Schema, String, String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Deprecated. Use `#createIdentTransformations()` instead.
createIntSchemaName(String, boolean, boolean) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates a name for an intentional schema based on a given schema.
createLine() - Static method in class uk.ac.ic.doc.automed.gui.SchemaManager
CreateListStatement - class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement.
CreateListStatement() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement
createMethod(String, String) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Adds a new method to the SMR.
createMethodArgument(int, int, String) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Adds a new argument to the method's arguments.
createModel() - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  Define a relational modelling language for the SQL standard, together with the JDBC protocol for accessing SQL compliant databases.
createModel(String) - Static method in class uk.ac.ic.doc.automed.MDR
  Creates a new data modelling language which can then have constructs added.
createModel(String) - Static method in class uk.ac.ic.doc.automed.reps.Model
  Creates a new model with the given name.
createPathway(Schema[]) - Static method in class uk.ac.ic.doc.automed.reps.Pathway
createPattern(String, String) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Adds a new pattern to the SSMDR.
createPattern(String, String) - Static method in class uk.ac.ic.doc.automed.ssd.Pattern
createPatternSobjAssociation(int, int, int, int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Add the association between ssdpattern and schema object to the SSMDR.
createPrimitiveTransformation(int, String[], String[], Vector) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Creates a primitive transformation and appends it in the STR.
createProtocol(String) - Static method in class uk.ac.ic.doc.automed.STR
  Add the given protocol to the STR.
createProtocol(String) - Static method in class uk.ac.ic.doc.automed.reps.Protocol
  Creates a new protocol.
createRenameTransformation(Schema, SchemaObject, Object[]) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates a RENAME transformation.
createRenameTransformation(Schema, SchemaObject, Object[], String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates a RENAME transformation.
createReturnArgument(TemplateArgumentSequence) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
createReturnedArgumentsDefinition(TemplateArgumentSequence) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Defines the values of the arguments that store returned values after the transformation's invocation.
createRhombus() - Static method in class uk.ac.ic.doc.automed.gui.SchemaManager
createSchema(String, boolean) - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Creates a new schema.
createSchema(String, boolean, boolean, boolean, int) - Static method in class uk.ac.ic.doc.automed.STR
  Adds a new schema to the STR.
createSchema(String, boolean, boolean, boolean, Schema) - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Creates a new schema.
createSchemaObject(Construct, Object[]) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Creates a schema object.
createSchemaObject(int, int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Adds a new schema object to the STR.
createSchemaObject(Schema, Construct, Object[]) - Static method in class uk.ac.ic.doc.automed.reps.SchemaObject
  All schemaobjects belong to schemas Creates a new schema object.
createSchemaObjectFromDB(int, Schema) - Static method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Instantiates a `SchemaObject` whose record already exists in the STR.
createScheme(int, int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Adds a scheme to the STR.
createSSDFormat(String) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Adds a new ssdformat to the SSMDR.
createSSDFormat(String, Schema) - Static method in class uk.ac.ic.doc.automed.ssd.SSDFormat
  Create a SSDFormat
createSSDPattern(int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Adds a ssdpattern to the SSMDR.
createSSDPattern(Pattern) - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
createStatement(String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Adds a new statement to the TTSR.
createStatementDefinition(int, int, String, String, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Adds a new argument definition to the statement's definitions of arguments.
createStatementExecution(int, Statement, TemplateArgumentSequence) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Defines the statement to be invoked at a particular program counter.
createTransformation(String, int, int, int, int, String, String) - Static method in class uk.ac.ic.doc.automed.STR
  Adds a transformation to the STR between two existing schemas, which must not already have a transformation between them.
currentArgumentPosition - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
currentForeachVariables - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
currentKey - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
currentlyDisplayedSchema - Variable in class uk.ac.ic.doc.automed.templates.gui.SchemaFrame
currentScopeStack - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
cx - Variable in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalVertex
cy - Variable in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalVertex

## D

d - Variable in class uk.ac.ic.doc.automed.editor.DrawArc
DATA_SIZE - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  A feature option to model the size in bytes of a column as part of a column in any `Schema` the factory generates
data_source - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
DATA_TYPE - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  A feature option to model the datatype of a column as part of a column in any `Schema` the factory generates
data() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns the Object contained in the Cell
DataSourceException - exception uk.ac.ic.doc.automed.wrappers.DataSourceException.
  Generated when some problem occurs when accessing a data source, such as the wrong password being supplied.
DataSourceException(String) - Constructor for class uk.ac.ic.doc.automed.wrappers.DataSourceException
  Creates an DataSourceException when there has been no Exception that caused the error to discovered.
DataSourceException(String, Exception) - Constructor for class uk.ac.ic.doc.automed.wrappers.DataSourceException
  Creates an DataSourceException when it is acting as a wrapper for other Exceptions.
DataSourceRepository - class uk.ac.ic.doc.automed.DataSourceRepository.
  Deprecated. Old name for `DSR`
DataSourceRepository() - Constructor for class uk.ac.ic.doc.automed.DataSourceRepository
  Deprecated.
DataSourceRepositoryException - exception uk.ac.ic.doc.automed.DataSourceRepositoryException.
  Deprecated. Old name for `DSRException`.
DataSourceRepositoryException(String) - Constructor for class uk.ac.ic.doc.automed.DataSourceRepositoryException
  Deprecated.
dataType() - Method in class uk.ac.bbk.dcs.automed.hdmstore.Span
  Get the dataType
dataType() - Method in class uk.ac.bbk.dcs.automed.hdmstore.EdgeElement
  get the dataType
DataTypeModule - class uk.ac.ic.doc.automed.matching.modules.DataTypeModule.
DataTypeModule(ArrayList, ArrayList) - Constructor for class uk.ac.ic.doc.automed.matching.modules.DataTypeModule
DATE_TOKEN - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
dateValue() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTime
DAY - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedTime
  Granularity of one day
debug - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
debug - Variable in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
Debug - class uk.ac.bbk.dcs.automed.hdmstore.Debug.
  The Debug class allows debugging messages to be sent from a calling application.
DEBUG_SECTION_GOBBLE_PATH - Static variable in class uk.ac.ic.doc.automed.STR
DEBUG_SECTION_GUI - Static variable in class uk.ac.ic.doc.automed.STR
Debug() - Constructor for class uk.ac.bbk.dcs.automed.hdmstore.Debug
  Standard constructor, default message level, no logging, print to output.
Debug(int) - Constructor for class uk.ac.bbk.dcs.automed.hdmstore.Debug
  Constructor with message level parameter , no logging, print to output.
Debug(int, boolean, boolean) - Constructor for class uk.ac.bbk.dcs.automed.hdmstore.Debug
  Constructor with message level, logging and print to output all parameters.
Debug(int, boolean, boolean, String) - Constructor for class uk.ac.bbk.dcs.automed.hdmstore.Debug
  Constructor with message level, logging, print to output and log file name all parameters.
debugPrintStackTrace(Throwable, int) - Static method in class uk.ac.ic.doc.automed.STR
  Print an throwable's stack trace, but only at a certain debug level
debugString() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  A String representation of this object useful for debugging code
debugString() - Method in class uk.ac.ic.doc.automed.reps.Schema
  A String representation of this object useful for debugging code
debugString() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  A String representation of this object useful for debugging code
DefaultDrawConstraintArc - class uk.ac.ic.doc.automed.editor.DefaultDrawConstraintArc.
DefaultDrawConstraintArc(EditorPanel, Positionable, Positionable[]) - Constructor for class uk.ac.ic.doc.automed.editor.DefaultDrawConstraintArc
DefaultDrawConstraintVertex - class uk.ac.ic.doc.automed.editor.DefaultDrawConstraintVertex.
DefaultDrawConstraintVertex(EditorPanel, Positionable) - Constructor for class uk.ac.ic.doc.automed.editor.DefaultDrawConstraintVertex
DefaultDrawConstraintVertex(EditorPanel, Positionable, Positionable[]) - Constructor for class uk.ac.ic.doc.automed.editor.DefaultDrawConstraintVertex
DefaultDrawLinkArc - class uk.ac.ic.doc.automed.editor.DefaultDrawLinkArc.
DefaultDrawLinkArc(EditorPanel, Positionable, Positionable[]) - Constructor for class uk.ac.ic.doc.automed.editor.DefaultDrawLinkArc
DefaultDrawLinkNodalArc - class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalArc.
DefaultDrawLinkNodalArc(EditorPanel, Positionable, Positionable[]) - Constructor for class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalArc
DefaultDrawLinkNodalVertex - class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalVertex.
DefaultDrawLinkNodalVertex(EditorPanel, Positionable, Positionable[]) - Constructor for class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalVertex
DefaultDrawLinkVertex - class uk.ac.ic.doc.automed.editor.DefaultDrawLinkVertex.
DefaultDrawLinkVertex(EditorPanel, Positionable) - Constructor for class uk.ac.ic.doc.automed.editor.DefaultDrawLinkVertex
DefaultDrawNodalVertex - class uk.ac.ic.doc.automed.editor.DefaultDrawNodalVertex.
DefaultDrawNodalVertex(EditorPanel, Positionable) - Constructor for class uk.ac.ic.doc.automed.editor.DefaultDrawNodalVertex
defaultModel - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
defaultModel() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
defaultModel() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
  Return the AutoMed `Model` that the template transformation will generate or delete `SchemaObject`s in
DefaultTemplate - class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate.
  The DefaultTemplate class enables the definition of template transformations at run-time.
DefaultTemplate() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
  Instantiates a template transformation.
DefaultTemplate(Model, String, String) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
  Instantiates a template transformation.
DEFINE_CONSTRAINTS(Object[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_CONSTRAINTS(Object[], String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_CONSTRAINTS(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_CONSTRAINTS(String, String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_FUNCTION(Object[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_FUNCTION(Object[], String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_FUNCTION(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_FUNCTION(String, String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_NAME(Object[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_NAME(Object[], String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_NAME(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_NAME(String, String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_STRING_STATEMENT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Statement to defined dynamic strings, used for functions, constraints definitions and more
DEFINE_STRING(Object[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_STRING(Object[], String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_STRING(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_STRING(String, String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_STRING(TemplateCompilerSimulator.STRINGLIST) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINE_STRING(TemplateCompilerSimulator.STRINGLIST, String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DefineStringStatement - class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement.
DefineStringStatement(int) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
defineTemplate() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
defineTemplate() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINING_FOREACH_VARIABLES - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINING_IF_VALRIABLES - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DEFINING_INPUT_VARIABLES - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DegreeCombinator - class uk.ac.ic.doc.automed.matching.DegreeCombinator.
DegreeCombinator(SimilarSchemaElementPair[]) - Constructor for class uk.ac.ic.doc.automed.matching.DegreeCombinator
delete - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
DELETE - Static variable in class uk.ac.ic.doc.automed.IntegrityException
  Exception caused by an operation doing some sort of deletion from the repository.
DELETE_ICON - Static variable in class uk.ac.ic.doc.automed.templates.gui.Accessories
DELETE() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT
DELETE(TemplateCompilerSimulator.CONSTRAINTS) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT
DELETE(TemplateCompilerSimulator.CONSTRAINTS, TemplateCompilerSimulator.FUNCTION) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT
DELETE(TemplateCompilerSimulator.FUNCTION) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT
DELETE(TemplateCompilerSimulator.FUNCTION, TemplateCompilerSimulator.CONSTRAINTS) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT
DELETE(TemplateCompilerSimulator.OBJECT) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DELETE(TemplateCompilerSimulator.OBJECT, TemplateCompilerSimulator.CONSTRAINTS) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DELETE(TemplateCompilerSimulator.OBJECT, TemplateCompilerSimulator.CONSTRAINTS, TemplateCompilerSimulator.FUNCTION) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DELETE(TemplateCompilerSimulator.OBJECT, TemplateCompilerSimulator.FUNCTION) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
DELETE(TemplateCompilerSimulator.OBJECT, TemplateCompilerSimulator.FUNCTION, TemplateCompilerSimulator.CONSTRAINTS) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
deleteButtonClicked(InputItem) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
deleted() - Method in class uk.ac.ic.doc.automed.reps.Network
  Return true when the Network class is finished with, after all Schemas have been deleted from it
deleteEdge(String, String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Check the node type is valid & and instance of the node with this value exists.
deleteIQL(ASG) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
deleteIQL(ASG) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapper
  Take the query and attempt to insert each of the values in the list into the database.
deleteNode(String, String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Check the node type is valid & and instance of the node with this value exists.
DeleteStatement - class uk.ac.ic.doc.automed.templates.wrapper.DeleteStatement.
DeleteStatement() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.DeleteStatement
dependent - Variable in class uk.ac.ic.doc.automed.editor.DrawVertex
describeTransformations(Vector) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns a `String` describing the transformations executed in the Vector given as a parameter
description - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
descriptionPane - Variable in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
descriptions - Variable in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
descriptionScroller - Variable in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
dialogueFinished(CompositeTransformationRecord) - Method in interface uk.ac.ic.doc.automed.templates.gui.DialogueLauncher
DialogueLauncher - interface uk.ac.ic.doc.automed.templates.gui.DialogueLauncher.
DialogueManager - interface uk.ac.ic.doc.automed.templates.gui.DialogueManager.
Difference - class uk.ac.bbk.dcs.automed.qproc.functions.Difference.
Difference() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Difference
differenceByName(Schema) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Return an `SchemaObject` array containing the difference by name between this schema (s1) and the schema passed as a parameter (s2).
DirectedGraph - class uk.ac.bbk.dcs.automed.graph.DirectedGraph.
  Class that abstracts a directed unlabelled graph.
DirectedGraph() - Constructor for class uk.ac.bbk.dcs.automed.graph.DirectedGraph
DirectedGraphNode - class uk.ac.bbk.dcs.automed.graph.DirectedGraphNode.
  Class that abstracts a node in a directed unlabelled graph.
DirectedGraphNode(String) - Constructor for class uk.ac.bbk.dcs.automed.graph.DirectedGraphNode
disableAll() - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
disableAll() - Method in interface uk.ac.ic.doc.automed.templates.gui.InteractiveSchemaDisplay
discoverRelationships() - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
Disjointness - class uk.ac.ic.doc.automed.matching.relationships.Disjointness.
disjoints - Variable in class uk.ac.ic.doc.automed.matching.Integrator
Disjunction - class uk.ac.bbk.dcs.automed.qproc.functions.Disjunction.
Disjunction() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Disjunction
dispatchCommand(String) - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
dispatchCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
  Invokes the method registered for the command args[0] with `#addCommand(String, Class)`.
display() - Method in class uk.ac.bbk.dcs.automed.hdmstore.Span
  return the node value using the HDM notation
display(LinkedList) - Static method in class uk.ac.bbk.dcs.automed.hdmstore.EdgeElement
  Pretty print an edge
displayCurrentInputForm() - Method in class uk.ac.ic.doc.automed.templates.gui.TemplateInputDialogue
displayReferenceLists() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
Divide - class uk.ac.bbk.dcs.automed.qproc.functions.Divide.
Divide() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Divide
divide(AutoMedFloat) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedFloat
  Return the division of two AutoMedFloats.
divide(AutoMedInteger) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedInteger
  Return the division of two AutoMedIntegers.
divide(BidirectionalDegree) - Method in class uk.ac.ic.doc.automed.matching.BidirectionalDegree
do_action(int, lr_parser, Stack, int) - Method in class uk.ac.bbk.dcs.automed.qproc.EnvParser
  Invoke a user supplied parse action.
do_action(int, lr_parser, Stack, int) - Method in class uk.ac.bbk.dcs.automed.qproc.QParser
  Invoke a user supplied parse action.
DO() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
doCreateCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
doCreatedbCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
  Reads the property CreateDB property for the data source and executes the value as an update on the databse connection
doDefaultCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
doDisplayCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
doDropdbCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
doesReference() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
doExitCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
doGetCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
doGetModelsCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.Editor
doGetNetworkCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.Editor
doGetNetworkNamesCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.Editor
doGetNetworksCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.Editor
doGetSchemaNetworkCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.Editor
doHelpCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
doHelpCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
doIsCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
doListSchemaCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.Editor
domDriver - Static variable in class uk.ac.bbk.dcs.automed.xml.XMLConstants
DOMMaterialiser - class uk.ac.bbk.dcs.automed.xml.DOMMaterialiser.
  TODO: Informed repository that global schema is an external data source, TODO: should I do something else (inform location of data source)? TODO: investigate what happens to text in mixed elements
DOMMaterialiser(DOMWrapper, String, String, String[], boolean) - Constructor for class uk.ac.bbk.dcs.automed.xml.DOMMaterialiser
DOMWrapper - class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapper.
  A lower level wrapper that conforms to the XMLWrapper class.
DOMWrapper(AccessMethod, String) - Constructor for class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapper
DOMWrapperFactory - class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapperFactory.
  A lower level wrapper factory for accessing XML files using DOM.
DOMWrapperFactory() - Constructor for class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapperFactory
doPopulatedbCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
doPrintCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
doPrintNetworkCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.Editor
doQuitCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
doReloadCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
doRemoveCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
doSetCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
Dot - Static variable in class uk.ac.bbk.dcs.automed.qproc.FSym
DOUBLE_TOKEN - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
doubleValue() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTime
  Return the number of milliseconds since 1970 as a double
doubleValue() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedString
doubleValue() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTuple
  Return the arity (size) of the tuple as a double.
doubleValue() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedFloat
  Return the value of this AutoMedFloat as an double
doubleValue() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedInteger
  Return the value of this AutoMedInteger as a double
doubleValue() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedType
  Return the double representation of this AutoMedType.
doubleValue() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedBoolean
  Return a double representation of this AutoMedBoolean, where true is 1.0 and false 0.0
draw() - Method in class uk.ac.ic.doc.automed.gui.Rhombus
draw() - Method in class uk.ac.ic.doc.automed.gui.Line
draw() - Method in class uk.ac.ic.doc.automed.gui.Box
draw() - Method in class uk.ac.ic.doc.automed.gui.Arc
Drawable - interface uk.ac.ic.doc.automed.editor.Drawable.
DrawableArc - interface uk.ac.ic.doc.automed.editor.DrawableArc.
DrawableVertex - interface uk.ac.ic.doc.automed.editor.DrawableVertex.
DrawArc - class uk.ac.ic.doc.automed.editor.DrawArc.
DrawArc(EditorPanel, Positionable[]) - Constructor for class uk.ac.ic.doc.automed.editor.DrawArc
  Pass in the array of objects that this connects together.
DrawArc(EditorPanel, Positionable, Positionable[]) - Constructor for class uk.ac.ic.doc.automed.editor.DrawArc
  Pass in the array of objects that this connects together.
drawDiamond(Graphics2D, int, int, int, int) - Static method in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkVertex
DrawingObject - class uk.ac.ic.doc.automed.templates.gui.DrawingObject.
DrawingObject(int) - Constructor for class uk.ac.ic.doc.automed.templates.gui.DrawingObject
drawMap(String[][]) - Static method in class uk.ac.ic.doc.automed.reps.SchemaMapGenerator
drawMap(String[][], boolean) - Static method in class uk.ac.ic.doc.automed.reps.SchemaMapGenerator
DrawVertex - class uk.ac.ic.doc.automed.editor.DrawVertex.
DrawVertex(EditorPanel, Positionable) - Constructor for class uk.ac.ic.doc.automed.editor.DrawVertex
DrawVertex(EditorPanel, Positionable, Positionable[]) - Constructor for class uk.ac.ic.doc.automed.editor.DrawVertex
driver - Variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
dropSequence() - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Older versions of Postgres do not automatically drop sequences created for primary keys etc when the table is dropped - this loops through dropping the sequences explicitly.
DSR - class uk.ac.ic.doc.automed.DSR.
  Reads data source definitions from a configuration file and provides methods to get a `Connection` for a data souce.
DSRException - exception uk.ac.ic.doc.automed.DSRException.
  The class of exceptions generated by `DSR`.
DSRException(String) - Constructor for class uk.ac.ic.doc.automed.DSRException
duplicateDOM(Document) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Method that creates and returns a new DOM representation of the input one.
duplicateDOM(String, boolean) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
duplicateTransformation(Schema) - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates a duplicate of the transformation.

## E

Edge - class uk.ac.bbk.dcs.automed.hdmstore.Edge.
  A Edge represents an HDM edge, which can be of any length, each element (or `Span`) can be a node or an edge and edges can be named (optionally).
EDGE_ADDED - Static variable in class uk.ac.ic.doc.automed.reps.NetworkChangeEvent
EDGE_REMOVED - Static variable in class uk.ac.ic.doc.automed.reps.NetworkChangeEvent
edge() - Method in class uk.ac.bbk.dcs.automed.hdmstore.EdgeElement
  get the edge
Edge(String, String[]) - Constructor for class uk.ac.bbk.dcs.automed.hdmstore.Edge
  Construct a representation of an edge from a string representing its type and an array of spans
edgeAdded(NetworkChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.NetworkChangeListener
edgeAdded(NetworkChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
EdgeElement - class uk.ac.bbk.dcs.automed.hdmstore.EdgeElement.
  An edge element represents a single element of an edge.
edgeExists(Span) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Test to see if an edge exists has been passed a `Span` structure - split this out into type and and value and return the result.
edgeExists(String, String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Does and edge with this type and value exist in the HDM store?
edgeInstanceExists(String, String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Check to see if an instance of this edge exists in the HDM store
edgeNameIsUnique(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Edge names dont have to be unique - the combination of edge name and types is unique i.e.
edgeOrNode() - Method in class uk.ac.bbk.dcs.automed.hdmstore.Span
  Get the edgeOrNode indicator
edgeRemoved(NetworkChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.NetworkChangeListener
edgeRemoved(NetworkChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
edgeSpan - Static variable in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
edgeTypeExists(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Given an edge type e.g.
edgeTypeForName(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Assuming edge name is unique (which need to be checked before calling) return its edge type e.g.
edgeValueAsString() - Method in class uk.ac.bbk.dcs.automed.hdmstore.Edge
  Get the edge values as a string
Editor - class uk.ac.ic.doc.automed.editor.Editor.
Editor(String[]) - Constructor for class uk.ac.ic.doc.automed.editor.Editor
EditorException - exception uk.ac.ic.doc.automed.editor.EditorException.
EditorException(String) - Constructor for class uk.ac.ic.doc.automed.editor.EditorException
EditorPanel - class uk.ac.ic.doc.automed.editor.EditorPanel.
EditorPanel(Gui.EditorFrame) - Constructor for class uk.ac.ic.doc.automed.editor.EditorPanel
EditorPanel(Map, Gui.EditorFrame) - Constructor for class uk.ac.ic.doc.automed.editor.EditorPanel
element - Static variable in class uk.ac.bbk.dcs.automed.xml.XMLConstants
ELEMENT_AT(int, Construct) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.LIST
ELEMENT_AT(int, int) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.LIST
elementArgSeq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement
elementAttributeQuery(String, String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
elementAttributeQuery(String, String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.SAXWrapper
elementAttributeQuery(String, String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapper
elementElementQuery(String, String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
elementElementQuery(String, String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.SAXWrapper
elementElementQuery(String, String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapper
elementElementQuery(String, String, int) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
elementElementQuery(String, String, int) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.SAXWrapper
  Nodes are compared based on elementName:count, not their whole UID
elementElementQuery(String, String, int) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapper
  Nodes are compared based on elementName:count, not their whole UID
ElementNameModule - class uk.ac.ic.doc.automed.matching.modules.ElementNameModule.
ElementNameModule(ArrayList, ArrayList) - Constructor for class uk.ac.ic.doc.automed.matching.modules.ElementNameModule
elementOrAttribute - Static variable in class uk.ac.bbk.dcs.automed.xml.XMLConstants
elementOrPCData - Static variable in class uk.ac.bbk.dcs.automed.xml.XMLConstants
elementPCDataQuery(String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
elementPCDataQuery(String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.SAXWrapper
elementPCDataQuery(String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapper
elementPCDataQuery(String, int) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
elementPCDataQuery(String, int) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.SAXWrapper
elementPCDataQuery(String, int) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapper
elementQuery(String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
elementQuery(String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.SAXWrapper
elementQuery(String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapper
elementType() - Method in class uk.ac.bbk.dcs.automed.hdmstore.EdgeElement
  get the elementType;
ElementVectorRepresentation - class uk.ac.ic.doc.automed.matching.modules.ElementVectorRepresentation.
ElementVectorRepresentation(SchemaElement, double[]) - Constructor for class uk.ac.ic.doc.automed.matching.modules.ElementVectorRepresentation
emptyQuery() - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  Returns the ASG representation of the empty query.
enabled - Variable in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
END() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
endDocument() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLDSSSAX
endElement(String, String, String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLDSSSAX
ENDFOREACH() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
Environment - class uk.ac.bbk.dcs.automed.qproc.Environment.
Environment() - Constructor for class uk.ac.bbk.dcs.automed.qproc.Environment
Environment(File) - Constructor for class uk.ac.bbk.dcs.automed.qproc.Environment
Environment(String) - Constructor for class uk.ac.bbk.dcs.automed.qproc.Environment
EnvLexer - class uk.ac.bbk.dcs.automed.qproc.EnvLexer.
EnvLexer(InputStream) - Constructor for class uk.ac.bbk.dcs.automed.qproc.EnvLexer
EnvLexer(Reader) - Constructor for class uk.ac.bbk.dcs.automed.qproc.EnvLexer
EnvParser - class uk.ac.bbk.dcs.automed.qproc.EnvParser.
  CUP v0.10j generated parser.
EnvParser() - Constructor for class uk.ac.bbk.dcs.automed.qproc.EnvParser
  Default constructor.
EnvParser(Scanner) - Constructor for class uk.ac.bbk.dcs.automed.qproc.EnvParser
  Constructor which sets the default scanner.
EnvSym - class uk.ac.bbk.dcs.automed.qproc.EnvSym.
  CUP generated class containing symbol constants.
EnvSym() - Constructor for class uk.ac.bbk.dcs.automed.qproc.EnvSym
EOF - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
EOF - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
EOF - Static variable in class uk.ac.bbk.dcs.automed.qproc.EnvSym
EOF - Static variable in class uk.ac.bbk.dcs.automed.qproc.FSym
EOF_sym() - Method in class uk.ac.bbk.dcs.automed.qproc.EnvParser
  `EOF` Symbol index.
EOF_sym() - Method in class uk.ac.bbk.dcs.automed.qproc.QParser
  `EOF` Symbol index.
EOL - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
ep - Variable in class uk.ac.ic.doc.automed.editor.DrawVertex
ep - Variable in class uk.ac.ic.doc.automed.editor.DrawArc
Equal - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
EQUAL - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
  SQL equality predicate for use within WHERE expressions
Equals - class uk.ac.bbk.dcs.automed.qproc.functions.Equals.
Equals() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Equals
equals(AutoMedType) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTime
equals(AutoMedType) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedString
equals(AutoMedType) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTuple
equals(AutoMedType) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedFloat
equals(AutoMedType) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedInteger
equals(AutoMedType) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedType
  Test two AutoMedTypes for equality, performing conversions as appropriate.
equals(AutoMedType) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedBoolean
equals(BidirectionalDegree) - Method in class uk.ac.ic.doc.automed.matching.BidirectionalDegree
equals(Object) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
equals(Object) - Method in class uk.ac.ic.doc.automed.reps.Construct
equals(Object) - Method in class uk.ac.bbk.dcs.automed.qproc.SchemeInfo
equals(Object) - Method in class uk.ac.ic.doc.automed.matching.SchemaElementPair
equals(Object) - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
equals(Object) - Method in class uk.ac.ic.doc.automed.matching.Instance
equals(Object) - Method in class uk.ac.ic.doc.automed.matching.relationships.Subsumption
equals(Object) - Method in class uk.ac.ic.doc.automed.matching.relationships.SemanticRelationship
equals(Object) - Method in class uk.ac.ic.doc.automed.matching.relationships.Overlapness
equals(Object) - Method in class uk.ac.ic.doc.automed.matching.relationships.Incompatibility
equals(Object) - Method in class uk.ac.ic.doc.automed.matching.relationships.Equivalence
equals(Object) - Method in class uk.ac.ic.doc.automed.matching.relationships.Disjointness
Equivalence - class uk.ac.ic.doc.automed.matching.relationships.Equivalence.
equivalents - Variable in class uk.ac.ic.doc.automed.matching.Integrator
error - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
error - Static variable in class uk.ac.bbk.dcs.automed.qproc.EnvSym
error - Static variable in class uk.ac.bbk.dcs.automed.qproc.FSym
ERROR - Static variable in class uk.ac.bbk.dcs.automed.hdmstore.Debug
error_sym() - Method in class uk.ac.bbk.dcs.automed.qproc.EnvParser
  `error` Symbol index.
error_sym() - Method in class uk.ac.bbk.dcs.automed.qproc.QParser
  `error` Symbol index.
error(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.Debug
  Write an error level message
escapeSQLString(String) - Static method in class uk.ac.ic.doc.automed.STR
  Take a string, and escape its characters such the \ character will be stored in SQL correctly.
escapeString(String) - Static method in class uk.ac.ic.doc.automed.reps.Syntax
  Take a string, and escape its characters such the \ character will print correctly.
evaluate(ASG) - Method in class uk.ac.bbk.dcs.automed.qproc.Evaluator
  Evaluates g to normal form.
evaluate(Cell) - Method in class uk.ac.bbk.dcs.automed.qproc.Evaluator
  Evaluates the graph of which root is the root to normal form.
evaluateSize() - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
evaluateXPath(Document, String, int) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
Evaluator - class uk.ac.bbk.dcs.automed.qproc.Evaluator.
  The class that coordinates the evaluation of IQL queries.
Evaluator(FunctionTable) - Constructor for class uk.ac.bbk.dcs.automed.qproc.Evaluator
  Constructs an Evaluator object that will use the ft for the evaluation of built-in functions.
exactlyTwo(Object[]) - Static method in class uk.ac.ic.doc.automed.editor.Gui
EXECUTE_ICON - Static variable in class uk.ac.ic.doc.automed.templates.gui.Accessories
executeCreateListStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Executes a `CREATE_LIST` statement.
executeDefineStringStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Executes a `DEFINE_STRING` statement.
executedStatementNR - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
executedStatements - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
executedStatementsArguments - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
executeForEachStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Executes a `foreach` statement.
executeIndexListStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
executeInvocationStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Executes a `transformation_invocation` statement.
executeIQL(ASG) - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapper
executeIQL(ASG) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Execute an IQL query on the datasource.
executeIQL(ASG) - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
executeIQL(ASG) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
executeIQL(ASG) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapper
  Takes `ASG` query and passes it to a `LowLevelWrapperHdm` for processing.
executeLocalQuery(AutoMedQuery) - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapper
executeLocalQuery(AutoMedQuery) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Execute a query in the datasource's native query language, and obtain a result in an AutoMedResult class
executeLocalQuery(AutoMedQuery) - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
executeLocalQuery(AutoMedQuery) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
executeLocalQuery(AutoMedQuery) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapper
  This is a stub required as the AutoMedWrapper requires it
executeNewObjectStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Executes a `new_object` statement.
executePrimitiveTransformationStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Executes a `primitive_transformation` statement.
executeQuery(String) - Static method in class uk.ac.ic.doc.automed.MDR
  Execute a SQL query on the repository, and return the result in a `Vector`
executeQuery(String) - Static method in class uk.ac.ic.doc.automed.STR
  Execute a SQL query on the repository, and return the result in a `Vector`
executeSchemeListStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
executeSQLQuery(SQLQuery) - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapper
  Execute a query on the data source, returning the result in the standard format for instances of SQL queries.
executeStatement(String, Connection, OutputStream) - Static method in class uk.ac.ic.doc.automed.Util
executeStatement(String, Connection, OutputStream, Set) - Static method in class uk.ac.ic.doc.automed.Util
executeStatement(String, Connection, Writer) - Static method in class uk.ac.ic.doc.automed.Util
  Executes the sql statement on the JDBC Concection and returns either a ResultSet, an Integer representing the update count or an SQLException if thrown when executing the command.
executeStatement(String, Connection, Writer, Set) - Static method in class uk.ac.ic.doc.automed.Util
executeStatement(String, String, boolean) - Static method in class uk.ac.ic.doc.automed.DSR
executeStatement(String, String, boolean, Set) - Static method in class uk.ac.ic.doc.automed.DSR
executeStatements(String, String, boolean) - Static method in class uk.ac.ic.doc.automed.DSR
executeStatements(String, String, boolean, Set) - Static method in class uk.ac.ic.doc.automed.DSR
executeStatements(String, String, Connection, OutputStream) - Static method in class uk.ac.ic.doc.automed.Util
executeStatements(String, String, Connection, OutputStream, Set) - Static method in class uk.ac.ic.doc.automed.Util
executeStatements(String, String, Connection, Writer) - Static method in class uk.ac.ic.doc.automed.Util
  Calls {link #executeStatement(String, Connection, Writer)} with each each statement in sql seperated by del.
executeStatements(String, String, Connection, Writer, Set) - Static method in class uk.ac.ic.doc.automed.Util
executeTransformation() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList
executeTransformation(int, InteractiveSchemaDisplay, Frame) - Static method in class uk.ac.ic.doc.automed.templates.gui.TemplateInputDialogue
executeTransformation(int, int, Frame) - Static method in class uk.ac.ic.doc.automed.templates.gui.TemplateInputDialogue
executeTransformation(int, int, InteractiveSchemaDisplay, Frame) - Static method in class uk.ac.ic.doc.automed.templates.gui.TemplateInputDialogue
executeTransformation(int, int, String[], HashMap, int, String[], String[], Vector, Vector) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Main method which executes a composite transformation.
executeUpdate(String) - Static method in class uk.ac.ic.doc.automed.MDR
  Execute a SQL update on the repository.
executeUpdate(String) - Static method in class uk.ac.ic.doc.automed.STR
  Execute a SQL update on the repository.
executeXMLQuery(ASG) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
  Given an IQL query, this method queries the XML file using DOM, then returns the answer in ASG format.
executeYattaQuery(YattaQuery) - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
exists(int) - Static method in class uk.ac.ic.doc.automed.reps.Model
exists(int) - Static method in class uk.ac.ic.doc.automed.ssd.SSDFormat
  Returns true if the format for the specified schema identifier exists
exists(String) - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Returns true is the named schema exists
exists(String) - Static method in class uk.ac.ic.doc.automed.reps.Protocol
  Determine if a given named protocol exists in the repository
exists(String) - Static method in class uk.ac.ic.doc.automed.reps.Model
exists(String) - Static method in class uk.ac.ic.doc.automed.ssd.SSDFormat
  Returns true if the format for the specified ssdformat exists
exists(String) - Static method in class uk.ac.ic.doc.automed.ssd.Pattern
existsIn(SchemaElement, SchemaElementPair[], int) - Method in class uk.ac.ic.doc.automed.matching.Integrator
existsIn(String, SchemaObject[]) - Method in class uk.ac.ic.doc.automed.matching.Integrator
exitCommandLine() - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
exitCommandLine(int) - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
exitHelp - Static variable in class uk.ac.ic.doc.automed.editor.CommandLineDriver
exitSyntax - Static variable in class uk.ac.ic.doc.automed.editor.CommandLineDriver
exportConstructs(OutputStream) - Method in class uk.ac.ic.doc.automed.reps.Model
exportConstructs(PrintWriter) - Method in class uk.ac.ic.doc.automed.reps.Model
exportSchemaObjects(OutputStream) - Method in class uk.ac.ic.doc.automed.reps.Schema
exportSchemaObjects(PrintWriter) - Method in class uk.ac.ic.doc.automed.reps.Schema
exportSchemes(OutputStream) - Method in class uk.ac.ic.doc.automed.reps.Construct
exportSchemes(PrintWriter) - Method in class uk.ac.ic.doc.automed.reps.Construct
extend - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
EXTEND(Construct, Object[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
EXTEND(Construct, Object[], TemplateCompilerSimulator.CONSTRAINTS) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
EXTEND(Construct, Object[], TemplateCompilerSimulator.CONSTRAINTS, TemplateCompilerSimulator.FUNCTION) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
EXTEND(Construct, Object[], TemplateCompilerSimulator.FUNCTION) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
EXTEND(Construct, Object[], TemplateCompilerSimulator.FUNCTION, TemplateCompilerSimulator.CONSTRAINTS) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
extendEnvironment(File) - Method in class uk.ac.bbk.dcs.automed.qproc.Environment
extendEnvironment(String) - Method in class uk.ac.bbk.dcs.automed.qproc.Environment
ExtendStatement - class uk.ac.ic.doc.automed.templates.wrapper.ExtendStatement.
ExtendStatement() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.ExtendStatement
extendToMatch(Schema) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Create a new Schema which contains the same set of constructs as the current schema, plus all those constructs of another schema, which are defined via extend operators.
extendToMatch(Schema, Schema) - Static method in class uk.ac.ic.doc.automed.matching.Integrator
EXTGENSCHEME_STATEMENT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Statement to extend an ER generalization's scheme

## F

factoryInUse - Variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
features - Static variable in class uk.ac.ic.doc.automed.matching.modules.StatisticsModule
FIELD - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
FIELD_TYPE_AUTOMEDQUERY - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
  A field that can hold a AutoMedQuery
FIELD_TYPE_INTEGER - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
  A field that can hold an Integer constant
FIELD_TYPE_INTEGER - Static variable in class uk.ac.ic.doc.automed.wrappers.SchemeQuery
  A field that can hold an Integer constant
FIELD_TYPE_ONE_OR_MORE - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
  Used when the previous field type may be repeated any number of times.
FIELD_TYPE_ONE_OR_MORE - Static variable in class uk.ac.ic.doc.automed.wrappers.SchemeQuery
  Used when the previous field type may be repeated any number of times.
FIELD_TYPE_SCHEMEQUERY - Static variable in class uk.ac.ic.doc.automed.wrappers.SchemeQuery
  A field that can hold a SchemeQuery
FIELD_TYPE_STRING - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
  A field that can hold a String constant
FIELD_TYPE_STRING - Static variable in class uk.ac.ic.doc.automed.wrappers.SchemeQuery
  A field that can hold a String constant
fileCreate(String, String, String) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Creates a new file named "fileName" in path "filePath", with only the root, named "rootName", and returns its DOM representation.
fillDiamond(Graphics2D, int, int, int, int) - Static method in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkVertex
Filter - class uk.ac.ic.doc.automed.matching.Filter.
Filter(SchemaElement[], SchemaElement[]) - Constructor for class uk.ac.ic.doc.automed.matching.Filter
Filter(SchemaElementPair[]) - Constructor for class uk.ac.ic.doc.automed.matching.Filter
finalize() - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
findAtomicRelationships(SchemaObject[], SchemaObject[]) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
findAtomicRelationships(SchemaObject, SchemaObject[]) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
findAttachedDataSources() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns an array of Schema's that are connected to this schema by some transformation pathway and are data sources (including this schema itself if it is a data source).
findAttachedExtDBs() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns an array of Schema's that are connected to this schema by some transformation pathway and have extensional data (including this schema itself if it has extensional data).
findAttachedExtSchemas() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns an array of Schema's that are connected to this schema by some transformation pathway and are extensional schemas (including this schema itself if it is an extensional schema).
findAutoMedFile(String) - Static method in class uk.ac.ic.doc.automed.Util
findFile(String) - Static method in class uk.ac.ic.doc.automed.Util
  Returns a URL for the given name using several methods to make it useful for locating configuration files, resources etc.
findmax(Cell) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Max
findmin(Cell) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Min
findPath(Node, Node, LinkedList, LinkedList) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
findRelated(SchemaObject[], SchemaObject[], SemanticRelationship, boolean) - Method in class uk.ac.ic.doc.automed.matching.Integrator
findShortestPath(Schema) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns an array of schemas such that: There is a transformation between each pair of adjacent schamas.
findShortestPathway(Schema, Schema) - Static method in class uk.ac.ic.doc.automed.reps.Pathway
  Find the shortest path containing the fewest number of steps between two schemas.
findShortestPathway(String, String) - Static method in class uk.ac.ic.doc.automed.reps.Pathway
FINISHED - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
First - class uk.ac.bbk.dcs.automed.qproc.functions.First.
First() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.First
firstCharKeyword - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
Flatmap - class uk.ac.bbk.dcs.automed.qproc.functions.Flatmap.
Flatmap() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Flatmap
flattenSchemes(Object[]) - Static method in class uk.ac.ic.doc.automed.STR
  Converts an `Object` array representation of a schema object's scheme into a `String` representation.
FLexer - class uk.ac.bbk.dcs.automed.qproc.FLexer.
FLexer(InputStream) - Constructor for class uk.ac.bbk.dcs.automed.qproc.FLexer
FLexer(Reader) - Constructor for class uk.ac.bbk.dcs.automed.qproc.FLexer
FLOAT - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
FLOAT - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedType
  Type to represent a floating point atomic type
FLOAT_TOKEN - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
floatValue() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedFloat
  Return the value of this AutoMedFloat as an float
fm - Static variable in class uk.ac.ic.doc.automed.editor.DrawVertex
fm - Static variable in class uk.ac.ic.doc.automed.editor.DrawArc
focusItem(InputItem) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
FoldFunction - class uk.ac.bbk.dcs.automed.qproc.optimise.FoldFunction.
FoldFunction(String, int, String) - Constructor for class uk.ac.bbk.dcs.automed.qproc.optimise.FoldFunction
FoldFunction(String, int, String, String, String) - Constructor for class uk.ac.bbk.dcs.automed.qproc.optimise.FoldFunction
FoldFunctionTable - class uk.ac.bbk.dcs.automed.qproc.optimise.FoldFunctionTable.
FoldFunctionTable() - Constructor for class uk.ac.bbk.dcs.automed.qproc.optimise.FoldFunctionTable
Foldl - class uk.ac.bbk.dcs.automed.qproc.functions.Foldl.
Foldl() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Foldl
FoldNilRule - class uk.ac.bbk.dcs.automed.qproc.optimise.FoldNilRule.
FoldNilRule(FoldFunctionTable) - Constructor for class uk.ac.bbk.dcs.automed.qproc.optimise.FoldNilRule
Foldr - class uk.ac.bbk.dcs.automed.qproc.functions.Foldr.
Foldr() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Foldr
FOREACH_STATEMENT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Statement to iterate on lists
FOREACH() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
foreachArgSeq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
foreachBlock - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
foreachStack - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
ForeachStatement - class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement.
ForeachStatement() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
FOREIGN_KEY - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  A feature option to model foreign keys in any `Schema` the factory generates
Forest - class uk.ac.bbk.dcs.automed.graph.Forest.
  Class that abstracts the structure of a forest.
Forest() - Constructor for class uk.ac.bbk.dcs.automed.graph.Forest
formattedString() - Method in class uk.ac.bbk.dcs.automed.qproc.ASG
  Given that the ASG represents a list the string returned has each element separated by carriage returns for more legible output.
formattedString(ASG) - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  If g is an ASG list the string returned has each element separated by carriage returns for more legible output.
formattedString(Cell) - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  If n is the root of an ASG that represents a list, the string returned has each element separated by carriage returns for more legible output.
FragmentProcessor - class uk.ac.bbk.dcs.automed.qproc.FragmentProcessor.
  The purpose of this class is to replace all schemes with wrapper objects.
FragmentProcessor() - Constructor for class uk.ac.bbk.dcs.automed.qproc.FragmentProcessor
FROM - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
  The first field can contain a SQLQuery WHERE
fromASG(ASG) - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  Returns the text IQL of g.
fromASG(Cell) - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  returns the text IQL of the abstract syntax graph of which n is the root.
fromASGList(ASG) - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  If g represents a list this returns an ArrayList of its Cells.
fromASGList(Cell) - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  If n is the root of an ASG that represents a list, this returns an ArrayList of its Cells.
fromASGTuple(ASG) - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  If g represents a tuple this returns an ArrayList of its Cells.
fromASGTuple(Cell) - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  If n is the root of an ASG that represents a tuple, this returns an ArrayList of its Cells.
fromObjectARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
fromObjectARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
fromObjectARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
fromSchemaARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TStatement
FSym - class uk.ac.bbk.dcs.automed.qproc.FSym.
  CUP generated class containing symbol constants.
FSym() - Constructor for class uk.ac.bbk.dcs.automed.qproc.FSym
function - Static variable in class uk.ac.bbk.dcs.automed.qproc.Cell
Function - Static variable in class uk.ac.bbk.dcs.automed.qproc.EnvSym
FUNCTION - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TConstants
functionARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
functionARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
functionARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
FunctionTable - class uk.ac.bbk.dcs.automed.qproc.FunctionTable.
  Class containing a HashMap that keeps the function names.
FunctionTable() - Constructor for class uk.ac.bbk.dcs.automed.qproc.FunctionTable
  Constructs a FunctionTable object representing an empty table.
FunctionTable(BuiltInFunction[], String[]) - Constructor for class uk.ac.bbk.dcs.automed.qproc.FunctionTable
  Constructs a FunctionTable object.

## G

generateId - class uk.ac.ic.doc.automed.wrappers.ssdfunctions.generateId.
generateId() - Constructor for class uk.ac.ic.doc.automed.wrappers.ssdfunctions.generateId
genericRootName - Static variable in class uk.ac.bbk.dcs.automed.graph.Forest
get(int) - Method in class uk.ac.ic.doc.automed.reps.Pathway
  Returns the `Schema` at the given index of the pathway.
get(int) - Method in class uk.ac.ic.doc.automed.matching.modules.Vectors
getAbsoluteDegrees(ArrayList, ArrayList) - Static method in class uk.ac.ic.doc.automed.matching.modules.ClustererClassifier
getAccessMethod() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Returns the `AccessMethod` associated with this wrapper, which holds the details of the datasource being wrapped.
getAccessMethod(int) - Static method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Returns the `AccessMethod` held with the given identifier in in the STR.
getAccessMethodAWFFeatures(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the feature settings of the specified access method.
getAccessMethodBySID(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns all the access method identifiers (AMID) that point to the access methods for the specified schema.
getAccessMethodDBDriver(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the database driver of the specified access method.
getAccessMethodPassword(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the password of the specified access method.
getAccessMethodPID(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the protocol identifier (PID) of the specified access method.
getAccessMethodProperty(int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Access Method Property
getAccessMethods() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Find the `AccessMethod`s that may be used to access the physical database system that holds this `Schema`.
getAccessMethodSID(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the schema identifier (SID) to which the specified access method connects.
getAccessMethodURL(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the URL of the specified access method.
getAccessMethodUsername(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the username of the specified access method.
getAccessMethodWrapper(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the feature settings of the specified access method.
getAction() - Method in class uk.ac.ic.doc.automed.tml.TML
getActionFrom(Schema) - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the action of the transformation.
getActionNameFrom(Schema) - Method in class uk.ac.ic.doc.automed.reps.Transformation
getActionNameTo(Schema) - Method in class uk.ac.ic.doc.automed.reps.Transformation
getActionString() - Method in class uk.ac.ic.doc.automed.tml.TML
getActionTo(Schema) - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the action of the transformation.
getAdjacent() - Method in class uk.ac.ic.doc.automed.reps.Node
  Returns all nodes that are adjacent to this node - that is, nodes for which a transformation is defined between its schema and this node's schema.
getAllCombinations(Object[], Object[]) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
getAllCombinations(Object[], Object[]) - Method in class uk.ac.ic.doc.automed.matching.Integrator
getAllCompositeTransformations() - Static method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns an array of all CompositeTransformation objects.
getAllNodes() - Method in class uk.ac.ic.doc.automed.reps.Network
getAllPairs() - Method in class uk.ac.ic.doc.automed.matching.Filter
getAllPatternNames() - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the vector of patterns'name
getAllPatternNames() - Static method in class uk.ac.ic.doc.automed.ssd.Pattern
getAllPatterns(String) - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool
getAllProtocols() - Static method in class uk.ac.ic.doc.automed.STR
  Returns the name of all the protocols found in the STR.
getAllReferencedSchemaObjects() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns all the schema objects referenced in a transformation, including those referenced in its query.
  The result of this method is the union of the results returned by the methods `Transformation.getReferencedSchemaObjects()` and `Transformation.getReferencedSchemaObjectsInQuery()`.
getAllSchemaNames() - Static method in class uk.ac.ic.doc.automed.STR
  Returns the name of all the schemas found in the STR.
getAllSchemeNames() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns an `Object` array of schemes of all the schema objects that belong to the schema.
getAllSchemeNames(boolean) - Method in class uk.ac.ic.doc.automed.reps.Schema
getAllSchemeNames(boolean, int, int) - Method in class uk.ac.ic.doc.automed.reps.Schema
getAllSchemeNames(boolean, int, int, boolean) - Method in class uk.ac.ic.doc.automed.reps.Schema
getAllSchemeNames(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns an `Object` array of all objects' schemes of a schema.
getAllSchemeNamesString() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the scheme representation (of type `String`) of the schemes of all the schema objects that belong to the schema.
getAllSchemeNamesString(boolean) - Method in class uk.ac.ic.doc.automed.reps.Schema
getAllSchemeNamesString(boolean, int, int) - Method in class uk.ac.ic.doc.automed.reps.Schema
getAllSchemeNamesString(boolean, int, int, boolean) - Method in class uk.ac.ic.doc.automed.reps.Schema
getAllSchemeNamesString(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the scheme representation (of type `String`) of all objects' schemes of a schema.
getAllTrans() - Static method in class uk.ac.ic.doc.automed.reps.Transformation
getAMID() - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Returns the access method identifier (AMID).
getAppearances() - Method in class uk.ac.ic.doc.automed.matching.Instance
getAppearances(String[], char) - Static method in class uk.ac.ic.doc.automed.matching.Util
getArcDrawable() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Returns the name of the class implementing drawable that should be used to draw arc elements of this construct.
getArcs() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
getArgConstruct() - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Returns the `Construct` type of the `ConstructScheme`.
getArgument() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
getArgument() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.ITEM
getArgumentAt(int) - Method in class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
  Returns a particular TemplateArgument in this TemplateArgumentSequence.
getArgumentAt(int) - Method in class uk.ac.ic.doc.automed.templates.RuntimeArgumentSequence
  Returns a particular RuntimeArgument in this RuntimeArgumentSequence.
getArgumentDefinitionAt(int) - Method in class uk.ac.ic.doc.automed.templates.Statement
  Returns a particular StatementArgumentDefinition in the Statements's argument definition list.
getArgumentDefinitionAt(int) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns a particular TransformationArgumentDefinition in the CompositeTransformations's argument definition list.
getArgumentDefinitions() - Method in class uk.ac.ic.doc.automed.templates.Statement
  Returns an array of all the StatementArgumentDefinition objects of this Statement.
getArgumentDefinitions() - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns an array of all the TransformationArgumentDefinition objects in this CompositeTransformation.
getArgumentDefinitions(boolean) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns an array of TransformationArgumentDefinition objects.
getArgumentDefinitionsForStatement(int) - Static method in class uk.ac.ic.doc.automed.templates.StatementArgumentDefinition
  Returns all the StatementArgumentDefinition objects of the specified statement.
getArgumentDefinitionsForTransformation(int) - Static method in class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
  Returns all the TransformationArgumentDefinition objects of the specified transformation.
getArgumentDescription(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement
getArgumentDescription(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.SchemeListStatement
getArgumentDescription(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement
getArgumentDescription(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatement
getArgumentDescription(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
getArgumentDescription(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
getArgumentDescription(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
getArgumentDescription(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
getArgumentDescription(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
getArguments() - Method in class uk.ac.ic.doc.automed.gui.ArgumentsDialog
  Returns the values for the argument sequence.
getArguments() - Method in class uk.ac.ic.doc.automed.gui.ArgPane
  Returns the arguments defined by the user in this ArgPane.
getArguments() - Method in class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
  Returns an array of all the TemplateArguments in this TemplateArgumentSequence.
getArguments() - Method in class uk.ac.ic.doc.automed.templates.RuntimeArgumentSequence
  Returns an array of all the RuntimeArguments in this RuntimeArgumentSequence.
getArgumentsArgIdList() - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns a list of identifiers of all the sequences of arguments
getArgumentsArgIdList() - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a list of identifiers of all the sequences of arguments
getArgumentsArgIdRef(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular argument's `arg_id_ref` field
getArgumentsArgIdRefList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular's sequence of arguments list of `arg_id_ref` fields.
getArgumentsArgPosList(int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns a particular's sequence of arguments list of positions.
getArgumentsArgPosList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular's sequence of arguments list of positions.
getArgumentsArgPosRef(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular argument's `arg_pos_ref` field
getArgumentsArgPosRefList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular's sequence of arguments list of `arg_pos_ref` fields.
getArgumentSequence() - Method in class uk.ac.ic.doc.automed.templates.StatementExecution
  Returns the TemplateArgumentSequence of this StatementExecution.
getArgumentSequence() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
getArgumentsForSequence(int) - Static method in class uk.ac.ic.doc.automed.templates.TemplateArgument
  Returns all the TemplateArgument objects of the specified sequence of arguments.
getArgumentsForSequence(int) - Static method in class uk.ac.ic.doc.automed.templates.RuntimeArgument
  Returns all RuntimeArgument objects of the specified sequence of arguments.
getArgumentsValue(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns a particular argument's `value` field
getArgumentsValue(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular argument's `value` field
getArgumentsValueList(int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns a particular's sequence of arguments list of `value` fields.
getArgumentsValueList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular's sequence of arguments list of values.
getArgumentValues() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
getArity() - Method in interface uk.ac.bbk.dcs.automed.qproc.BuiltInFunction
  Returns the arity of the function.
getArity() - Method in class uk.ac.ic.doc.automed.wrappers.ssdfunctions.generateId
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Flatmap
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Foldr
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.BagIntersect
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Monus
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Foldl
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Equals
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Comprehension
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Sort
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.LessEqual
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Minus
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.SortDistinct
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.And
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Not
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Member
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.GreaterEqual
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.SubBag
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.LoadListFromFile
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Count
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Less
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Group
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.CallToWrapper
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Plus
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Sum
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.If
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Multiply
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Id
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Append
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.SetUnion
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Single
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.First
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Let
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Or
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Greater
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Map
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.GroupCompute
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.NotEqual
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Min
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Second
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Difference
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Average
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Divide
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Max
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Disjunction
getArity() - Method in class uk.ac.bbk.dcs.automed.qproc.optimise.FoldFunction
getAtomicRelationship(SchemaElementPair) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
getAtomicRelationshipCombinations(SchemaObject[], SchemaObject[]) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
getAttribute(int) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTuple
  Return a particular attribute from a tuple (counting from one)
getAttributeType(int) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTuple
getAttributeType(int) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedResult
  Returns the type of an attribute in the tuple that the cursor currently points at.
getAutoMedFile(String) - Static method in class uk.ac.ic.doc.automed.Util
getAutoMedModel() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Return the AutoMed oriented `Model` used to represent the `Schema` of the datasource.
getAutoMedModel() - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  Return the AutoMed relational `Model` used to represent the `Schema` for the SQL datasource wrapper.
getAutoMedModel() - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapperFactory
  Return the AutoMed oriented `Model`, which is the same as the source oriented `Model` for the semistructured datasource
getAutoMedModel() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapperFactory
getAutoMedModel() - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapperFactory
getAutoMedModelName() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Find the name of the `Model` that will be used to represent an AutoMed oriented view of the data source.
getAutoMedQueryToken() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
  Return the AutoMedQueryToken of this node; ie the type of object query node represents.
getAutoMedTuple() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedResult
  Return the tuple which the cursor current points at.
getAutoMedTuple(int) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedResult
  Move the cursor and get the tuple that is at the point
getAutoMedWrapper(AccessMethod) - Static method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Equivalent to calling newAutoMedWrapper(am,null)
getAutoMedWrapper(AccessMethod, String) - Static method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Return the wrapper asspciated to a stored AccessMethod.
getAutoMedWrapperFactory() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Return the AutoMedWrapperFactory currently associated with this wrapper.
getAutoMedWrapperFactoryFeatures() - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Returns the feature settings as used with associated `AutoMedWrapperFactory`
getAverage(double[]) - Static method in class uk.ac.ic.doc.automed.matching.Util
getAverageAppearances(String[], char) - Static method in class uk.ac.ic.doc.automed.matching.Util
getBackgroundColor() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getBackgroundColor() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Return the default background colour to be used from drawing `SchemaObject`s of this `Construct`.
getBackgroundColor() - Method in class uk.ac.ic.doc.automed.reps.Network
getBackgroundColor() - Method in class uk.ac.ic.doc.automed.reps.Schema
getBackgroundColor() - Method in class uk.ac.ic.doc.automed.reps.Model
  Return the default background colour to be used from drawing `SchemaObject`s of this `Model`.
getBackgroundColor() - Method in interface uk.ac.ic.doc.automed.editor.Positionable
getBackwardDegree() - Method in class uk.ac.ic.doc.automed.matching.BidirectionalDegree
getBidirectionalDegrees() - Method in class uk.ac.ic.doc.automed.matching.modules.AbstractModule
getBidirectionalDegrees(Hashtable, Hashtable) - Static method in class uk.ac.ic.doc.automed.matching.modules.AbstractModule
getBidirectionalSimilarity(SchemaElementPair) - Method in class uk.ac.ic.doc.automed.matching.modules.AbstractModule
getBoundingBox() - Method in class uk.ac.ic.doc.automed.gui.SchemaManager
getBoundingBox() - Method in class uk.ac.ic.doc.automed.gui.Rhombus
getBoundingBox() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getBoundingBox() - Method in class uk.ac.ic.doc.automed.gui.Box
getBoundingBox() - Method in class uk.ac.ic.doc.automed.gui.Arc
getBounds() - Method in interface uk.ac.ic.doc.automed.editor.DrawableVertex
  Describe the rectangular area within the `EditorPanel` where this `Drawable` vertex is to be painted.
getBounds() - Method in class uk.ac.ic.doc.automed.editor.DrawVertex
getBounds() - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalVertex
getBounds() - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawConstraintVertex
getCause() - Method in class uk.ac.ic.doc.automed.RepositoryAccessException
getCause() - Method in class uk.ac.ic.doc.automed.reps.AutoRepException
getCause() - Method in class uk.ac.ic.doc.automed.gui.GUIException
getCause() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateDefinitionException
getCenter() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
getCentre() - Method in interface uk.ac.ic.doc.automed.editor.DrawableVertex
  Describe where the centre of the `Drawable` visually appears to a viewer.
getCentre() - Method in class uk.ac.ic.doc.automed.editor.DrawVertex
  Describe where the centre of the `Drawable` visually appears to a viewer.
getCentre() - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalVertex
getCentreOffset() - Method in interface uk.ac.ic.doc.automed.editor.DrawableVertex
  Describe where the centre of the `Drawable` visually appears to a viewer.
getCentreOffset() - Method in class uk.ac.ic.doc.automed.editor.DrawVertex
  Implements the `Drawable`
getCentreOffset() - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalVertex
getChildCount(Node) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Counts the children of the given node.
getChildren() - Method in class uk.ac.ic.doc.automed.reps.Node
  If the network this node belongs to is directed then returns all the adjacent nodes that are children of this node, otherwise its behaviour is defined by the type of network but the children will be a subset of adjacent.
getChildren() - Method in class uk.ac.bbk.dcs.automed.graph.TreeNode
getCID() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Returns the construct identifier (CID) of the construct.
getCID() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
getClassName() - Method in class uk.ac.ic.doc.automed.IntegrityException
  Return the className of the object that the manipulation of caused this exception.
getClassName(int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Returns the class name of the method specified by `meth_id`
getClassNameList() - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Returns the class names of all the methods found in the SMR
getCloseSchemeBracket() - Static method in class uk.ac.ic.doc.automed.STR
  Return String used to close schemes
getCloseSchemeBracket() - Static method in class uk.ac.ic.doc.automed.reps.Schema
  find what string is used to deliminate the closing of a scheme name, such as the ">>" in "<<person>>" or "<<person,name>>".
getClusters() - Method in class uk.ac.ic.doc.automed.matching.modules.Clusterer
getColumnDetailsSchemeLength() - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  Return the number of fields in a full source table scheme that are used to represent the structure and type of one column (ie its name, data type, size, null, ...)
getColumnNames(ResultSet) - Static method in class uk.ac.ic.doc.automed.Util
getColumns(SchemaObject, ArrayList) - Method in class uk.ac.ic.doc.automed.matching.SQLRelationshipExtractor
getColumnsOfTable(Schema, SchemaObject) - Method in class uk.ac.ic.doc.automed.matching.SQLIntegrator
getColumnTypes(ResultSet) - Static method in class uk.ac.ic.doc.automed.Util
getCombinations(Object[]) - Method in class uk.ac.ic.doc.automed.matching.Integrator
getCombinationsOverMultipleArrays(ArrayList[]) - Method in class uk.ac.ic.doc.automed.matching.Integrator
getCommandClass() - Static method in class uk.ac.ic.doc.automed.DSR
getCommonRelationship(SchemaElementPairRelationship[]) - Static method in class uk.ac.ic.doc.automed.matching.Integrator
getCommonSchema(Transformation) - Method in class uk.ac.ic.doc.automed.reps.Transformation
getCompatibles(double) - Method in class uk.ac.ic.doc.automed.matching.Filter
getCompositeTransformation(int) - Static method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns a reference to a CompositeTransformation.
getCompositeTransformation(String) - Static method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns a reference to a CompositeTransformation.
getCompositeTransformationByName(String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the ID (`trans_id`) of the composite transformation specified by name
getCompositeTransformationDefinitionArgPosList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular transformation's list of argument positions.
getCompositeTransformationDefinitionArgPosList(int, boolean) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular transformation's list of argument positions.
getCompositeTransformationDefinitionDescription(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular transformation's argument definition (only the `description` field).
getCompositeTransformationDefinitionDescriptionList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular transformation's list of argument definitions (only the `description` field).
getCompositeTransformationDefinitionDescriptionList(int, boolean) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular transformation's list of argument definitions (only the `description` field).
getCompositeTransformationDefinitionElementNR(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepositoryExtension
getCompositeTransformationDefinitionFieldName(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular transformation's argument definition (only the `field_name` field).
getCompositeTransformationDefinitionFieldNameList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular transformation's list of argument definitions (only the `field_name` field).
getCompositeTransformationDefinitionFieldNameList(int, boolean) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular transformation's list of argument definitions (only the `field_name` field).
getCompositeTransformationDefinitionIsReturnedValue(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns whether a particular transformation's argument stores a returned value after the transformation's invocation, or not.
getCompositeTransformationDefinitionIsReturnedValueList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular transformation's list of argument types (if they store a returned value or not).
getCompositeTransformationDefinitionRefPos(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepositoryExtension
getCompositeTransformationDefinitionTableName(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular transformation's argument definition (only the `table_name` field).
getCompositeTransformationDefinitionTableNameList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular transformation's list of argument definitions (only the `table_name` field).
getCompositeTransformationDefinitionTableNameList(int, boolean) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular transformation's list of argument definitions (only the `table_name` field).
getCompositeTransformationDefinitionType(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepositoryExtension
getCompositeTransformationDefinitionTypeInstance(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepositoryExtension
getCompositeTransformationDescription(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the description of the composite transformation specified by `trans_id`
getCompositeTransformationExecutionArgId(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns a sequence of arguments ID in the execution of a particular composite transformation
getCompositeTransformationExecutionArgIdList(int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns a list of sequence of arguments identifiers of a particular composite transformation's execution
getCompositeTransformationExecutionPcList(int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns a list of program counters of a particular composite transformation's execution.
getCompositeTransformationExecutionStId(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns the statement ID in the execution of a particular composite transformation
getCompositeTransformationExecutionStIdList(int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns a list of statement identifiers of a particular composite transformation's execution.
getCompositeTransformationExecutionTransIdList() - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns a list of sequence of transformation identifiers that are being executed
getCompositeTransformationInvocationArgIdList() - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns a list of sequence of arguments identifiers in the invocation of transformations
getCompositeTransformationName(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the name of the composite transformation specified by `trans_id`
getCompositeTransformationPreservesEquivalence(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns whether the composite transformation specified by `trans_id` preserves schema equivalence.
getCompositeTransformationProgramArgId(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the sequence of arguments ID that is going to be used at the specified pc of a transformation's template program.
getCompositeTransformationProgramArgIdList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a list of sequence of arguments identifiers of a particular composite transformation's template program, ie the sequences of arguments that are going to be used at each program counter.
getCompositeTransformationProgramPcList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a list of program counters of a particular composite transformation's template program.
getCompositeTransformationProgramStId(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the statement ID of the statement that is going to be executed at the specified pc of a transformation's template program.
getCompositeTransformationProgramStIdList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a list of statement identifiers of a particular composite transformation's template program, ie the statements that are going to be executed at each program counter.
getCompositeTransformationRecord() - Method in class uk.ac.ic.doc.automed.templates.gui.TemplateInputDialogue
getCompositeTransformationReturnedValuesDefinitionArgId(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the sequence of arguments ID that defines the returned values of the transformation
getCompositeTransformations(boolean) - Static method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns an array of CompositeTransformation objects.
getCompositeTransformationsDescriptionList() - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the descriptions of all the composite transformations found in the TTR
getCompositeTransformationsDescriptionList(boolean) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the descriptions of all the composite transformations found in the TTR that preserve schema equivalence
getCompositeTransformationsNameList() - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the names of all the composite transformations found in the TTR
getCompositeTransformationsNameList(boolean) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the names of all the composite transformations found in the TTR that preserve schema equivalence
getCompositeTransformationsPreservesEquivalenceList() - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the `preserves_equivalence` field of all the composite transformations found in the TTR
getCompositeTransformationsTransIdList() - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the IDs of all the composite transformations found in the TTR
getCompositeTransformationsTransIdList(boolean) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the IDs of all the composite transformations found in the TTR that preserve schema equivalence
getConcatenationOp() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
getConfigFileName() - Static method in class uk.ac.ic.doc.automed.DSR
  Returns the name of the file used for data source definitions.
getConnectionPoint(Point) - Method in interface uk.ac.ic.doc.automed.editor.DrawableVertex
  Calculate the `Point` where a `DrawableArc` connecting to this `DrawableVertex` should be drawn to, no
getConnectionPoint(Point) - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkVertex
getConnectionPoint(Point) - Method in class uk.ac.ic.doc.automed.editor.DrawVertex
getConnectionPoint(Point) - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawNodalVertex
getConnectionPoint(Point) - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawConstraintVertex
getConstraint() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the constraint associated with the transformation.
getConstraint() - Method in class uk.ac.ic.doc.automed.tml.TML
getConstraintDefinition(String) - Method in class uk.ac.ic.doc.automed.reps.Construct
  Return the definition of a constraint used within this `Construct`.
getConstraintReferencedConstructs(SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns all the objects in a SchemaObject's scheme that are correspond to positions in the SchemaObject's scheme of type `SCHEME_TYPE_CONSTRUCT`
getConstraints() - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
getConstruct() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Returns the construct type of the schema object.
getConstruct() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getConstruct() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
getConstruct() - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
getConstruct(int) - Static method in class uk.ac.ic.doc.automed.reps.Construct
  Returns the `Construct` identified by the given construct identifier (CID).
getConstruct(String) - Method in class uk.ac.ic.doc.automed.reps.Model
  Returns the named construct in the model or throws an AutoMedException if the construct name doesn't exist in the model.
getConstructByCID(int) - Static method in class uk.ac.ic.doc.automed.reps.ConstructWithModelingProgram
getConstructClass() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Returns the class of the construct.
getConstructClass(int) - Static method in class uk.ac.ic.doc.automed.MDR
getConstructClassString(int) - Static method in class uk.ac.ic.doc.automed.reps.Construct
getConstructConstraint(int, String) - Static method in class uk.ac.ic.doc.automed.MDR
getConstructDescription() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Returns a printable description of the construct including all of its schemes.
getConstructMID(int) - Static method in class uk.ac.ic.doc.automed.MDR
  Gets the Model Identifier for a given construct
getConstructModelingProgramMethod(int, int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Returns the method that is going to be invoked at the specified pc of a construct's modeling program.
getConstructModelingProgramMethodList(int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Returns a list of method invocations of a particular construct's modeling program, ie the methods that are going to be invoked at each program counter.
getConstructModelingProgramPcList(int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Returns a list of program counters of a particular construct's modeling program.
getConstructName(int) - Static method in class uk.ac.ic.doc.automed.MDR
getConstructNames(int) - Static method in class uk.ac.ic.doc.automed.MDR
  Gets a list of all construct names for a modelling language
getConstructProperty(int, int, String, boolean) - Static method in class uk.ac.ic.doc.automed.MDR
getConstructs() - Method in class uk.ac.ic.doc.automed.reps.Model
  Returns an array of all the constructs in the model.
getConstructs(int) - Static method in class uk.ac.ic.doc.automed.MDR
  Get the CIDs of all constructs for a modelling language
getConstructSchemeArgCID(int, int) - Static method in class uk.ac.ic.doc.automed.MDR
getConstructSchemeCount(int) - Static method in class uk.ac.ic.doc.automed.MDR
  Gets the count of construct scheme arguments for this construct, the number is also the highest index (argument pos) usable as the construct scheme numbering starts at 1
getConstructSchemeHDMType(int, int) - Static method in class uk.ac.ic.doc.automed.MDR
getConstructSchemeLowerBound(int, int) - Static method in class uk.ac.ic.doc.automed.MDR
getConstructSchemeType(int, int) - Static method in class uk.ac.ic.doc.automed.MDR
getConstructSchemeUpperBound(int, int) - Static method in class uk.ac.ic.doc.automed.MDR
getConstructType() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getCurrent(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
getCurrentModelSyntax - Static variable in class uk.ac.ic.doc.automed.editor.Editor
getCurrentSchema() - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
getCurrentToken() - Method in class uk.ac.ic.doc.automed.reps.Syntax.Tokenizer
getCurrentToken(int) - Method in class uk.ac.ic.doc.automed.reps.Syntax.Tokenizer
getCurrentToken(int, int) - Method in class uk.ac.ic.doc.automed.reps.Syntax.Tokenizer
getData() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTuple
  Return all the attributes of this tuple as an array
getDatafromYattaData(Vector) - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
getDataSourceConnection(String) - Static method in class uk.ac.ic.doc.automed.DSR
  Gets a connection to the named data souce.
getDataSourceConnection(String, String, String) - Static method in class uk.ac.ic.doc.automed.DSR
  Gets a connection to the named data souce.
getDataSourceName() - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns the name of the repository in the local database.
getDataSourceName() - Static method in class uk.ac.ic.doc.automed.MDR
  Returns the name of the repository in the local database.
getDataSourceName() - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns the name of the repository in the local database.
getDataSourceName() - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Returns the name of the repository in the local database.
getDataSourceName() - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Returns the name of the repository in the local database.
getDataSourceName() - Static method in class uk.ac.ic.doc.automed.STR
  Returns the name of the repository in the local database.
getDataSourceName() - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the name of the repository in the local database.
getDataSourceProperty(String, String) - Static method in class uk.ac.ic.doc.automed.DSR
  Returns the named property for the named data source as defined in the configuration file.
getDataType() - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
getDBDriver() - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Returns the database driver used for connecting to the database.
getDebugLevel() - Static method in class uk.ac.ic.doc.automed.STR
  Return the value of the debug level at set by `STR.setDebugLevel(int)`
getDefaultDataSource() - Static method in class uk.ac.ic.doc.automed.DSR
getDefaultSchemaName(AutoMedWrapper) - Method in class uk.ac.ic.doc.automed.wrappers.TransactSQLWrapperFactory
getDefaultSchemaName(AutoMedWrapper) - Method in class uk.ac.ic.doc.automed.wrappers.OracleWrapperFactory
getDefaultSchemaName(AutoMedWrapper) - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  Return the name of the default schema for the type of database being wrapped.
getDefaultSchemaName(AutoMedWrapper) - Method in class uk.ac.ic.doc.automed.wrappers.PostgresWrapperFactory
getDefaultUserName() - Static method in class uk.ac.ic.doc.automed.DSR
getDefaultWrapperFactory() - Method in class uk.ac.ic.doc.automed.wrappers.TransactSQLWrapper
  Returns a new instance of the default wrapper factory for this wrapper
getDefaultWrapperFactory() - Method in class uk.ac.ic.doc.automed.wrappers.OracleWrapper
  Returns a new instance of the default wrapper factory for this wrapper
getDefaultWrapperFactory() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Return the default `AutoMedWrapperFactory` that is used to generate `Schema` instances from information in a data sources
getDefaultWrapperFactory() - Method in class uk.ac.ic.doc.automed.wrappers.PostgresWrapper
  Returns a new instance of the default wrapper factory for this wrapper
getDefaultWrapperFactory() - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
  Returns a new instance of the default wrapper factory for this wrapper
getDefaultWrapperFactory() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
  Returns a new instance of the default wrapper factory for this wrapper
getDefaultWrapperFactory() - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapper
  Returns a new instance of the default wrapper factory for this wrapper
getDegree() - Method in class uk.ac.ic.doc.automed.matching.SimilarSchemaElementPair
getDelta() - Method in class uk.ac.ic.doc.automed.reps.NetworkChangeEvent
getDelta() - Method in class uk.ac.ic.doc.automed.reps.SchemaChangeEvent
getDependentSchemaObjects() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Return all `SchemaObject`s which have a reference to this `SchemaObject` in their scheme.
getDependentSchemaObjects(Construct) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Return those `SchemaObject`s of a particular `Construct` which have a reference to this `SchemaObject` in their scheme.
getDependentSchemaObjects(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the object identifiers (OBID) in ascending order of all the schema objects that depedent on the existanace of some other object.
getDependentSchemaObjects(SchemaObject) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Return all `SchemaObject`s of a particular `Construct` in this `Schema` which have a reference to the given `SchemaObject` in their scheme.
getDependentSchemaObjects(SchemaObject, Construct) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Return those `SchemaObject`s of a particular `Construct` in this `Schema` which have a reference to the given `SchemaObject` in their scheme.
getDepth(Document) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
getDescription() - Method in class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
  Returns the description of this TransformationArgumentDefinition.
getDescription() - Method in class uk.ac.ic.doc.automed.templates.StatementArgumentDefinition
  Returns the description of this StatementArgumentDefinition.
getDescription() - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns the description of this CompositeTransformation.
getDescription() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
getDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
  Returns the description of the template transformation
getDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
getDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
getDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
getDistinctInstances() - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
getDoc() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapper
getDouble() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns the value of the double contained in the Cell
getDrawingObject(int) - Static method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
getDrawingObject(SchemaObject, Construct) - Static method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
getDrawingObjectRepresenting(SchemaObject) - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
getDriver() - Static method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
  The name of the driver string that identifies this wrapper
getE() - Method in class uk.ac.bbk.dcs.automed.qproc.optimise.FoldFunction
getEdgeInstances(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Return all the instances of the passed edge type as a `LinkedList` of `Span` elements, each `Span` representing an instance of an edge.
getEdgePosition(Point) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
getEdgePosition(Point) - Method in class uk.ac.ic.doc.automed.gui.Line
getEdgePosition(Point) - Method in class uk.ac.ic.doc.automed.gui.Box
getEdgePosition(Point) - Method in class uk.ac.ic.doc.automed.gui.Arc
getEdges() - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
getEditorPanel() - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
getElement() - Method in class uk.ac.ic.doc.automed.matching.modules.ElementVectorRepresentation
getElement(int) - Method in class uk.ac.ic.doc.automed.matching.SchemaElementPair
getElement(SchemaObject, boolean) - Static method in class uk.ac.ic.doc.automed.matching.SchemaElement
getElement(String, boolean) - Static method in class uk.ac.ic.doc.automed.matching.SchemaElement
getElementByUID(Document, String) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Returns the node in the input doc that has an AutoMedID with the value of elementUID
getElementByUIDNoSchema(Document, String) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  This method will return the first occurrence of an element containing an AutoMedID whose suffix after "schemaName:" matches the input elementUID.
getElementChildCount(Node) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Counts the element children of the given node.
getElementLevel(Node, int) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Returns all the element nodes in a given level.
getElementNodeOrder(Node) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Returns the order of element node n in its parent's children NodeList - takes into account only elements.
getElements() - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
getElements() - Method in class uk.ac.ic.doc.automed.matching.modules.SimilarCluster
getElements() - Method in class uk.ac.ic.doc.automed.matching.modules.Clusterer
getElements() - Method in class uk.ac.ic.doc.automed.matching.modules.Cluster
getElements(SchemaObject[], boolean) - Static method in class uk.ac.ic.doc.automed.matching.Integrator
getElementsByUID(Document, String) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Given a schema UID (schemaName:elementName:counter), this method runs through the given instance, and returns all elements with an instance UID starting with the given schema UID.
getEntityEdgePosition(Point) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
getEnvironment() - Method in class uk.ac.bbk.dcs.automed.qproc.Evaluator
getExpression() - Method in class uk.ac.ic.doc.automed.reps.HDMConstraint
getExtend(boolean) - Method in class uk.ac.ic.doc.automed.gui.SchemaManager
getFeatureNames() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Return the list of feature names provided by the wrapper factory.
getFeatureNames() - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  Return a string list of features supported by this wrapper, where the first one is bit zero in the feature bit map, second bit one, etc
getFeatures() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Return the bitwise or of all the features in use for a wrapper.
getField(int) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
  Return a field from the query node, where fields are counted from zero.
getField(int) - Method in class uk.ac.ic.doc.automed.wrappers.SchemeQuery
  Return a field from the query node.
getFieldName() - Method in class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
  Returns the fieldname of this TransformationArgumentDefinition.
getFieldName() - Method in class uk.ac.ic.doc.automed.templates.StatementArgumentDefinition
  Returns the fieldname of this StatementArgumentDefinition.
getFile(String) - Static method in class uk.ac.ic.doc.automed.Util
getFinalDoc() - Method in class uk.ac.bbk.dcs.automed.xml.XMLTransformer
getFinalSchema() - Method in class uk.ac.bbk.dcs.automed.xml.XMLTransformer
getFinalSchema() - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformationRecord
getFinalSchemaName() - Method in class uk.ac.bbk.dcs.automed.xml.XMLTransformer
getFirstElement() - Method in class uk.ac.ic.doc.automed.matching.SchemaElementPair
getFoldFunction(String) - Method in class uk.ac.bbk.dcs.automed.qproc.optimise.FoldFunctionTable
getFontMetrics() - Method in class uk.ac.ic.doc.automed.editor.EditorPanel
  Utility method for all editor drawing tools to use when they need to obtain the `FontMetrics` of an `EditorPanel`
getFontMetrics(JComponent) - Static method in class uk.ac.ic.doc.automed.editor.Gui
  Utility method for all editor drawing tools to use when they need to obtain the `FontMetrics` of a `JComponent`
getForegroundColor() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getForegroundColor() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Return the default foreground colour to be used from drawing `SchemaObject`s of this `Construct`.
getForegroundColor() - Method in class uk.ac.ic.doc.automed.reps.Network
getForegroundColor() - Method in class uk.ac.ic.doc.automed.reps.Schema
getForegroundColor() - Method in class uk.ac.ic.doc.automed.reps.Model
  Return the default foreground colour to be used from drawing `SchemaObject`s of this `Model`.
getForegroundColor() - Method in interface uk.ac.ic.doc.automed.editor.Positionable
getForest() - Method in class uk.ac.bbk.dcs.automed.graph.Forest
getForwardDegree() - Method in class uk.ac.ic.doc.automed.matching.BidirectionalDegree
getFrame() - Static method in class uk.ac.ic.doc.automed.editor.Gui
getFromOBID() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the schema object identifier (OBID) of the input of the transformaiton (fromObject).
getFromObject() - Method in class uk.ac.ic.doc.automed.tml.TML
getFromObjectsUnmatched() - Method in class uk.ac.ic.doc.automed.reps.SchemasNotIdenticalException
getFromSchema() - Method in class uk.ac.ic.doc.automed.reps.SchemasNotIdenticalException
getFromSchema() - Method in class uk.ac.ic.doc.automed.tml.TML
getFromSID() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the schema identifier (SID) of the originating schema.
getFunction() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the function of the transformation.
getFunction() - Method in class uk.ac.ic.doc.automed.tml.TML
getFunction(String) - Method in class uk.ac.bbk.dcs.automed.qproc.Environment
getFunction(String) - Method in class uk.ac.bbk.dcs.automed.qproc.FunctionTable
  Returns the BuiltInFunction corresponding to the string name.
getGenEdgePosition() - Method in class uk.ac.ic.doc.automed.gui.Rhombus
getGeneralConstruct() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getGeneralConstruct(SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns a SchemaObject corresponding to the "general" entity of a generalization.
getGeneralisationExtend() - Method in class uk.ac.ic.doc.automed.gui.SchemaManager
getGraph() - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraph
getGraphicObject(SchemaObject) - Method in class uk.ac.ic.doc.automed.gui.SchemaManager
getGraphics() - Method in class uk.ac.ic.doc.automed.gui.SchemaManager
getGroupNo(int, int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the group no of ssdpattern and schemaobject in the SSMDR.
getGroupNoByOBID(int) - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getHDMNetwork() - Method in class uk.ac.ic.doc.automed.reps.Schema
getHDMType() - Method in class uk.ac.ic.doc.automed.reps.Scheme
getHDMType() - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Returns the HDM type of the `ConstructScheme`.
getHDMTypeString(int) - Static method in class uk.ac.ic.doc.automed.reps.ConstructScheme
getHDMTypeString(int, boolean) - Static method in class uk.ac.ic.doc.automed.reps.ConstructScheme
getIcon(String) - Static method in class uk.ac.ic.doc.automed.templates.gui.Accessories
getIconHeight() - Method in class uk.ac.ic.doc.automed.gui.ArrowIcon
getIconWidth() - Method in class uk.ac.ic.doc.automed.gui.ArrowIcon
getIncomingEdges() - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraphNode
getInput(int) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
getInput(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
getInputArguments() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList
getInputDoc() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLDSSDOM
getInputItems() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
getInsertableSQLValue(Object, int) - Static method in class uk.ac.ic.doc.automed.Util
getInstanceDoc() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLDSSDOM
getInstancesSorted() - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
getInt(int) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTuple
  Return a particular attribute from a tuple (counting from one) as a 32 bit integer
getIntegerConstructProperty(int, int, String) - Static method in class uk.ac.ic.doc.automed.MDR
getIntegratedSchema() - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
getIsReturnedValue() - Method in class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
  Returns the type of this TransformationArgumentDefinition.
getKnownSchemaObject(int) - Static method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Similiar to `SchemaObject.getSchemaObject(int)` except that it throws a runtime exception `InconsistentException` if the obid is not found.
getKnownSchemaObject(int) - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Use instead of `#getSchemaObject(int)` where you are sure that the sid is valid for the transformation.
getKnownSchemaObject(Schema) - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Use instead of `Transformation.getSchemaObject(Schema)` where you are sure that the `Schema` is valid for the transformation.
getKnownTransformation(Schema, Schema) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
getLabel() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Get the text used to label this SchemaObject.
getLabel() - Method in class uk.ac.ic.doc.automed.reps.Network
  Get the text used to label this Network.
getLabel() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Get the text used to label this Schema.
getLabel() - Method in interface uk.ac.ic.doc.automed.editor.Positionable
getLabelPosition() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getLabelPosition() - Method in class uk.ac.ic.doc.automed.reps.Network
getLabelPosition() - Method in class uk.ac.ic.doc.automed.reps.Schema
getLabelPosition() - Method in interface uk.ac.ic.doc.automed.editor.Positionable
getLabelXPos() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getLabelXPos() - Method in class uk.ac.ic.doc.automed.reps.Network
getLabelXPos() - Method in class uk.ac.ic.doc.automed.reps.Schema
getLabelXPos() - Method in interface uk.ac.ic.doc.automed.editor.Positionable
getLabelYPos() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getLabelYPos() - Method in class uk.ac.ic.doc.automed.reps.Network
getLabelYPos() - Method in class uk.ac.ic.doc.automed.reps.Schema
getLabelYPos() - Method in interface uk.ac.ic.doc.automed.editor.Positionable
getLastExtSchema() - Method in class uk.ac.ic.doc.automed.reps.Pathway
  Returns the last extentional `Schema` in the pathway.
getLeafs() - Method in class uk.ac.ic.doc.automed.reps.Network
getLevel(Node, int) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Returns all the nodes in a given level.
getListElement() - Method in class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement
getLocation() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getLower() - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Returns the lower bound indicating the minimum occurence of the `ConstructScheme`.
getManager() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getMappings() - Method in class uk.ac.ic.doc.automed.matching.Aggregator
getMaximum(double[]) - Static method in class uk.ac.ic.doc.automed.matching.Util
getMDR_DataSourceName() - Static method in class uk.ac.ic.doc.automed.MDR
  Deprecated. use `MDR.getDataSourceName()` instead
getMedium(double[]) - Static method in class uk.ac.ic.doc.automed.matching.Util
getMethodArgumentsPosList(int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Returns a particular methods's list of argument positions.
getMethodArgumentsType(int, int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Returns a particular method's argument type.
getMethodArgumentsTypeList(int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Returns a particular methods's list of argument types.
getMethodByName(String, String) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Returns the ID (`meth_id`) of the method specified by name and class, or `-1` if a method with the specified name doesn't exist in the specified class.
getMethodCall() - Method in class uk.ac.ic.doc.automed.reps.ModelingStatement
  Returns the method to be called by this ModelingStatement.
getMethodName(int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Returns the name of the method specified by `meth_id`
getMethodsMethIdList() - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Returns the IDs of all the methods found in the SMR
getMethodsNameList() - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Returns the names of all the methods found in the SMR
getMID() - Method in class uk.ac.ic.doc.automed.reps.Model
  Returns the repository identifer of the model.
getMinimum(double[]) - Static method in class uk.ac.ic.doc.automed.matching.Util
getModel() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Return the `Model` to which this Construct belongs
getModel() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Return the source oriented `Model` used to represent the `Schema` of the datasource.
getModel() - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  Return the `raw' relational `Model` used to represent the `Schema` for the SQL datasource wrapper.
getModel() - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapperFactory
  Return the source oriented `Model`, YATTA Model, used to represent the semistructured datasource.
getModel() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapperFactory
getModel() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
  Returns the model of the template transformation
getModel() - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapperFactory
getModel(int) - Static method in class uk.ac.ic.doc.automed.reps.Model
  Returns a reference to the `Model` with the given MID.
getModel(String) - Static method in class uk.ac.ic.doc.automed.reps.Model
  Returns a reference to the `Model` with the given modelName.
getModelBaseName() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Return text used as basis for generating `Model` names
getModelByName(String) - Static method in class uk.ac.ic.doc.automed.MDR
getModelDescription() - Method in class uk.ac.ic.doc.automed.reps.Model
  Returns a description of the model, each construct along with their schemes is listed in a way suitable for printing.
getModelDescription(boolean) - Method in class uk.ac.ic.doc.automed.reps.Model
  Returns a description of the model, each construct along with its schemes are listed in a way suitable for printing.
getModelingProgram() - Method in class uk.ac.ic.doc.automed.reps.ConstructWithModelingProgram
  Returns the ModelingProgram that defines the graphical representation of this Construct.
getModelingProgramByCID(int) - Static method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Returns the ModelingProgram of a Construct.
getModelingStatementAt(int) - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Returns the statement at the specified program counter in this program.
getModelingStatements() - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Returns an array containing all of the statements in this program in the correct order.
getModelName() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Find the name of the `Model` that will be used when a new wrapper is generated
getModelName(int) - Static method in class uk.ac.ic.doc.automed.MDR
getModelNames() - Static method in class uk.ac.ic.doc.automed.MDR
  Gets a list of all modelling language names in the MDR
getModels() - Static method in class uk.ac.ic.doc.automed.MDR
  Gets a list of all modelling language identifiers in the MDR
getModels() - Static method in class uk.ac.ic.doc.automed.reps.Model
  Returns an array of all models.
getModelsHelp - Static variable in class uk.ac.ic.doc.automed.editor.Editor
getModelsSyntax - Static variable in class uk.ac.ic.doc.automed.editor.Editor
getName() - Method in class uk.ac.ic.doc.automed.reps.HDMElement
getName() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Returns the name of the construct.
getName() - Method in class uk.ac.ic.doc.automed.reps.Network
getName() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Find the name of the schema.
getName() - Method in class uk.ac.ic.doc.automed.reps.Protocol
  Returns the name of the protocol.
getName() - Method in class uk.ac.ic.doc.automed.reps.Model
  Returns the name of the model.
getName() - Method in class uk.ac.bbk.dcs.automed.graph.TreeNode
getName() - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraphNode
getName() - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getName() - Method in class uk.ac.ic.doc.automed.ssd.Pattern
getName() - Method in class uk.ac.bbk.dcs.automed.qproc.optimise.FoldFunction
getName() - Method in class uk.ac.ic.doc.automed.templates.Statement
  Returns the name of this Statement.
getName() - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns the name of this CompositeTransformation.
getName() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
getName() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
  Returns the name of the template transformation
getName() - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
getName() - Method in class uk.ac.ic.doc.automed.matching.relationships.Subsumption
getName() - Method in class uk.ac.ic.doc.automed.matching.relationships.SemanticRelationship
getName() - Method in class uk.ac.ic.doc.automed.matching.relationships.Overlapness
getName() - Method in class uk.ac.ic.doc.automed.matching.relationships.Incompatibility
getName() - Method in class uk.ac.ic.doc.automed.matching.relationships.Equivalence
getName() - Method in class uk.ac.ic.doc.automed.matching.relationships.Disjointness
getName(int) - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the name of a schema from its SID without instantiating it
getNegativePostconditions() - Method in class uk.ac.ic.doc.automed.tml.TML
getNegativePreconditions() - Method in class uk.ac.ic.doc.automed.tml.TML
getNetwork() - Method in class uk.ac.ic.doc.automed.reps.Node
  Returns the network this node belongs to
getNetwork(Schema, String) - Static method in class uk.ac.ic.doc.automed.reps.Network
  Returns the complete undirected network that contains schema s.
getNetworkHelp - Static variable in class uk.ac.ic.doc.automed.editor.Editor
getNetworkNamesHelp - Static variable in class uk.ac.ic.doc.automed.editor.Editor
getNetworkNamesSyntax - Static variable in class uk.ac.ic.doc.automed.editor.Editor
getNetworks() - Static method in class uk.ac.ic.doc.automed.reps.Network
  Return a List that contains all Networks held in the repository.
getNetworks(boolean) - Static method in class uk.ac.ic.doc.automed.reps.Network
  Return a list that contains all Networks held in the repository.
getNetworksHelp - Static variable in class uk.ac.ic.doc.automed.editor.Editor
getNetworksSyntax - Static variable in class uk.ac.ic.doc.automed.editor.Editor
getNetworkSyntax - Static variable in class uk.ac.ic.doc.automed.editor.Editor
getNextItemInList(InputItem) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
getNextKey() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
getNextRow() - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
getNextToken() - Method in class uk.ac.ic.doc.automed.reps.Syntax.Tokenizer
getNextToken(int) - Method in class uk.ac.ic.doc.automed.reps.Syntax.Tokenizer
getNextToken(int, int) - Method in class uk.ac.ic.doc.automed.reps.Syntax.Tokenizer
getNode(int) - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraph
getNode(Node) - Method in class uk.ac.ic.doc.automed.reps.Network
  Deprecated.
getNode(Schema) - Static method in class uk.ac.ic.doc.automed.reps.Node
  returns the node for a schema if one exists or null otherwise
getNode(Schema) - Method in class uk.ac.ic.doc.automed.reps.Network
  Returns the network node representing the supplied schema
getNode(String) - Static method in class uk.ac.ic.doc.automed.reps.Node
  returns the node for a schema if one exists or null otherwise
getNode(String) - Method in class uk.ac.ic.doc.automed.reps.Network
  Returns the network node representing the named schema
getNode(String) - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraph
getNodeDepth(Node) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Returns the depth of node n.
getNodeInstances(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Given a node type return all the instances in the HDM store as a `LinkedList` with elements of type `Span`, each element representing an instance
getNodeOrder(Node) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
getNodes() - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
getNonAtomicRelationship(SchemaElementPair) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
getNumbers(String[]) - Static method in class uk.ac.ic.doc.automed.matching.Util
getOBID() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Returns the schema object identifier (OBID) of a schema object.
getOBID() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
getOBIDBySFIDSPID(int, int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the ID of schemaobject in the SSMDR for the particular ssdformat and ssdpattern.
getOBIDBySPID(int) - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getObjectID() - Method in class uk.ac.ic.doc.automed.IntegrityException
  Return the object indentifier of the the object, that the manipulation of caused this exception.
getObjectSchemeNames(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns an `Object` array of an object's scheme.
getObjectSchemeNamesString(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the scheme representation (of type `String`}) of an object's scheme.
getOpenSchemeBracket() - Static method in class uk.ac.ic.doc.automed.STR
  Return String used to open schemes
getOpenSchemeBracket() - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Find what string is used to deliminate the opening of a scheme name, such as the "<<" in "<<person>>" or "<<person,name>>".
getOperation() - Method in class uk.ac.ic.doc.automed.IntegrityException
  Return the operation attempted on the object that caused this exception.
getOperator() - Method in class uk.ac.ic.doc.automed.wrappers.SchemeQuery
  Return the operator type that this query node represents.
getOption(String) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Return an option setting.
getOptionKeys() - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapper
  Return the list of option setting key provided by the wrapper.
getOptionKeys() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Return the list of option setting key provided by the wrapper factory.
getOpts(String, String[]) - Static method in class uk.ac.ic.doc.automed.Util
getOriginalSchemas() - Method in class uk.ac.ic.doc.automed.reps.Transformation
getOtherSchema(Schema) - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the schemas of the transformation.
getOutgoingEdges() - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraphNode
getOutput(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
getOutput(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
getPairs() - Method in class uk.ac.ic.doc.automed.matching.Aggregator
getParent() - Method in class uk.ac.bbk.dcs.automed.graph.TreeNode
getParents() - Method in class uk.ac.ic.doc.automed.reps.Node
  If the network this node belongs to is directed then returns all the adjacent nodes that are parents of this node, otherwise its behaviour is defined by the type of network but the parents will be a subset of adjacent.
getPassword() - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Returns the password of the user, if it exists
getPath(Node) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
getPattern() - Method in class uk.ac.ic.doc.automed.ssd.SSDPattern
getPattern() - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getPattern() - Method in class uk.ac.ic.doc.automed.matching.modules.ElementVectorRepresentation
getPattern() - Method in class uk.ac.ic.doc.automed.matching.modules.Cluster
getPattern(String) - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool
getPatternByName(String) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the pattern identifier (PID).
getPatternByName(String) - Static method in class uk.ac.ic.doc.automed.ssd.Pattern
getPatternIDs() - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the IDs of all the patterns found in the SSMDR.
getPatternName(int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the name of the pattern.
getPatternSize() - Method in class uk.ac.ic.doc.automed.matching.modules.Clusterer
getPatternValue() - Method in class uk.ac.ic.doc.automed.ssd.SSDPattern
getPatternValue(int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the value (an actual pattern in regular expression) of the pattern.
getPc() - Method in class uk.ac.ic.doc.automed.templates.StatementExecution
  Returns the program counter of this StatementExecution.
getPCDATAChildCount(Node) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Counts the element children of the given node.
getPCDATANodeOrder(Node) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
getPID() - Method in class uk.ac.ic.doc.automed.reps.Protocol
  Returns the protocol identifier (PID).
getPID() - Method in class uk.ac.ic.doc.automed.ssd.Pattern
getPIDByName(String) - Static method in class uk.ac.ic.doc.automed.ssd.Pattern
getPIDBySPID(int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the ssdpattern identifier (SPID).
getPK(SchemaObject, ArrayList) - Method in class uk.ac.ic.doc.automed.matching.SQLRelationshipExtractor
getPKColumns(SchemaObject, ArrayList) - Method in class uk.ac.ic.doc.automed.matching.SQLRelationshipExtractor
getPosition() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getPosition() - Method in class uk.ac.ic.doc.automed.reps.Network
getPosition() - Method in class uk.ac.ic.doc.automed.reps.Schema
getPosition() - Method in interface uk.ac.ic.doc.automed.editor.Positionable
getPosition() - Method in class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
  Returns the position in the transformation's argument definition list of this TransformationArgumentDefinition.
getPosition() - Method in class uk.ac.ic.doc.automed.templates.TemplateArgument
  Returns the position of this TemplateArgument.
getPosition() - Method in class uk.ac.ic.doc.automed.templates.StatementArgumentDefinition
  Returns the position in the statement's argument definition list of this StatementArgumentDefinition.
getPosition() - Method in class uk.ac.ic.doc.automed.templates.RuntimeArgument
  Returns the position of this RuntimeArgument.
getPosition() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
getPosition() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
getPositionable() - Method in interface uk.ac.ic.doc.automed.editor.DrawableVertex
getPositionable() - Method in class uk.ac.ic.doc.automed.editor.DrawVertex
getPositionInReferencedArgumentSequence() - Method in class uk.ac.ic.doc.automed.templates.TemplateArgument
  Returns the position in the referenced arguments sequence.
getPositivePostconditions() - Method in class uk.ac.ic.doc.automed.tml.TML
getPositivePreconditions() - Method in class uk.ac.ic.doc.automed.tml.TML
getPreferredSize() - Method in class uk.ac.ic.doc.automed.gui.ToolTip
getPrimaryKeyOfTable(Schema, SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns the primary key of a table SchemaObject.
getProjected() - Method in class uk.ac.ic.doc.automed.matching.modules.MapDisplay
getProperty(String) - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Returns a property associated with this AccessMethod.
getProtocol() - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Returns the `Protocol` used for connecting to the database.
getProtocol() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Returns the `Protocol` associated with the Wrapper.
getProtocol(int) - Static method in class uk.ac.ic.doc.automed.reps.Protocol
  Returns the `Protocol` with the given PID.
getProtocol(String) - Static method in class uk.ac.ic.doc.automed.reps.Protocol
  Returns the `Protocol` with the given protocolName.
getProtocolByName(String) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the protocol identifier (PID) of the specified protocol name.
getProtocolName() - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapper
  The name of the `Protocol` in the repository used to represent JDBC connections.
getProtocolName() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  The name of the `Protocol` that this wrapper uses
getProtocolName() - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
  The name of the `Protocol` in the repository used to represent flat files with a YATTA schema.
getProtocolName() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.SAXWrapper
  The name of the `Protocol` in the repository used to represent JDBC connections.
getProtocolName() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapper
getProtocolName() - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapper
  The name of the `Protocol` in the repository used to represent the HDM store.
getProtocolName(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the name of the given protocol identifier (PID).
getQuerySchemaObjects(int, String, Schema) - Static method in class uk.ac.ic.doc.automed.tml.TML
  Returns an ArrayList of OBIDs referenced by the given query.
getQueryScheme() - Method in class uk.ac.ic.doc.automed.wrappers.YattaQuery
getQueryVariables() - Method in class uk.ac.ic.doc.automed.wrappers.YattaQuery
getRandomInstance() - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
getRefAction() - Method in class uk.ac.ic.doc.automed.tml.TempTML
getRefActionString() - Method in class uk.ac.ic.doc.automed.tml.TempTML
getRefConstraint() - Method in class uk.ac.ic.doc.automed.tml.TempTML
getRefConstructName() - Method in class uk.ac.ic.doc.automed.tml.TempTML
getReferencedArgumentsAsArray() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
getReferencedArgumentsAsVector() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
getReferencedArgumentSequence() - Method in class uk.ac.ic.doc.automed.templates.TemplateArgument
  Returns the TemplateArgumentSequence this TemplateArgument refers to.
getReferencedConstruct() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getReferencedConstruct(SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns the object a SchemaObject is attached to.
getReferencedConstructs() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getReferencedConstructs(SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns all the objects in a SchemaObject's scheme that are correspond to positions in the SchemaObject's scheme of type `SCHEME_TYPE_CONSTRUCT` that are of NODAL class.
getReferencedField() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getReferencedField(SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns the field of a primary key SchemaObject.
getReferencedObjects(SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns all the objects in a SchemaObject's scheme that are correspond to positions in the SchemaObject's scheme of type `SCHEME_TYPE_CONSTRUCT`.
getReferencedSchemaObjects() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Returns the set of SchemaObjects that are referenced directly or indirectly by this SchemaObject.
getReferencedSchemaObjects() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns all the schema objects referenced in a transformation.
getReferencedSchemaObjectsInQuery() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns all the schema objects referenced in the query of a transformation.
getReferencedTable() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getReferencedTable(SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns the table of a primary key SchemaObject.
getReferencePosition() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
getReferringObjects(Schema, SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns the SchemaObject objects that include `object` in their schemes.
getRefFromObjName() - Method in class uk.ac.ic.doc.automed.tml.TempTML
getRefFunction() - Method in class uk.ac.ic.doc.automed.tml.TempTML
getRefModelName() - Method in class uk.ac.ic.doc.automed.tml.TempTML
getRefPos() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
getRefSchemaObject() - Method in class uk.ac.ic.doc.automed.reps.Scheme
  Returns the `SchemaObject` that this `Scheme` wraps
getRefToObjName() - Method in class uk.ac.ic.doc.automed.tml.TempTML
getRelatedTables(ArrayList) - Method in class uk.ac.ic.doc.automed.matching.SQLIntegrator
getRelationship() - Method in class uk.ac.ic.doc.automed.matching.SchemaElementPairRelationship
getRelationship() - Static method in class uk.ac.ic.doc.automed.matching.relationships.Superset
getRelationship() - Static method in class uk.ac.ic.doc.automed.matching.relationships.Subset
getRelationship() - Static method in class uk.ac.ic.doc.automed.matching.relationships.Overlapness
getRelationship() - Static method in class uk.ac.ic.doc.automed.matching.relationships.Incompatibility
getRelationship() - Static method in class uk.ac.ic.doc.automed.matching.relationships.Equivalence
getRelationship() - Static method in class uk.ac.ic.doc.automed.matching.relationships.Disjointness
getRelationship(BidirectionalDegree) - Method in class uk.ac.ic.doc.automed.matching.BidirectionalMap
getRelationship(SchemaElementPair) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
getRelationship(SchemaElementPair) - Method in class uk.ac.ic.doc.automed.matching.Integrator
getRelationship(SchemaElementPairRelationship[]) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
getRelationships() - Method in class uk.ac.ic.doc.automed.matching.SQLRelationshipExtractor
getRelationships() - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
getRelationships(ArrayList) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
getRelationships(BidirectionalMap) - Method in class uk.ac.ic.doc.automed.matching.DegreeCombinator
getRelationshipsColumnEdges(double, double, double, double) - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
getRelationshipsColumns(double, double, double, double) - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
getRelationshipsTables(double, double, double, double) - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
getRelativeDegrees(ArrayList, ArrayList) - Static method in class uk.ac.ic.doc.automed.matching.modules.ClustererClassifier
getRelativeTo() - Method in interface uk.ac.ic.doc.automed.editor.DrawableVertex
getRelativeTo() - Method in class uk.ac.ic.doc.automed.editor.DrawVertex
  If the coordinates of the Positionable that this Drawable is for are specified relatitive to some other Positionables, return those other Positionables
getRenamedObject() - Method in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
getRepObject() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getRepObject() - Method in class uk.ac.ic.doc.automed.reps.Network
getRepObject() - Method in class uk.ac.ic.doc.automed.reps.Schema
getRepObject() - Method in interface uk.ac.ic.doc.automed.editor.Positionable
getRepTran() - Method in class uk.ac.ic.doc.automed.tml.TML
getRequiredNumberOfElements() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
getResult() - Method in class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement
getReturnedArgumentsDefinition() - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns the arguments that store returned values after the transformation's invocation.
getReverseTransformation() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the reverse transformation of the given transformation.
getRoots() - Method in class uk.ac.ic.doc.automed.reps.Network
getRuntimeArgumentSequence(int) - Static method in class uk.ac.ic.doc.automed.templates.RuntimeArgumentSequence
  Returns the reference to the RuntimeArgumentSequence with the given ID.
getRuntimeArgumentSequences() - Static method in class uk.ac.ic.doc.automed.templates.RuntimeArgumentSequence
  Returns an array of all RuntimeArgumentSequence objects that have RuntimeArgument objects.
getSchema() - Method in class uk.ac.ic.doc.automed.reps.Node
  Returns the schema at this node in the network
getSchema() - Method in class uk.ac.ic.doc.automed.reps.BadSchemaException
  Returns the bad schema.
getSchema() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Returns the `Schema` to which the SchemaObject belongs.
getSchema() - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Returns the schema that represents the database to which the access method connects.
getSchema() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Returns the `Schema` that represents in the datasource in terms of `SchemaObject`s in a data source oriented manner.
getSchema() - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getSchema(int) - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the `Schema object which has the given schema identifier (SID).`
getSchema(String) - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the `Schema` object with the given name.
getSchema(String) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  A method that creates in the repository a Schema and AccessMethod from the supplied information, together with a Protocol if necessary, and returns the AccessMethod.
getSchemaBackgroundColor(int) - Static method in class uk.ac.ic.doc.automed.STR
getSchemaByName(String) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the schema identifier (SID) of the schema specified by name.
  Assumption:schema names are unique.
getSchemaDoc() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
getSchemaForegroundColor(int) - Static method in class uk.ac.ic.doc.automed.STR
getSchemaId() - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
getSchemaId() - Method in interface uk.ac.ic.doc.automed.templates.gui.InteractiveSchemaDisplay
getSchemaIDs() - Static method in class uk.ac.ic.doc.automed.STR
  Returns the IDs of all the schemas found in the STR.
getSchemaIDs() - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Returns an array of SID of all the schemas found in the STR.
getSchemaLabelPos(int) - Static method in class uk.ac.ic.doc.automed.STR
getSchemaName() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
getSchemaName() - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
getSchemaName(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the name of the schema with the given schema identifier.
getSchemaNames() - Static method in class uk.ac.ic.doc.automed.STR
  Returns the name of all the schemas found in the STR.
getSchemaNames() - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Returns an array of names of all the schemas found in the STR.
getSchemaNetworkHelp - Static variable in class uk.ac.ic.doc.automed.editor.Editor
getSchemaNetworkSyntax - Static variable in class uk.ac.ic.doc.automed.editor.Editor
getSchemaObject() - Method in class uk.ac.ic.doc.automed.reps.Scheme
  Returns the `SchemaObject` that this Scheme element is contained within, i.e.
getSchemaObject() - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
getSchemaObject(int) - Static method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Returns the `SchemaObject` reference that has the given schema object identifier (OBID).
getSchemaObject(Schema) - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the `SchemaObject` of the transformation.
getSchemaObject(String) - Method in class uk.ac.ic.doc.automed.reps.Schema
getSchemaObject(String, int) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Return the `SchemaObject` that has the supplied name in this schema.
getSchemaObjectBackgroundColor(int) - Static method in class uk.ac.ic.doc.automed.STR
getSchemaObjectByName(String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Deprecated. Return the `SchemaObject` that has the supplied name in this schema. Note that the String supplied must match exactly the name of the `SchemaObject` as returned by `SchemaObject.getSchemeNamesString()`
getSchemaObjectByOBID(int) - Static method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Deprecated. use `SchemaObject.getSchemaObject(int)` instead
getSchemaObjectCID(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the construct identifier (CID) of the schema object.
getSchemaObjectForegroundColor(int) - Static method in class uk.ac.ic.doc.automed.STR
getSchemaObjectLabelPos(int) - Static method in class uk.ac.ic.doc.automed.STR
getSchemaObjectPos(int) - Static method in class uk.ac.ic.doc.automed.STR
getSchemaObjects() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Find all `SchemaObjects` that are instances of a particular Construct.
getSchemaObjects() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns an array of schema objects (of class `SchemaObject`) that belong to the schema.
getSchemaObjects(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the object identifiers (OBID) in ascending order of all the schema objects that belong to a particular schema.
getSchemaObjectsByCID(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the object identifiers (OBID) in ascending order of all the schema objects that are instances of a certain construct type, in order of the OBID to which they belong
getSchemaObjectSID(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the schema identifier (SID) that a schema object belongs to.
getSchemaObjectTextColor(int) - Static method in class uk.ac.ic.doc.automed.STR
getSchemaObjectValue(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the name (value) of the schema object.
getSchemaPos(int) - Static method in class uk.ac.ic.doc.automed.STR
getSchemas() - Method in class uk.ac.ic.doc.automed.reps.Pathway
  Return as an array the `Schema`s that appear in the `Transformation`s of this Pathway.
getSchemas() - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Find all `Schema` instances held in the repository.
getSchemas() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the schemas of the transformation.
getSchemas() - Method in class uk.ac.ic.doc.automed.matching.SQLIntegrator
getSchemas() - Method in class uk.ac.ic.doc.automed.matching.Integrator
getSchemaSIDs() - Static method in class uk.ac.ic.doc.automed.STR
  Returns the schema identifier (SID) of all the schemas found in the STR.
getSchemaSubnetSID(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the subnet schema id of this schema.
getSchemaTextColor(int) - Static method in class uk.ac.ic.doc.automed.STR
getSchemaUIDDoc() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
getSchemaUIDDoc() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLDSSSAX
getSchemaUIDDoc() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLDSSDOM
getScheme() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Returns an array of `ConstructScheme` objects representing the scheme of the construct.
getSchemeArray(Construct, String[]) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  This method is used to retrieve the Object [] which defines the schema of a newly added object.
getSchemeDefinition() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  All SchemaObjects when they are created by methods such as `Schema.createSchemaObject`, `Schema.applyAddTransformation` and `Transformation.createAddTransformation` require that an Object array be supplied that defines the scheme of the new SchemaObject.
getSchemeList() - Method in class uk.ac.ic.doc.automed.templates.wrapper.SchemeListStatement
getSchemeNames() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  A shorthand for `#getSchemeNames(false)`
getSchemeNames(boolean) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Return the names of all objects in the scheme of this SchemaObject.
getSchemeNames(int, int) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getSchemeNames(int, int, boolean) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getSchemeNamesString() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Same as calling `#Schema.getSchemaNameString(false)`
getSchemeNamesString(boolean) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Returns the scheme representation this `SchemaObject` using brackets as set by `Schema.setOpenCloseSchemeBracket`.
getSchemeNamesString(int, int) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getSchemeNamesString(int, int, boolean) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getSchemeOBIDList(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns a list of all schema object identifiers (OBID) by which a particular schema object is referenced.
getSchemeObjects() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Returns an array of schema objects that are contained in the scheme of this schema object.
getSchemePos() - Method in class uk.ac.ic.doc.automed.reps.Scheme
  Returns the position of this `Scheme` in the definition of the `SchemaObject` it defines.
getSchemePosList(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns a list of positions in the scheme of a particular schema object.
getSchemeSOBID(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the object identifier (SOBID) of the referenced schema object in the specified schema object's scheme at the given position.
getSchemeSOBIDList(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns a list of all schema object identifiers (SOBID) referenced by a particular schema object.
getSchemeString() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getSchemeString(Schema) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getSchemeType() - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Returns the scheme type of the `ConstructScheme`.
getSchemeTypeString(int) - Static method in class uk.ac.ic.doc.automed.reps.ConstructScheme
getSchemeTypeString(int, boolean) - Static method in class uk.ac.ic.doc.automed.reps.ConstructScheme
getSecondElement() - Method in class uk.ac.ic.doc.automed.matching.SchemaElementPair
getSectionDebugLevel(int) - Static method in class uk.ac.ic.doc.automed.STR
  Gets the debug level which the section of code has been set to.
getSequenceId() - Method in class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
  Returns the sequence ID of this TemplateArgumentSequence.
getSequenceId() - Method in class uk.ac.ic.doc.automed.templates.TemplateArgument
  Returns the sequence identifier of this TemplateArgument.
getSequenceId() - Method in class uk.ac.ic.doc.automed.templates.RuntimeArgumentSequence
  Returns the sequence ID of this RuntimeArgumentSequence.
getSequenceId() - Method in class uk.ac.ic.doc.automed.templates.RuntimeArgument
  Returns the sequence identifier of this RuntimeArgument.
getSFID() - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getSFID(String) - Static method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getSFIDByName(String) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the ssd format identifier (SFID) of the ssd format specified by name.
  Assumption:ssd format names are unique.
getSFIDBySID(int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the ssdformat identifier (SFID) of the ssd format specified by schema identifier (SID).
getShape() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getSID() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns the schema identifier (SID) of the schema.
getSIDBySFID(int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the schema identifier (SID) of the ssd format specified by ssd format identifier (SFID).
getSimilarityDegree() - Method in class uk.ac.ic.doc.automed.matching.modules.SimilarCluster
getSize() - Method in class uk.ac.ic.doc.automed.matching.modules.ElementVectorRepresentation
getSmartQuoting() - Static method in class uk.ac.ic.doc.automed.reps.Syntax
getSMR_DataSourceName() - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Deprecated, use getDataSourceName instead
getSpans(int, int) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  For the edge specified return a `LinkedList` with each element of type `Span` representing a span in that edge.
getSpecEdgePosition() - Method in class uk.ac.ic.doc.automed.gui.Rhombus
getSpecialConstructs() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getSpecialConstructs(SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns an array of SchemaObject objects corresponing to the sub-entities of a generalization.
getSPID() - Method in class uk.ac.ic.doc.automed.ssd.SSDPattern
getSPID(int) - Method in class uk.ac.ic.doc.automed.ssd.SSDPattern
getSPIDByOBID(int) - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getSPIDByPID(int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the recent ssdpattern identifier (SPID) of the specified pattern.
getSPIDBySFIDOBID(int, int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the ID of ssdpattern in the SSMDR for the particular ssdformat and schemaobject.
getSPIDsBySFID(int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the IDs of all the ssdpatterns found in the SSMDR.
getSQLQuery(int) - Method in class uk.ac.ic.doc.automed.wrappers.SQLQuery
  Return the SQLQuery held in a certain field, or null if the field is empty.
getSQLTableReference(Object[]) - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  Given the scheme of a table, get the name SQL uses to reference that table.
getSQLType(String) - Static method in class uk.ac.ic.doc.automed.Util
getSQLTypeName(int) - Static method in class uk.ac.ic.doc.automed.Util
getSSDFormat() - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
getSSDFormat(int) - Static method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getSSDFormat(String) - Static method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getSSDFormatBySchema(Schema) - Static method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getSSDFormatIDs() - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the IDs of all the ssd formats found in the SSMDR.
getSSDFormatName(int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the name of the ssd format with the given ssd format identifier.
getSSDFormatName(int) - Static method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getSSDFormatNames() - Static method in class uk.ac.ic.doc.automed.SSMDR
  Returns the name of all the ssd formats found in the SSMDR.
getSSDPatternBySPID(int) - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getSSDPatternIDs() - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
getSSDSource() - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
getSSMDR_DataSourceName() - Static method in class uk.ac.ic.doc.automed.SSMDR
  Deprecated. use getDataSourceName()
getStandardDeviation(double[]) - Static method in class uk.ac.ic.doc.automed.matching.Util
getStandardDeviation(double[], double) - Static method in class uk.ac.ic.doc.automed.matching.Util
getStatement() - Method in class uk.ac.ic.doc.automed.templates.StatementExecution
  Returns the Statement of this StatementExecution.
getStatement(int) - Static method in class uk.ac.ic.doc.automed.templates.Statement
  Returns a reference to a Statement.
getStatement(String) - Static method in class uk.ac.ic.doc.automed.templates.Statement
  Returns a reference to a Statement.
getStatementByName(String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Returns the ID (`st_id`) of the statement specified by name, or `-1` if a statement with the specified name doesn't exist in the TTSR.
getStatementDefinitionArgPosList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Returns a particular statement's list of argument positions.
getStatementDefinitionDescription(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Returns a particular statement's argument definition (only the `description` field).
getStatementDefinitionDescriptionList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Returns a particular statement's list of argument definitions (only the `description` field).
getStatementDefinitionFieldName(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Returns a particular statement's argument definition (only the `field_name` field).
getStatementDefinitionFieldNameList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Returns a particular statement's list of argument definitions (only the `field_name` field).
getStatementDefinitionTableName(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Returns a particular statement's argument definition (only the `table_name` field).
getStatementDefinitionTableNameList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Returns a particular statement's list of argument definitions (only the `table_name` field).
getStatementDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement
getStatementDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.SchemeListStatement
getStatementDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement
getStatementDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatement
getStatementDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
getStatementDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
getStatementDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
getStatementDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
getStatementDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
getStatementExecutionAt(int) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns a particular StatementExecution in the CompositeTransformations's template program.
getStatementExecutions() - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns an array of all the StatementExecution objects in this CompositeTransformation.
getStatementExecutionsForTransformation(int) - Static method in class uk.ac.ic.doc.automed.templates.StatementExecution
  Returns all the StatementExecution objects of the specified composite transformation.
getStatementName(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Returns the name of the statement specified by `st_id`
getStatements() - Static method in class uk.ac.ic.doc.automed.templates.Statement
  Returns an array of all Statement objects.
getStatementsNameList() - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Returns the names of all the statements found in the TTSR
getStatementsStIdList() - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Returns the IDs of all the statements found in the TTSR
getStId() - Method in class uk.ac.ic.doc.automed.templates.StatementArgumentDefinition
  Returns the statement identifier defining which statement this StatementArgumentDefinition belongs to.
getStId() - Method in class uk.ac.ic.doc.automed.templates.Statement
  Returns the ID of this Statement.
getSTR_DataSourceName() - Static method in class uk.ac.ic.doc.automed.STR
  Deprecated. use getDataSourceName()
getStrength() - Method in class uk.ac.ic.doc.automed.matching.relationships.Subsumption
getStrength() - Method in class uk.ac.ic.doc.automed.matching.relationships.SemanticRelationship
getStrength() - Method in class uk.ac.ic.doc.automed.matching.relationships.Overlapness
getStrength() - Method in class uk.ac.ic.doc.automed.matching.relationships.Incompatibility
getStrength() - Method in class uk.ac.ic.doc.automed.matching.relationships.Equivalence
getStrength() - Method in class uk.ac.ic.doc.automed.matching.relationships.Disjointness
getString() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRAINTS
getString() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.FUNCTION
getString() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
getString(int) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
  Return a field as a String value.
getString(int) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTuple
  Return a particular attribute from a tuple (counting from one) as a String
getStringConstructProperty(int, int, String) - Static method in class uk.ac.ic.doc.automed.MDR
getSubGraphs() - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraph
getSubnetSchema() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Find the extensional schema in the same subnetwork as this SchemaObject.
getSubnetSchema() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Find the extensional schema in the same subnetwork as this Schema.
getTableDetailsSchemeLength() - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  Return the number of fields in a full source table scheme used to reprsent the table details
getTableForeignKeyPoints() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getTableForeignKeyPoints(SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns the table that a foreign key SchemaObject points.
getTableName() - Method in class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
  Returns the tablename of this TransformationArgumentDefinition.
getTableName() - Method in class uk.ac.ic.doc.automed.templates.StatementArgumentDefinition
  Returns the tablename of this StatementArgumentDefinition.
getTables(Schema) - Method in class uk.ac.ic.doc.automed.matching.SQLIntegrator
getTableWithForeignKey() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getTableWithForeignKey(SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns the table of a foreign key SchemaObject.
getTemplateArgumentSequence(int) - Static method in class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
  Returns the reference to the TemplateArgumentSequence with the given ID.
getTemplateArgumentSequences() - Static method in class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
  Returns an array of all TemplateArgumentSequence objects that have TemplateArgument objects.
getTemplateName() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList
getTempPathway(Pathway) - Static method in class uk.ac.ic.doc.automed.tml.TempPathway
getTextColor() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getTextColor() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Return the default text colour to be used from drawing `SchemaObject`s of this `Construct`.
getTextColor() - Method in class uk.ac.ic.doc.automed.reps.Network
getTextColor() - Method in class uk.ac.ic.doc.automed.reps.Schema
getTextColor() - Method in class uk.ac.ic.doc.automed.reps.Model
  Return the default text colour to be used from drawing `SchemaObject`s of this `Model`.
getTextColor() - Method in interface uk.ac.ic.doc.automed.editor.Positionable
getTextNodes(Node) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
getTML(Schema, Schema) - Static method in class uk.ac.ic.doc.automed.tml.TML
getTmlList() - Method in class uk.ac.ic.doc.automed.tml.TempPathway
getToOBID() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the schema object identifier (OBID) of the output of the transformaiton (toObject).
getToObject() - Method in class uk.ac.ic.doc.automed.tml.TML
getToObjectsUnmatched() - Method in class uk.ac.ic.doc.automed.reps.SchemasNotIdenticalException
getTool(Object[]) - Static method in class uk.ac.ic.doc.automed.editor.PathwayOptimiserTool
getTool(Object[]) - Static method in class uk.ac.ic.doc.automed.editor.PatternWritingTool
getTool(Object[]) - Static method in class uk.ac.ic.doc.automed.editor.MatchingTool
getToSchema() - Method in class uk.ac.ic.doc.automed.reps.SchemasNotIdenticalException
getToSchema() - Method in class uk.ac.ic.doc.automed.tml.TML
getToSID() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the schema identifier (SID) of the resultant schema.
getTranAction(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the action of transformation between two schemas.
getTranConstraint(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the constraint of a transformation between two schemas.
getTranFromObject(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the schema object to be transformed in a transformation.
getTranFromSchema(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns a list of schema identifiers (SID) from which a particular schema can be derived.
getTranFunction(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the function of a transformation between two schemas.
getTransformation(int, int) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the transformation between two given schemas.
getTransformation(Schema, Schema) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the transformation between two given schemas.
getTransformationObject(int) - Static method in class uk.ac.ic.doc.automed.reps.SchemaObject
getTransformations() - Static method in class uk.ac.ic.doc.automed.STR
  Returns a vector representing all transformations in the repository
getTransformations() - Method in class uk.ac.ic.doc.automed.reps.Pathway
  Return as an array the `Transformation`s that make up this Pathway.
getTransformations() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Find the set of `Transformation`s that involve this SchemaObject.
getTransformations() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Return an array of all `Transformation` that go out from a particular schema.
getTransformations() - Static method in class uk.ac.ic.doc.automed.reps.Transformation
getTransformations() - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformationRecord
getTransformationsByOBID(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the pairs of schema identifiers (SID) of all the schema transformations that involve the supplied OBID
getTransformationsFrom() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns an array of `Transformation`'s that have this schema as the `fromSchema` field in the transformation table of the STR.
getTransformationsTo() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Returns an array of `Transformation`'s that have this schema as the `toSchema` field in the transformation table of the STR.
getTransId() - Method in class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
  Returns the composite transformation identifier defining which transformation this TransformationArgumentDefinition belongs to.
getTransId() - Method in class uk.ac.ic.doc.automed.templates.StatementExecution
  Returns the transformation identifier of the composite transformation this StatementExecution belongs to.
getTransId() - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns the ID of this CompositeTransformation.
getTransId() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
getTranToObject(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the schema object as a result of a transformation.
getTranToSchema(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns a list of schema identifiers (SID) which are derived from a particular schema.
getTree() - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree
getTreeModel() - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree
getType() - Method in class uk.ac.ic.doc.automed.reps.NetworkChangeEvent
getType() - Method in class uk.ac.ic.doc.automed.reps.SchemaChangeEvent
getType() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTime
getType() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedString
getType() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTuple
getType() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedFloat
getType() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedInteger
getType() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedType
  Return the Type (INTEGER, TUPLE, ...) of this AutoMedType
getType() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedBoolean
getType() - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraphNode
getType() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
getType() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
getType() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
getType() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
getType(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
getType(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
getTypeID() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
getTypeID() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
getTypeID() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
getTypeID() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
getTypeInstance() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
getTypeInstance() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
getTypeInstance() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
getTypeInstance() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
getUIDDoc() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapper
getUnderlyingText(Node, String) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Returns a concatenated string of all text nodes under this node - not only its children's text nodes.
getUpper() - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Returns the upper bound indicating the maximum occurence of the `ConstructScheme`.
getURI() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
getURL() - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Returns the URL of the database to which the access method connects.
getUsername() - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Returns the username used for connecting to the database.
getValue() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Returns the name/value of the schema object.
getValue() - Method in class uk.ac.ic.doc.automed.ssd.Pattern
getValue() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getValue() - Method in class uk.ac.ic.doc.automed.templates.TemplateArgument
  Returns this TemplateArgument's value field.
getValue() - Method in class uk.ac.ic.doc.automed.templates.RuntimeArgument
  Returns this RuntimeArgument's value field.
getValue() - Method in class uk.ac.ic.doc.automed.matching.Instance
getValueForTemplateArgument(int, int, String, String[], HashMap) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns the value for a template argument.
getValueForTemplateArgumentPointingToArgId(int, int, String, String[], HashMap, Vector, boolean) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  .
getValuePosInScheme() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Returns the position in the construct's scheme where the construct's name is, i.e.
getValuesDisplaying() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
getVertexComponent(Positionable) - Method in class uk.ac.ic.doc.automed.editor.EditorPanel
getVertexComponent(Positionable) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
  Get a JComponent that is the visualisation of a class that implements the `Positionable` interface
getVertexDrawable() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Returns the name of the class implementing drawable that should be used to draw nodal elements of this construct.
getVertexDrawable(Positionable) - Method in class uk.ac.ic.doc.automed.editor.EditorPanel
getVertices() - Method in class uk.ac.ic.doc.automed.reps.HDMEdge
getWeakestRelationship(SemanticRelationship[]) - Static method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
getWellformedErrorMsg() - Method in class uk.ac.ic.doc.automed.reps.Pathway
getWrapper() - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Returns the wrapper used for connecting to the database.
getWrapperSchema() - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
getXMLDSS() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
getXPos() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getXPos() - Method in class uk.ac.ic.doc.automed.reps.Network
getXPos() - Method in class uk.ac.ic.doc.automed.reps.Schema
getXPos() - Method in interface uk.ac.ic.doc.automed.editor.Positionable
getXPos() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
getYattaRootNode(Schema) - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
getYPos() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getYPos() - Method in class uk.ac.ic.doc.automed.reps.Network
getYPos() - Method in class uk.ac.ic.doc.automed.reps.Schema
getYPos() - Method in interface uk.ac.ic.doc.automed.editor.Positionable
getYPos() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
GraphicSchemaObject - class uk.ac.ic.doc.automed.gui.GraphicSchemaObject.
GraphicSchemaObject(GraphicManager, Schema, SchemaObject) - Constructor for class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
Greater - class uk.ac.bbk.dcs.automed.qproc.functions.Greater.
Greater() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Greater
GreaterEqual - class uk.ac.bbk.dcs.automed.qproc.functions.GreaterEqual.
GreaterEqual() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.GreaterEqual
GREATERTHAN - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
GREATERTHANEQUAL - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
Group - class uk.ac.bbk.dcs.automed.qproc.functions.Group.
Group() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Group
GroupCompute - class uk.ac.bbk.dcs.automed.qproc.functions.GroupCompute.
GroupCompute() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.GroupCompute
grouplist(ModifiedArray) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Group
Gui - class uk.ac.ic.doc.automed.editor.Gui.
Gui.EditorFrame - class uk.ac.ic.doc.automed.editor.Gui.EditorFrame.
  A frame inside the main window to represent either All Networks, the contents of a Network (ie a connect set of Schemas), or the contents of a Schema
GUIException - exception uk.ac.ic.doc.automed.gui.GUIException.
  The class of exceptions generated by the GUI.
GUIException(String) - Constructor for class uk.ac.ic.doc.automed.gui.GUIException
GUIException(String, Exception) - Constructor for class uk.ac.ic.doc.automed.gui.GUIException
GUITool - class uk.ac.ic.doc.automed.editor.GUITool.
  A GUITool instance provides a window in which as user make interact with the repository.
GUITool() - Constructor for class uk.ac.ic.doc.automed.editor.GUITool
GUITool(String) - Constructor for class uk.ac.ic.doc.automed.editor.GUITool
GUITool(String, boolean, Object) - Constructor for class uk.ac.ic.doc.automed.editor.GUITool
  Create a new window that follows the AutoMed GUITool conventions.

## H

handleNonStatementArgument(int, String[], HashMap, Vector, boolean) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Creates an execution argument sequence according to a template argument sequence.
hashCode() - Method in class uk.ac.ic.doc.automed.matching.SchemaElementPair
hashCode() - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
hasObject(SchemaObject) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Determines if the schema contains the given schema object.
hasTextNodes(Node) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
hdm_constraint - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
hdm_edge - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
hdm_node - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
hdm_none - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
hdm_reference - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
HDM_TYPE_C - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
  Scheme relates to a constraint sentence in HDM
HDM_TYPE_E - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
  Scheme relates to edge name in HDM when instantiating the containing construct, this scheme position takes the name of the new edge to be created in HDM
HDM_TYPE_MAXIMUM - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
HDM_TYPE_MINIMUM - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
HDM_TYPE_N - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
  Scheme relates to node name in HDM.
HDM_TYPE_N1 - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
  Deprecated.
HDM_TYPE_N2 - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
  Deprecated.
HDM_TYPE_P1 - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
  Deprecated.
HDM_TYPE_P2 - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
  Deprecated.
HDM_TYPE_R - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
  Scheme relates to node or edge name/s in HDM and to other Construct/s in the automed.reps API.
HDM_TYPE_Z - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
  Scheme has no HDM representation
HDMConstraint - class uk.ac.ic.doc.automed.reps.HDMConstraint.
HDMConstraint() - Constructor for class uk.ac.ic.doc.automed.reps.HDMConstraint
HDMConstraint(String) - Constructor for class uk.ac.ic.doc.automed.reps.HDMConstraint
HDMEdge - class uk.ac.ic.doc.automed.reps.HDMEdge.
HDMEdge() - Constructor for class uk.ac.ic.doc.automed.reps.HDMEdge
HDMEdge(String) - Constructor for class uk.ac.ic.doc.automed.reps.HDMEdge
HDMEdge(String, HDMElement[]) - Constructor for class uk.ac.ic.doc.automed.reps.HDMEdge
HDMElement - class uk.ac.ic.doc.automed.reps.HDMElement.
HDMElement() - Constructor for class uk.ac.ic.doc.automed.reps.HDMElement
HDMElement(String) - Constructor for class uk.ac.ic.doc.automed.reps.HDMElement
HDMNetwork - class uk.ac.ic.doc.automed.reps.HDMNetwork.
HDMNetwork() - Constructor for class uk.ac.ic.doc.automed.reps.HDMNetwork
HDMNode - class uk.ac.ic.doc.automed.reps.HDMNode.
HDMNode() - Constructor for class uk.ac.ic.doc.automed.reps.HDMNode
HDMNode(String) - Constructor for class uk.ac.ic.doc.automed.reps.HDMNode
HdmStore - class uk.ac.bbk.dcs.automed.hdmstore.HdmStore.
  A HdmStore allows data to be stored and queried in an HDM repository which is implemented in a Postgres databas).
HdmStore() - Constructor for class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Default constructor assumes only error messages should be displayed (not debugs)
HdmStore(Debug) - Constructor for class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Constructor is passed debug class to send debug & error messages to
HdmStoreCmd - class uk.ac.bbk.dcs.automed.hdmstore.HdmStoreCmd.
  A command line processor for the HDM store which can be used as an alternative to the API..
HdmStoreCmd(String[]) - Constructor for class uk.ac.bbk.dcs.automed.hdmstore.HdmStoreCmd
  Construct a HdmStoreCmd and process the command line arguments
HdmStoreException - exception uk.ac.bbk.dcs.automed.hdmstore.HdmStoreException.
  The class of exceptions generated by `DataSourceRepository`.
HdmStoreException(String) - Constructor for class uk.ac.bbk.dcs.automed.hdmstore.HdmStoreException
hdmStoreExists(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Is there an HDM store with the passed name in the repository?
HdmWrapper - class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapper.
  A Wrapper for the HDM data store.
HdmWrapper() - Constructor for class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapper
HdmWrapperFactory - class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapperFactory.
HdmWrapperFactory() - Constructor for class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapperFactory
helpGetCurrentModel - Static variable in class uk.ac.ic.doc.automed.editor.Editor
helpHelp - Static variable in class uk.ac.ic.doc.automed.editor.CommandLineDriver
helpSyntax - Static variable in class uk.ac.ic.doc.automed.editor.CommandLineDriver
hid() - Method in class uk.ac.bbk.dcs.automed.hdmstore.Span
  Get the hid
hid(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Given an HDM store name return its row id number (or -1 if it does not exist)
hidden - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.ITEM
hide() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.ITEM
hideInternalSeperators(String) - Static method in class uk.ac.bbk.dcs.automed.hdmstore.Edge
  Remove commas that are not at the 'top level' e.g.
hideInternalSpaces(String) - Static method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStoreCmd
  Change any spaces within an edge thats a span to another character
highlighted - Variable in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
highlightElseDisableObjectsWithCID(int) - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
highlightElseDisableObjectsWithCID(int) - Method in interface uk.ac.ic.doc.automed.templates.gui.InteractiveSchemaDisplay
highlightObjectsWithCID(int) - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
HORIZONTAL_EXT - Static variable in class uk.ac.ic.doc.automed.gui.Rhombus
HOUR - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedTime
  Granularity of one hour
hyphen - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token

## I

Id - class uk.ac.bbk.dcs.automed.qproc.functions.Id.
id() - Method in class uk.ac.bbk.dcs.automed.hdmstore.Span
  Get the id
Id() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Id
ident - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
identifier - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
IDENTIFIER_TOKEN - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
identifierSafe(String) - Static method in class uk.ac.ic.doc.automed.reps.Syntax
identifySubGraphs() - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraph
  Discovers the subGraphs in the graph
IdentToken - Static variable in class uk.ac.bbk.dcs.automed.qproc.FSym
If - class uk.ac.bbk.dcs.automed.qproc.functions.If.
If() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.If
ifStack - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
IllegalOperationException - exception uk.ac.ic.doc.automed.reps.IllegalOperationException.
IllegalOperationException(String) - Constructor for class uk.ac.ic.doc.automed.reps.IllegalOperationException
implementCompositeTransformation(InteractiveSchemaDisplay, Frame) - Static method in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
implementCompositeTransformation(int, InteractiveSchemaDisplay, Frame) - Static method in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
importConstructs(InputStream) - Method in class uk.ac.ic.doc.automed.reps.Model
importSchemaObjects(InputStream) - Method in class uk.ac.ic.doc.automed.reps.Schema
importSchemes(InputStream) - Method in class uk.ac.ic.doc.automed.reps.Construct
importTransformations(InputStream) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
importTransformations(InputStream, String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
In - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
IN_ROW - Static variable in class uk.ac.ic.doc.automed.gui.SchemaManager
IN(TemplateCompilerSimulator.CONSTRAINTS) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
IN(TemplateCompilerSimulator.CONSTRAINTSLIST) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
IN(TemplateCompilerSimulator.FUNCTION) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
IN(TemplateCompilerSimulator.FUNCTIONLIST) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
IN(TemplateCompilerSimulator.NAMELIST) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
IN(TemplateCompilerSimulator.OBJECTLIST) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
Incompatibility - class uk.ac.ic.doc.automed.matching.relationships.Incompatibility.
inconsistent - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
InconsistentException - exception uk.ac.ic.doc.automed.InconsistentException.
  A manipulation of the repository that should always succeed has failed.
InconsistentException(String) - Constructor for class uk.ac.ic.doc.automed.InconsistentException
  Creates an InconsistentException when there has been no Exception that caused the error to discovered.
InconsistentException(String, Exception) - Constructor for class uk.ac.ic.doc.automed.InconsistentException
  Creates an InconsistentException when it is acting as a wrapper for other Exceptions.
INDEX - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  A feature option to model SQL Indexes in any `Schema` the factory generates
INDEX_LIST_STATEMENT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
IndexListStatement - class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement.
IndexListStatement() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement
indexOf(Schema) - Method in class uk.ac.ic.doc.automed.reps.Pathway
  Returns the index of a given `Schema` within the pathway.
init_actions() - Method in class uk.ac.bbk.dcs.automed.qproc.EnvParser
  Action encapsulation object initializer.
init_actions() - Method in class uk.ac.bbk.dcs.automed.qproc.QParser
  Action encapsulation object initializer.
initialise() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
initialiseArguments() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList
initialiseToolbars() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
initialSchemaKey - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
inputData(int, String) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
inputData(String, String) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
InputForm - class uk.ac.ic.doc.automed.templates.gui.InputForm.
InputForm(boolean, boolean) - Constructor for class uk.ac.ic.doc.automed.templates.gui.InputForm
InputForm(int, boolean) - Constructor for class uk.ac.ic.doc.automed.templates.gui.InputForm
InputForm(TTemplateInputArgument) - Constructor for class uk.ac.ic.doc.automed.templates.gui.InputForm
inputObjectToTemplate(int, String) - Method in class uk.ac.ic.doc.automed.templates.gui.TemplateInputDialogue
inputObjectToTemplate(int, String) - Method in interface uk.ac.ic.doc.automed.templates.gui.DialogueManager
inputs - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
INPUTS() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
INPUTS() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
inputVariables - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
inRange(int) - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Determine if a certain number of instances of elements in a scheme matching this ConstructScheme are permissable.
InsertingStatement - class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement.
InsertingStatement() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
insertIQL(ASG) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Execute an IQL insert on the datasource.
insertIQL(ASG) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapper
insertIQL(ASG) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapper
  Take the query and attempt to insert each of the values in the list into the database.
INSIDE - Static variable in class uk.ac.ic.doc.automed.editor.UserActionClass
Instance - class uk.ac.ic.doc.automed.matching.Instance.
INSTANCE - Static variable in class uk.ac.ic.doc.automed.matching.relationships.Superset
INSTANCE - Static variable in class uk.ac.ic.doc.automed.matching.relationships.Subset
INSTANCE - Static variable in class uk.ac.ic.doc.automed.matching.relationships.Overlapness
INSTANCE - Static variable in class uk.ac.ic.doc.automed.matching.relationships.Incompatibility
INSTANCE - Static variable in class uk.ac.ic.doc.automed.matching.relationships.Equivalence
INSTANCE - Static variable in class uk.ac.ic.doc.automed.matching.relationships.Disjointness
Instance() - Constructor for class uk.ac.ic.doc.automed.matching.Instance
Instance(String, int) - Constructor for class uk.ac.ic.doc.automed.matching.Instance
INTEGER - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
  Token to represent the AutoMedWrapper.INTEGER atomic type
INTEGER - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedType
  Type to represent a twos-complement integer atomic type
INTEGER_TOKEN - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
IntegrateDialog - class uk.ac.ic.doc.automed.gui.IntegrateDialog.
  A dialog that can be used for schema integration by name.
IntegrateDialog(Frame, String, boolean) - Constructor for class uk.ac.ic.doc.automed.gui.IntegrateDialog
integrateSchemas(Schema, Schema) - Static method in class uk.ac.ic.doc.automed.gui.IntegrateDialog
Integrator - class uk.ac.ic.doc.automed.matching.Integrator.
Integrator() - Constructor for class uk.ac.ic.doc.automed.matching.Integrator
IntegratorException - exception uk.ac.ic.doc.automed.matching.IntegratorException.
IntegratorException() - Constructor for class uk.ac.ic.doc.automed.matching.IntegratorException
IntegratorException(String) - Constructor for class uk.ac.ic.doc.automed.matching.IntegratorException
IntegratorException(String, Throwable) - Constructor for class uk.ac.ic.doc.automed.matching.IntegratorException
IntegratorException(Throwable) - Constructor for class uk.ac.ic.doc.automed.matching.IntegratorException
IntegrityException - exception uk.ac.ic.doc.automed.IntegrityException.
  An attempt has be made to alter the repository (or data structure representing it) in a way that would make it inconsistent.
IntegrityException(String, String, int, int) - Constructor for class uk.ac.ic.doc.automed.IntegrityException
  Creates an IntegrityException, recording details of what operation was being attempted
IntegrityException(String, String, int, int, int) - Constructor for class uk.ac.ic.doc.automed.IntegrityException
  Creates an IntegrityException, recording details of what operation was being attempted
InteractiveSchemaDisplay - interface uk.ac.ic.doc.automed.templates.gui.InteractiveSchemaDisplay.
intersectionByName(Schema) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Return an `SchemaObject` array containing the intersection by name between this schema (s1) and the schema passed as a parameter (s2).
intValue() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedInteger
  Return the value of this AutoMedInteger as an int
INVALID_TYPE - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TConstants
InvalidElementException - exception uk.ac.ic.doc.automed.matching.InvalidElementException.
InvalidElementException() - Constructor for class uk.ac.ic.doc.automed.matching.InvalidElementException
InvalidElementException(String) - Constructor for class uk.ac.ic.doc.automed.matching.InvalidElementException
InvalidElementException(String, Throwable) - Constructor for class uk.ac.ic.doc.automed.matching.InvalidElementException
INVOCATION_STATEMENT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Statement to inve other template transformations
invoke(RuntimeArgumentSequence) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Invokes this CompositeTransformation with the specified RuntimeArgumentSequence as arguments.
IQLfromResult(AutoMedResult) - Method in class uk.ac.bbk.dcs.automed.wrappers.Translator
IQLfromResult(AutoMedResult) - Method in class uk.ac.bbk.dcs.automed.wrappers.SQLTranslator
IS(Construct) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRUCT
IS(Object[]) - Static method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.SCHEME
IS(String) - Static method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRAINTS
IS(String) - Static method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.FUNCTION
IS(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRUCT
IS(TemplateCompilerSimulator.CONSTRAINTS) - Static method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRAINTS
IS(TemplateCompilerSimulator.FUNCTION) - Static method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.FUNCTION
isAdjacent(Node) - Method in class uk.ac.ic.doc.automed.reps.Node
isApply() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if tag is apply
isArgument - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRAINTS
isArgument - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.FUNCTION
isAtomic() - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
isBeingDisplayed() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
isChangedRefTML() - Method in class uk.ac.ic.doc.automed.tml.TML
isComplete() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
isConsConstructor() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if tag is "Cons"
isConstant() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if tag is constant
isConstraints() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
isConstraints() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
isConstraints() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
isConstraints() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
isConstructor() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if tag is constructor
isConstructRoot(int) - Static method in class uk.ac.ic.doc.automed.MDR
isConstructSchemeKey(int, int) - Static method in class uk.ac.ic.doc.automed.MDR
isCyclic() - Method in class uk.ac.ic.doc.automed.reps.Network
isDataSource() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Determines whether or not the schema represents an external data source.
isDependentOn(Transformation) - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Determines whether or not the transformation is dependent on another transformation.
isDirected() - Method in class uk.ac.ic.doc.automed.reps.Network
isElementNode(Node) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Returns true if node n is an element node, false otherwise
isEmpty() - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Tests if this program is empty.
isEnabled() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
isExecuted() - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns false if the specified transformation is not currently being executed, true otherwise.
isExtDB() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Determines whether or not the schema represents an extentional database.
isExtSchema() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Determines whether or not the schema is an extentional schema.
isFeatureInUse(int) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Test if a certain group of features is being implemented in the representation of the datasource model in the AutoMed repository
isFunction() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if tag is function
isFunction() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
isFunction() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
isFunction() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
isFunction() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
isHidden() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.ITEM
isHighlighted() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
isInRepository() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
isKey - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
isKey() - Method in class uk.ac.ic.doc.automed.reps.Scheme
  Determine if this `Scheme` is part of the set of `Scheme`s that uniquely identify the parent `SchemaObject` in a particular `Schema`
isKey() - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Returns whether of not the `ConstructScheme` is part the key of the whole scheme.
isLambda() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if tag is lambda
isLeaf() - Method in class uk.ac.ic.doc.automed.reps.Node
  True if (and only if) this node belongs to a directed network and this is a leaf node.
isLeaf() - Method in class uk.ac.bbk.dcs.automed.graph.TreeNode
isList() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
isList() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
isList() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
isList() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
isName() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
isName() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
isName() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
isName() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
isNaN() - Method in class uk.ac.ic.doc.automed.matching.BidirectionalDegree
isNew() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
isNewTemplate - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
isNilConstructor() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if tag is "Nil"
isNode() - Method in class uk.ac.bbk.dcs.automed.hdmstore.Span
  Is this Span a node?
isNull() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedType
  Is this type a null value?
isNum() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if the Cell contains a double
isObject() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
isObject() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
isObject() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
isObject() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
isOutput() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
isPrimaryKeyForeignKey() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
isPrimaryKeyForeignKey(Schema, SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns whether a foreign-key field SchemaObject is also a primary-key.
isRedundant(Transformation) - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Determines whether or not the transformation and the given tran are redundant, e.g., two transformations are redundant if they transform the same schema object and their action is the opposite of the other (add/delete, extend/contract, etc.).
isRelated(SchemaObject, SchemaObject[], SemanticRelationship, boolean) - Method in class uk.ac.ic.doc.automed.matching.Integrator
isReturn - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
isRoot - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
isRoot() - Method in class uk.ac.ic.doc.automed.reps.Node
  True if (and only if) this node belongs to a directed network and this is a root node.
isRoot() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Returns whether or not the construct is a construct of its underlying model.
isRoot() - Method in class uk.ac.bbk.dcs.automed.graph.TreeNode
isSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
isSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
isSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
isSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
isSchemaDataSource(int) - Static method in class uk.ac.ic.doc.automed.STR
  Determines whether or not the specified schema represents a data source.
isSchemaExtDB(int) - Static method in class uk.ac.ic.doc.automed.STR
  Determines whether or not the specified schema represents an extensional database.
isSchemaExtSchema(int) - Static method in class uk.ac.ic.doc.automed.STR
  Determines whether or not the specified schema is an extensional schema.
isScheme() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if tag is scheme
isSet() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
isSpecial() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if tag is special
isString - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRAINTS
isString - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.FUNCTION
isString() - Method in class uk.ac.ic.doc.automed.reps.Scheme
  Determine if this `Scheme` defines a `String`, rather than a reference to some other `SchemaObject`
isString() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
isString() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
isString() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
isString() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
isStronger(SemanticRelationship) - Method in class uk.ac.ic.doc.automed.matching.relationships.SemanticRelationship
isSysVariable() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if tag is sysvariable
isTempARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
isTextNode(Node) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Returns true if node n is a text node, false otherwise
isTree() - Method in class uk.ac.ic.doc.automed.reps.Network
isUndefined() - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformationRecord
isValidMethId(int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  This method determines if a method with the specified `meth_id` exists in the SMR.
isValidStId(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  This method determines if a statement with the specified `st_id` exists in the TTSR.
isValidTransId(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  This method determines if a composite transformation with the specified `trans_id` exists in the TTR.
isVariable() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if tag is variable
isWellformed() - Method in class uk.ac.ic.doc.automed.reps.Pathway
isYattaModelandSource(Object[]) - Static method in class uk.ac.ic.doc.automed.editor.PatternWritingTool
itemGotFocus(InputItem) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
itemPosition(InputItem) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm

## J

JSomClusterer - class uk.ac.ic.doc.automed.matching.modules.JSomClusterer.
JSomClusterer(ElementVectorRepresentation[]) - Constructor for class uk.ac.ic.doc.automed.matching.modules.JSomClusterer
JSomClusterer(int) - Constructor for class uk.ac.ic.doc.automed.matching.modules.JSomClusterer
justDragged - Variable in class uk.ac.ic.doc.automed.templates.gui.DrawingObject

## K

keywords - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token

## L

l() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns a reference to the left child of the Cell
lambda - Static variable in class uk.ac.bbk.dcs.automed.qproc.Cell
Lambda - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
Lambda - Static variable in class uk.ac.bbk.dcs.automed.qproc.FSym
LArrow - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
LAST - Static variable in class uk.ac.ic.doc.automed.editor.MatchingTool
lastArgumentPosition - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
lastCharKeyword - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
lastConstructKeyword - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
lastKeyword - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
lastModelKeyword - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
lastSchema - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
lastSchemaKeyword - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
lastSchemeKeyword - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
lastTransformationKeyword - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
layDownAllInputItems() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
layoutContainer(Container) - Method in class uk.ac.ic.doc.automed.editor.PinBoardLayout
LCB - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
LDAB - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
LDAB - Static variable in class uk.ac.bbk.dcs.automed.qproc.FSym
LEFT_ARROW_ICON - Static variable in class uk.ac.ic.doc.automed.templates.gui.Accessories
leftBrace - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
leftBracket - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
Less - class uk.ac.bbk.dcs.automed.qproc.functions.Less.
Less() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Less
LessEqual - class uk.ac.bbk.dcs.automed.qproc.functions.LessEqual.
LessEqual() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.LessEqual
LESSTHAN - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
LESSTHANEQUAL - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
Let - class uk.ac.bbk.dcs.automed.qproc.functions.Let.
Let - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
Let() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Let
line - Variable in class uk.ac.ic.doc.automed.editor.GUITool
Line - class uk.ac.ic.doc.automed.gui.Line.
Line() - Constructor for class uk.ac.ic.doc.automed.gui.Line
link - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
link_nodal - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
list - Variable in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
LIST - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TConstants
LIST_ICON - Static variable in class uk.ac.ic.doc.automed.templates.gui.Accessories
LIST_SCHEMA_LONG - Static variable in class uk.ac.ic.doc.automed.reps.Schema
  Constant used to indicate where schemes in schemas must be listed with all details, including the OBID as returned by `SchemaObject.getOBID()` SchemaObject}, and the `Construct` as returned by `SchemaObject.getConstruct()`.
LIST_SCHEMA_NORMAL - Static variable in class uk.ac.ic.doc.automed.reps.Schema
  Constant used to indicate where schemes in schemas must be listed with all the type of each `SchemaObject` prefixing the scheme of each object.
LIST_SCHEMA_SHORT - Static variable in class uk.ac.ic.doc.automed.reps.Schema
  Constant used to indicate where schemes in schemas must be listed with the minimum of detail.
LIST_TYPE - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TConstants
listArgSeq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
listNodes() - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Want to display all the nodes so pass just a wildcard as a the pattern
listNodes(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  List the instance nodes of the passed nodeType (or wildcard)
listOfSchemes() - Method in class uk.ac.bbk.dcs.automed.qproc.ASG
  Returns a list of the schemes used in the ASG as String objects.
listOfSchemes(ASG) - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  Returns a list of the schemes used in the ASG as String objects.
listSchema() - Method in class uk.ac.ic.doc.automed.reps.Schema
  List the Schema to the current output in a form designed for human interpretation.
listSchema(PrintStream) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Shorthand for calling listSchema(out,LIST_SCHEMA_NORMAL)
listSchema(PrintStream, int) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Shorthand for calling listSchema(out,LIST_SCHEMA_NORMAL,false)
listSchema(PrintStream, int, boolean) - Method in class uk.ac.ic.doc.automed.reps.Schema
  List the Schema to an output stream, using the specified format.
listSchemaHelp - Static variable in class uk.ac.ic.doc.automed.editor.Editor
listSchemaSyntax - Static variable in class uk.ac.ic.doc.automed.editor.Editor
listScroller - Variable in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
listTransformationPathway() - Method in class uk.ac.bbk.dcs.automed.xml.XMLTransformer
  Prints out the transformation pathway created by the schema transformation algorithm.
load(Schema) - Method in class uk.ac.ic.doc.automed.gui.SchemaManager
  Loads the schema specified into this SchemaManager.
loadBrowseWindow() - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool
LoadDialog - class uk.ac.ic.doc.automed.gui.LoadDialog.
LoadDialog - class uk.ac.ic.doc.automed.templates.gui.LoadDialog.
LoadDialog(Frame, String, boolean) - Constructor for class uk.ac.ic.doc.automed.gui.LoadDialog
LoadDialog(Frame, String, boolean) - Constructor for class uk.ac.ic.doc.automed.templates.gui.LoadDialog
loadedSchemas - Variable in class uk.ac.ic.doc.automed.templates.gui.SchemaFrame
LoadListFromFile - class uk.ac.bbk.dcs.automed.qproc.functions.LoadListFromFile.
LoadListFromFile() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.LoadListFromFile
loadPatternWindow(String) - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool
loadSchema(int) - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
loadSchema(int) - Method in interface uk.ac.ic.doc.automed.templates.gui.InteractiveSchemaDisplay
loadSchema(Schema) - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
LONG_TOKEN - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
longValue() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedInteger
  Return the value of this AutoMedInteger as an long
loopStatementsStack - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
lowerBound - Static variable in class uk.ac.bbk.dcs.automed.qproc.QueryReformulator
LowLevelWrapperHdm - class uk.ac.bbk.dcs.automed.hdmstore.LowLevelWrapperHdm.
  The LowLevelWrapperHdm passes queries to the `HdmStore` and returns the results in the HDM specifc format of a Linked List of `EdgeElements` each representing a tuple.
LowLevelWrapperHdm(HdmStore) - Constructor for class uk.ac.bbk.dcs.automed.hdmstore.LowLevelWrapperHdm
  The constructor is passed the `HdmStore` to be used
LRB - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
LRB - Static variable in class uk.ac.bbk.dcs.automed.qproc.FSym
LSB - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym

## M

main(String[]) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
main(String[]) - Static method in class uk.ac.ic.doc.automed.DSR
  Provides a simple command line interface to enable the configuration file to be checked.
main(String[]) - Static method in class uk.ac.ic.doc.automed.MDR
  Executing this class invokes this method which supplies a command line interface to the MDR.
main(String[]) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
main(String[]) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
main(String[]) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
main(String[]) - Static method in class uk.ac.ic.doc.automed.STR
main(String[]) - Static method in class uk.ac.ic.doc.automed.SSMDR
main(String[]) - Static method in class uk.ac.ic.doc.automed.STRMethodTest
main(String[]) - Static method in class uk.ac.ic.doc.automed.reps.SchemaMapGenerator
main(String[]) - Static method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
main(String[]) - Static method in class uk.ac.ic.doc.automed.editor.PatternWritingTool
main(String[]) - Static method in class uk.ac.ic.doc.automed.editor.Gui
main(String[]) - Static method in class uk.ac.ic.doc.automed.editor.Editor
main(String[]) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
main(String[]) - Static method in class uk.ac.ic.doc.automed.gui.SchemaTool
main(String[]) - Static method in class uk.ac.ic.doc.automed.templates.gui.SchemaFrame
main(String[]) - Static method in class uk.ac.ic.doc.automed.templates.gui.Run
main(String[]) - Static method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStoreCmd
  main creates an HdmStoreCmd and passes the arguments
mainPanel - Variable in class uk.ac.ic.doc.automed.templates.gui.SchemaFrame
mainTemplate - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
makeIdentifierSafe(String) - Static method in class uk.ac.ic.doc.automed.reps.Syntax
makeQuery(String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
makeStringSafe(String) - Static method in class uk.ac.ic.doc.automed.reps.Syntax
makeUpdate(String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
Map - class uk.ac.bbk.dcs.automed.qproc.functions.Map.
Map() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Map
MapDisplay - class uk.ac.ic.doc.automed.matching.modules.MapDisplay.
MapDisplay(Map, Vectors) - Constructor for class uk.ac.ic.doc.automed.matching.modules.MapDisplay
  Creates new form MapDisplay
match(Schema) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Return a array of two Schemas, which are formed by extending two conformed schemes such that they are identical.
MatchingTool - class uk.ac.ic.doc.automed.editor.MatchingTool.
MatchingTool(Schema, Schema) - Constructor for class uk.ac.ic.doc.automed.editor.MatchingTool
materialiseSchema(Document) - Method in class uk.ac.bbk.dcs.automed.xml.DOMMaterialiser
Max - class uk.ac.bbk.dcs.automed.qproc.functions.Max.
MAX_CHARS - Static variable in class uk.ac.ic.doc.automed.matching.modules.StatisticsModule
Max() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Max
MDR - class uk.ac.ic.doc.automed.MDR.
  Properties used from the MDR data source
MDR_DataSourceName - Static variable in class uk.ac.ic.doc.automed.MDR
MDR() - Constructor for class uk.ac.ic.doc.automed.MDR
MDRException - exception uk.ac.ic.doc.automed.MDRException.
  The class of exceptions generated by `MDR`.
MDRException(String) - Constructor for class uk.ac.ic.doc.automed.MDRException
Member - class uk.ac.bbk.dcs.automed.qproc.functions.Member.
Member() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Member
merge(Hashtable, Hashtable) - Static method in class uk.ac.ic.doc.automed.matching.SimilarSchemaElementPair
mergeSchemas() - Method in class uk.ac.ic.doc.automed.matching.SQLIntegrator
mergeSchemas() - Method in class uk.ac.ic.doc.automed.matching.Integrator
METHOD_PREFIX - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  A character that prefixes the method calls in the DEFINE_STRING statement.
METHOD_PREFIX - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
mimicThisCell(Cell) - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns an exact copy of the input Cell
Min - class uk.ac.bbk.dcs.automed.qproc.functions.Min.
Min() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Min
minimumLayoutSize(Container) - Method in class uk.ac.ic.doc.automed.editor.PinBoardLayout
Minus - class uk.ac.bbk.dcs.automed.qproc.functions.Minus.
Minus() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Minus
MINUTE - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedTime
  Granularity of one minute
model - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
model - Static variable in class uk.ac.bbk.dcs.automed.xml.XMLConstants
Model - class uk.ac.ic.doc.automed.reps.Model.
  The Model class
ModelDefinitionsRepository - class uk.ac.ic.doc.automed.ModelDefinitionsRepository.
ModelDefinitionsRepository() - Constructor for class uk.ac.ic.doc.automed.ModelDefinitionsRepository
ModelDefinitionsRepositoryException - exception uk.ac.ic.doc.automed.ModelDefinitionsRepositoryException.
ModelDefinitionsRepositoryException(String) - Constructor for class uk.ac.ic.doc.automed.ModelDefinitionsRepositoryException
ModelingProgram - class uk.ac.ic.doc.automed.reps.ModelingProgram.
  Class representing the graphical representation of a Construct.
ModelingProgram() - Constructor for class uk.ac.ic.doc.automed.reps.ModelingProgram
  Constructs a new, empty ModelingProgram
ModelingStatement - class uk.ac.ic.doc.automed.reps.ModelingStatement.
  Class that defines the statement/method-call that can be used in a construct's graphical representation.
ModelingStatement(String) - Constructor for class uk.ac.ic.doc.automed.reps.ModelingStatement
  Constructs a new ModelingStatement.
modelName - Variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
ModifiedArray - class uk.ac.bbk.dcs.automed.qproc.functions.ModifiedArray.
ModifiedArray() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.ModifiedArray
ModifiedArray(Cell) - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.ModifiedArray
Monus - class uk.ac.bbk.dcs.automed.qproc.functions.Monus.
Monus() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Monus
monus(ModifiedArray, ModifiedArray) - Static method in class uk.ac.bbk.dcs.automed.qproc.functions.Utilities
mouseClicked(MouseEvent) - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
mouseClicked(MouseEvent) - Method in class uk.ac.ic.doc.automed.gui.SchemaCanvas
mouseDragged(MouseEvent) - Method in class uk.ac.ic.doc.automed.gui.SchemaCanvas
mouseEntered(MouseEvent) - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
mouseEntered(MouseEvent) - Method in class uk.ac.ic.doc.automed.gui.SchemaCanvas
mouseExited(MouseEvent) - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
mouseExited(MouseEvent) - Method in class uk.ac.ic.doc.automed.gui.SchemaCanvas
mouseMoved(MouseEvent) - Method in class uk.ac.ic.doc.automed.gui.SchemaCanvas
mousePressed(MouseEvent) - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
mousePressed(MouseEvent) - Method in class uk.ac.ic.doc.automed.gui.SchemaCanvas
mouseReleased(MouseEvent) - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
mouseReleased(MouseEvent) - Method in class uk.ac.ic.doc.automed.gui.SchemaCanvas
msg(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.Debug
  Write a normal level message
msg(String, int) - Method in class uk.ac.bbk.dcs.automed.hdmstore.Debug
  Write a message, severity level is a parameter
MULTI - Static variable in class uk.ac.ic.doc.automed.editor.UserActionClass
Multiply - class uk.ac.bbk.dcs.automed.qproc.functions.Multiply.
Multiply() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Multiply
multiply(AutoMedFloat) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedFloat
  Return the multiplication of two AutoMedFloats.
multiply(AutoMedInteger) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedInteger
  Return the multiplication of two AutoMedIntegers.
multiply(BidirectionalDegree) - Method in class uk.ac.ic.doc.automed.matching.BidirectionalDegree
my(TemplateCompilerSimulator.NAME) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
myArgument - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.ITEM
myCompiler - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.ITEM
mySchemaObject - Variable in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
myStatements - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
myTrans - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
myType - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument

## N

NaiveBayesModule - class uk.ac.ic.doc.automed.matching.modules.NaiveBayesModule.
NaiveBayesModule(ArrayList, ArrayList) - Constructor for class uk.ac.ic.doc.automed.matching.modules.NaiveBayesModule
name - Variable in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
NAME - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TConstants
NAME - Variable in class uk.ac.ic.doc.automed.matching.relationships.Subsumption
NAME - Variable in class uk.ac.ic.doc.automed.matching.relationships.Overlapness
NAME - Variable in class uk.ac.ic.doc.automed.matching.relationships.Incompatibility
NAME - Variable in class uk.ac.ic.doc.automed.matching.relationships.Equivalence
NAME - Variable in class uk.ac.ic.doc.automed.matching.relationships.Disjointness
name() - Method in class uk.ac.bbk.dcs.automed.hdmstore.Edge
  Get the edge name
nameDimensions - Variable in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
names - Variable in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
nestList - Static variable in class uk.ac.bbk.dcs.automed.xml.XMLConstants
Network - class uk.ac.ic.doc.automed.reps.Network.
NETWORK_ADDED - Static variable in class uk.ac.ic.doc.automed.reps.NetworkChangeEvent
NETWORK_MERGED - Static variable in class uk.ac.ic.doc.automed.reps.NetworkChangeEvent
NETWORK_REMOVED - Static variable in class uk.ac.ic.doc.automed.reps.NetworkChangeEvent
NETWORK_SPLIT - Static variable in class uk.ac.ic.doc.automed.reps.NetworkChangeEvent
Network(Schema[][]) - Constructor for class uk.ac.ic.doc.automed.reps.Network
  Constructs a directed network from the schema paths supplied.
Network(String, Schema[][]) - Constructor for class uk.ac.ic.doc.automed.reps.Network
  Constructs a directed network from the schema paths supplied.
Network(String, Schema[][], boolean, boolean) - Constructor for class uk.ac.ic.doc.automed.reps.Network
  Constructs a network from the schema paths supplied.
networkAdded(NetworkChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.NetworksListener
networkAdded(NetworkChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
NetworkChangeEvent - class uk.ac.ic.doc.automed.reps.NetworkChangeEvent.
NetworkChangeEvent(int, Object) - Constructor for class uk.ac.ic.doc.automed.reps.NetworkChangeEvent
NetworkChangeListener - interface uk.ac.ic.doc.automed.reps.NetworkChangeListener.
networkMerged(NetworkChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.NetworkChangeListener
networkMerged(NetworkChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
networkRemoved(NetworkChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.NetworkChangeListener
networkRemoved(NetworkChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.NetworksListener
networkRemoved(NetworkChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
NetworksListener - interface uk.ac.ic.doc.automed.reps.NetworksListener.
networkSplit(NetworkChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.NetworkChangeListener
networkSplit(NetworkChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
NEW_OBJECT_STATEMENT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Statement to create new objects
NEW_SCHEMA_Y_OFFSET - Static variable in class uk.ac.ic.doc.automed.reps.Schema
  Default distance to place a new schema created by a transformation from the schema it is created from
newapplyExtendTransformation(Construct, String, String, String) - Method in class uk.ac.ic.doc.automed.reps.Schema
newAutoMedSchema(String) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Returns the `Schema` that represents in the datasource in terms of `SchemaObject`s in an AutoMed oriented manner.
newAutoMedWrapper(AccessMethod) - Static method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Deprecated. use getAutoMedWrapper(am) instead
newAutoMedWrapper(AccessMethod, String) - Static method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Deprecated. use getAutoMedWrapper
newAutoMedWrapper(String, String, String, String, String, AutoMedWrapperFactory) - Static method in class uk.ac.ic.doc.automed.wrappers.TransactSQLWrapper
  Create an AutoMed `Schema` containing `SchemaObject`s that represent a database, in such a form that queries on that schema can be mapped by executeQuery in the query lanuage of the database.
newAutoMedWrapper(String, String, String, String, String, AutoMedWrapperFactory) - Static method in class uk.ac.ic.doc.automed.wrappers.OracleWrapper
  Create an AutoMed `Schema` containing `SchemaObject`s that represent a database, in such a form that queries on that schema can be mapped by executeQuery in the query lanuage of the database.
newAutoMedWrapper(String, String, String, String, String, AutoMedWrapperFactory) - Static method in class uk.ac.ic.doc.automed.wrappers.PostgresWrapper
  Create an AutoMed `Schema` containing `SchemaObject`s that represent a database, in such a form that queries on that schema can be mapped by executeQuery in the query lanuage of the database.
newAutoMedWrapper(String, String, String, String, String, AutoMedWrapperFactory) - Static method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
  Create an AutoMed `Schema` containing `SchemaObject`s that represent a database, in such a form that queries on that schema can be mapped by executeQuery in the query lanuage of the database.
newAutoMedWrapper(String, String, String, String, String, AutoMedWrapperFactory) - Static method in class uk.ac.bbk.dcs.automed.xml.wrappers.SAXWrapper
newAutoMedWrapper(String, String, String, String, String, AutoMedWrapperFactory) - Static method in class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapper
newInconsistentException(String, Exception) - Static method in class uk.ac.ic.doc.automed.InconsistentException
  Create a new InconsistentException only if necessary.
newInput(TemplateCompilerSimulator.ITEM) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
newNameARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
newObjectArgSeq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
newScope() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
next_token() - Method in class uk.ac.bbk.dcs.automed.qproc.EnvLexer
next_token() - Method in class uk.ac.bbk.dcs.automed.qproc.QLexer
next_token() - Method in class uk.ac.bbk.dcs.automed.qproc.FLexer
next() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedResult
  Returns true if the cursor can be moved to a next row
nextStatement(TStatement) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
NilOptimiser - class uk.ac.bbk.dcs.automed.qproc.optimise.NilOptimiser.
NilOptimiser() - Constructor for class uk.ac.bbk.dcs.automed.qproc.optimise.NilOptimiser
NO_EXT - Static variable in class uk.ac.ic.doc.automed.gui.Rhombus
nodal - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
Node - class uk.ac.ic.doc.automed.reps.Node.
NODE_ADDED - Static variable in class uk.ac.ic.doc.automed.reps.NetworkChangeEvent
NODE_REMOVED - Static variable in class uk.ac.ic.doc.automed.reps.NetworkChangeEvent
node() - Method in class uk.ac.bbk.dcs.automed.hdmstore.EdgeElement
  is this element a node?
nodeAdded(NetworkChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.NetworkChangeListener
nodeAdded(NetworkChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
nodeExists(Span) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  For the node instance specifed in the `Span` data structure check if it exists in the HDM store
nodeExists(String, String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  For the node instance specifed by node type & value, check if it exists in the HDM store
nodeRemoved(NetworkChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.NetworkChangeListener
nodeRemoved(NetworkChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
nodeSpan - Static variable in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
nodeTypeExists(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Check whether any instances of this node type are currently stored in the HDM store
NodeUtility - class uk.ac.bbk.dcs.automed.xml.NodeUtility.
  Implements useful operation on nodes.
NodeUtility() - Constructor for class uk.ac.bbk.dcs.automed.xml.NodeUtility
nodeValue() - Method in class uk.ac.bbk.dcs.automed.hdmstore.EdgeElement
  get the nodeValue
NONE - Static variable in class uk.ac.bbk.dcs.automed.hdmstore.Debug
NONSCALAR_COMPOUND_KEY - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
NORMAL - Static variable in class uk.ac.bbk.dcs.automed.hdmstore.Debug
Not - class uk.ac.bbk.dcs.automed.qproc.functions.Not.
NOT - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
NOT_EQUAL - Static variable in class uk.ac.ic.doc.automed.IntegrityException
  Exception caused by an operation doing some sort comparison where .
Not() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Not
NotEqual - class uk.ac.bbk.dcs.automed.qproc.functions.NotEqual.
NOTEQUAL - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
NotEqual() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.NotEqual
NotFoundException - exception uk.ac.ic.doc.automed.NotFoundException.
  A request has be made for details of an object where the object is not present in the repository
NotFoundException(String) - Constructor for class uk.ac.ic.doc.automed.NotFoundException
  Creates an NotFoundException when there has been no Exception that caused the error to discovered.
NotFoundException(String, Exception) - Constructor for class uk.ac.ic.doc.automed.NotFoundException
  Creates an NotFoundException when it is acting as a wrapper for other Exceptions.
NotImplementedException - exception uk.ac.ic.doc.automed.NotImplementedException.
  Some part of the AutoMed code that should present has not yet been implemented..
NotImplementedException() - Constructor for class uk.ac.ic.doc.automed.NotImplementedException
  Creates an NotImplementedException with no message
NotImplementedException(String) - Constructor for class uk.ac.ic.doc.automed.NotImplementedException
  Creates an NotImplementedException detailing what has not been implemented! .
NotOptimisableException - exception uk.ac.ic.doc.automed.tml.NotOptimisableException.
  A request for optimisatiing a pathway has been made where the pathway is not optimisable
NotOptimisableException(String) - Constructor for class uk.ac.ic.doc.automed.tml.NotOptimisableException
  Creates an NotOptimisableException when there has been no Exception that caused the error to discovered.
NotOptimisableException(String, Exception) - Constructor for class uk.ac.ic.doc.automed.tml.NotOptimisableException
  Creates an NotOptimisableException when it is acting as a wrapper for other Exceptions.
nul - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
NULL_CONSTRAINT - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  A feature option to model the null/notnull distinction as part of a column in any `Schema` the factory generates
NULL_STR - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedType
  String to use to represent null values
nullAction(Object[]) - Static method in class uk.ac.ic.doc.automed.editor.Gui
number - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
NumberInstancesModule - class uk.ac.ic.doc.automed.matching.modules.NumberInstancesModule.
NumberInstancesModule(ArrayList, ArrayList) - Constructor for class uk.ac.ic.doc.automed.matching.modules.NumberInstancesModule
numberOfElements() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
numberOfElements() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
numberOfElements() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
numberOfElements() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
numberOfElements(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement
numberOfElements(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.SchemeListStatement
numberOfElements(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement
numberOfElements(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatement
numberOfElements(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
numberOfElements(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
numberOfElements(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
numberOfElements(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
numberOfElements(TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
numberOfReturns - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
numberOfRowsInResultSet(ResultSet) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Given a result set - how many rows are in it?
numOfInstances() - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
NumToken - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
nval - Variable in class uk.ac.ic.doc.automed.reps.Syntax.Token

## O

obid - Variable in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
OBJECT - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TConstants
OBJECT_ADDED - Static variable in class uk.ac.ic.doc.automed.reps.SchemaChangeEvent
OBJECT_CHANGED - Static variable in class uk.ac.ic.doc.automed.reps.SchemaChangeEvent
OBJECT_HDISTANCE - Static variable in class uk.ac.ic.doc.automed.gui.SchemaManager
OBJECT_REMOVED - Static variable in class uk.ac.ic.doc.automed.reps.SchemaChangeEvent
OBJECT_VDISTANCE - Static variable in class uk.ac.ic.doc.automed.gui.SchemaManager
objectAdded(SchemaChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.SchemaChangeListener
objectAdded(SchemaChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
objectChanged(SchemaChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.SchemaChangeListener
objectChanged(SchemaChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
objectClicked(int, String) - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
objectMovedAt(DrawingObject, int, int) - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
objectRemoved(SchemaChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.SchemaChangeListener
objectRemoved(SchemaChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
okButton - Variable in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
okToAddEdge(Edge) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Given an `Edge` is it OK to add the edge e.g.
oldRetract() - Method in class uk.ac.ic.doc.automed.reps.Schema
openScheme - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
optimise() - Method in class uk.ac.ic.doc.automed.reps.Pathway
optimise(ASG) - Method in class uk.ac.bbk.dcs.automed.qproc.optimise.NilOptimiser
optimise(ASG) - Method in interface uk.ac.bbk.dcs.automed.qproc.optimise.Optimiser
optimise(boolean) - Method in class uk.ac.ic.doc.automed.reps.Pathway
optimise(boolean, PathwayOptimiserTool) - Method in class uk.ac.ic.doc.automed.reps.Pathway
optimise(Cell) - Method in class uk.ac.bbk.dcs.automed.qproc.optimise.NilOptimiser
optimise(Cell) - Method in interface uk.ac.bbk.dcs.automed.qproc.optimise.Optimiser
optimisePathway(Pathway) - Static method in class uk.ac.ic.doc.automed.tml.PathwayOptimiser
optimisePathway(Pathway, boolean) - Static method in class uk.ac.ic.doc.automed.tml.PathwayOptimiser
optimisePathway(Pathway, boolean, PathwayOptimiserTool) - Static method in class uk.ac.ic.doc.automed.tml.PathwayOptimiser
Optimiser - interface uk.ac.bbk.dcs.automed.qproc.optimise.Optimiser.
OPTION_SCHEMA_NAME - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapper
  An option key setting, the value of which should be the SQL schema which is the only one to be mapped in this wrapping
OPTIONAL - Static variable in class uk.ac.ic.doc.automed.editor.CommandLineDriver
OpToken - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
Or - class uk.ac.bbk.dcs.automed.qproc.functions.Or.
OR - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
  SQL logical OR binary operator for use within WHERE expressions
Or() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Or
OracleWrapper - class uk.ac.ic.doc.automed.wrappers.OracleWrapper.
  A lower level wrapper for the conforming to the AutoMed SQL high level wrapper for Oracle SQL databases.
OracleWrapper(AccessMethod, String) - Constructor for class uk.ac.ic.doc.automed.wrappers.OracleWrapper
  Generate a new wrapper instance from information held in the repository about how to access a data source.
OracleWrapperFactory - class uk.ac.ic.doc.automed.wrappers.OracleWrapperFactory.
  A lower level wrapper factory for Oracle SQL databases conforming to the AutoMed SQL high level wrapper factory.
OracleWrapperFactory() - Constructor for class uk.ac.ic.doc.automed.wrappers.OracleWrapperFactory
outerMostVariables - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
outputs - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
overFunction(double) - Method in class uk.ac.ic.doc.automed.matching.BidirectionalDegree
Overlapness - class uk.ac.ic.doc.automed.matching.relationships.Overlapness.
overlaps - Variable in class uk.ac.ic.doc.automed.matching.Integrator
owner - Variable in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher

## P

p - Variable in class uk.ac.ic.doc.automed.editor.DrawVertex
  The underlying `Positionable` that this `Drawable` instace is representing
p - Variable in class uk.ac.ic.doc.automed.editor.DrawArc
paint(Graphics) - Method in class uk.ac.ic.doc.automed.gui.ToolTip
paint(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkArc
  Modify the basic drawing of arcs to set the arc colour based on the foreground colour of the first positionable connected
paint(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalArc
  Choose the colour to be that which the first connected Positionable is drawn in
paint(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.DrawVertex
paint(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.DrawArc
paint(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawConstraintArc
paint(Graphics2D) - Method in interface uk.ac.ic.doc.automed.editor.Drawable
paint(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.drawables.YattaDrawSequence
  Modify the basic drawing of arcs to set the arc colour based on the foreground colour of the first positionable connected
paint(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.drawables.YattaDrawLinkNodalLink
  Draw a Yatta Arc by linking all parents to child
paintArcs(Graphics2D) - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
paintChildren(Graphics) - Method in class uk.ac.ic.doc.automed.editor.EditorPanel
paintChildren(Graphics) - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
paintComponent(Graphics) - Method in class uk.ac.ic.doc.automed.gui.SchemaCanvas
paintComponent(Graphics) - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
paintIcon(Component, Graphics, int, int) - Method in class uk.ac.ic.doc.automed.gui.ArrowIcon
paintSpecificShapes(Graphics) - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
paintSymbol(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkVertex
paintSymbol(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.DrawVertex
paintSymbol(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalVertex
  Draw a circle to represent the attribute vertex
paintSymbol(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawNodalVertex
  Replace the paintSymbol method of `DrawVertex` with one that draws a rectangle rather that a oval.
paintSymbol(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawConstraintVertex
  Draw a rounded box to represent a constraint
paintText(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.DrawVertex
paintText(Graphics2D) - Method in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalVertex
panelsOfSchemas - Variable in class uk.ac.ic.doc.automed.templates.gui.SchemaFrame
parent - Variable in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
parentStatement() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
parseFile(String, boolean) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Parses the input file and returns its DOM representation
password - Variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
PATH - Static variable in class uk.ac.ic.doc.automed.editor.UserActionClass
path() - Method in class uk.ac.bbk.dcs.automed.hdmstore.Edge
  Get the edge value as a path of spans
Pathway - class uk.ac.ic.doc.automed.reps.Pathway.
  The Pathway class
PathwayOptimiser - class uk.ac.ic.doc.automed.tml.PathwayOptimiser.
PathwayOptimiser() - Constructor for class uk.ac.ic.doc.automed.tml.PathwayOptimiser
PathwayOptimiserTool - class uk.ac.ic.doc.automed.editor.PathwayOptimiserTool.
  A PathwayOptimiserTool instance provides a dialog box displaying the result of running pathway optimisation on the given pathway.
PathwayOptimiserTool(Schema[]) - Constructor for class uk.ac.ic.doc.automed.editor.PathwayOptimiserTool
Pattern - class uk.ac.ic.doc.automed.ssd.Pattern.
  The Pattern class represents a pattern of a semistructured datasource in regular expression.
Pattern(int) - Constructor for class uk.ac.ic.doc.automed.ssd.Pattern
Pattern(String, String) - Constructor for class uk.ac.ic.doc.automed.ssd.Pattern
PatternRule - class uk.ac.bbk.dcs.automed.qproc.optimise.PatternRule.
PatternRule(String, String) - Constructor for class uk.ac.bbk.dcs.automed.qproc.optimise.PatternRule
patterns - Variable in class uk.ac.ic.doc.automed.matching.modules.Clusterer
patternSize - Variable in class uk.ac.ic.doc.automed.matching.modules.Clusterer
PatternWritingTool - class uk.ac.ic.doc.automed.editor.PatternWritingTool.
PatternWritingTool.DynamicTree - class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree.
PatternWritingTool.DynamicTree() - Constructor for class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree
PatternWritingTool(Schema) - Constructor for class uk.ac.ic.doc.automed.editor.PatternWritingTool
pcdata - Static variable in class uk.ac.bbk.dcs.automed.xml.XMLConstants
perform(Cell[], Evaluator) - Method in interface uk.ac.bbk.dcs.automed.qproc.BuiltInFunction
  Returns a Cell object that is the root of a graph that represents the result of applying the built-in function to the arguments args.
perform(Cell[], Evaluator) - Method in class uk.ac.ic.doc.automed.wrappers.ssdfunctions.generateId
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Flatmap
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Foldr
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.BagIntersect
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Monus
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Foldl
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Equals
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Comprehension
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Sort
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.LessEqual
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Minus
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.SortDistinct
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.And
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Not
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Member
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.GreaterEqual
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.SubBag
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.LoadListFromFile
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Count
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Less
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Group
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.CallToWrapper
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Plus
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Sum
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.If
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Multiply
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Id
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Append
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.SetUnion
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Single
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.First
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Let
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Or
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Greater
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Map
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.GroupCompute
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.NotEqual
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Min
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Second
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Difference
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Average
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Divide
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Max
perform(Cell[], Evaluator) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.Disjunction
PinBoardLayout - class uk.ac.ic.doc.automed.editor.PinBoardLayout.
PinBoardLayout(Map, Map) - Constructor for class uk.ac.ic.doc.automed.editor.PinBoardLayout
pks - Variable in class uk.ac.ic.doc.automed.matching.SQLRelationshipExtractor
Plus - class uk.ac.bbk.dcs.automed.qproc.functions.Plus.
Plus() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Plus
populateDatabaseId(char, int) - Method in class uk.ac.bbk.dcs.automed.hdmstore.Span
  Populate the id of the span in the database
populateEdgeValue(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.Span
  Populate specific values for an edge
populateNodeValue(String, String, String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.Span
  Populate specific values for a node
populateSchema(AutoMedWrapper) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Read the metadata from the wrapper connection, and store in existing Schema within the wrapper.
populateSchema(AutoMedWrapper) - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
populateSchema(AutoMedWrapper) - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapperFactory
  Read the metadata from the wrapper connection, and store in the Schema and SSDFormat within the wrapper.
populateSchema(AutoMedWrapper) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.SAXWrapperFactory
populateSchema(AutoMedWrapper) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.DOMWrapperFactory
populateSchema(AutoMedWrapper) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapperFactory
POPUP_ICON - Static variable in class uk.ac.ic.doc.automed.templates.gui.Accessories
popUpArgumentValues(TTemplateInputArgument[]) - Method in class uk.ac.ic.doc.automed.templates.gui.TemplateInputDialogue
popupSchema(Schema) - Static method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
position - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
Positionable - interface uk.ac.ic.doc.automed.editor.Positionable.
PostgresWrapper - class uk.ac.ic.doc.automed.wrappers.PostgresWrapper.
  A lower level wrapper for the conforming to the AutoMed SQL high level wrapper for Postgres SQL databases.
PostgresWrapper(AccessMethod, String) - Constructor for class uk.ac.ic.doc.automed.wrappers.PostgresWrapper
  Generate a new wrapper instance from information held in the repository about how to access a data source.
PostgresWrapperFactory - class uk.ac.ic.doc.automed.wrappers.PostgresWrapperFactory.
  A lower level wrapper factory for Postgres SQL databases conforming to the AutoMed SQL high level wrapper factory.
PostgresWrapperFactory() - Constructor for class uk.ac.ic.doc.automed.wrappers.PostgresWrapperFactory
PrecisionModule - class uk.ac.ic.doc.automed.matching.modules.PrecisionModule.
PrecisionModule(ArrayList, ArrayList) - Constructor for class uk.ac.ic.doc.automed.matching.modules.PrecisionModule
preferredLayoutSize(Container) - Method in class uk.ac.ic.doc.automed.editor.PinBoardLayout
prefixAllNodalNames(String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Create a new Schema which contains the same set of constructs as an existing, except each has been renamed to have a common prefix if it is of `Construct` type Nodal.
prefixSchemaObjectName(String, SchemaObject) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Create a new Schema if the `SchemaObject` is a Nodal object, where the SchemaObject has had a prefix applied to the node name,
preservesEq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
preservesEquivalence() - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Returns whether this CompositeTransformation preserves schema equivalence.
prettyPrint(Node) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Outputs the subtree with root n to System.out with identation, without any respect to the file's original identation
prettyPrint(Node, String) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Outputs the subtree with root n to System.out with identation, without any respect to the file's original identation.
previous() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedResult
  Returns true if the cursor can be moved back to a previous row
PRIMARY_KEY - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  A feature option to model primary keys in any `Schema` the factory generates
PRIMITIVE_TRANSFORMATION_STATEMENT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Statement to execute primitive transformations
primitiveArgSeq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
primitiveArgSeq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
primitiveArgSeq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
print() - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
print() - Method in class uk.ac.ic.doc.automed.tml.TempPathway
print() - Method in class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
print() - Method in class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
print() - Method in class uk.ac.ic.doc.automed.templates.TemplateArgument
print() - Method in class uk.ac.ic.doc.automed.templates.StatementExecution
print() - Method in class uk.ac.ic.doc.automed.templates.StatementArgumentDefinition
print() - Method in class uk.ac.ic.doc.automed.templates.Statement
print() - Method in class uk.ac.ic.doc.automed.templates.RuntimeArgumentSequence
print() - Method in class uk.ac.ic.doc.automed.templates.RuntimeArgument
print() - Method in class uk.ac.ic.doc.automed.matching.modules.MapDisplay
printDate(String) - Static method in class uk.ac.ic.doc.automed.matching.Util
printDocument(Document) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Outputs Document doc in System.out exactly as it is in the DOM.
printDocument(Document, File) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Outputs Document doc in File f exactly as it is in the DOM.
printElements() - Static method in class uk.ac.ic.doc.automed.matching.SchemaElement
printForest() - Method in class uk.ac.bbk.dcs.automed.graph.Forest
printGraph(DirectedGraph) - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraph
printNetworkHelp - Static variable in class uk.ac.ic.doc.automed.editor.Editor
printNetworkSyntax - Static variable in class uk.ac.ic.doc.automed.editor.Editor
printObject(Object, OutputStream) - Static method in class uk.ac.ic.doc.automed.Util
printObject(Object, Writer) - Static method in class uk.ac.ic.doc.automed.Util
printResultSet(ResultSet, OutputStream) - Static method in class uk.ac.ic.doc.automed.Util
printResultSet(ResultSet, Writer) - Static method in class uk.ac.ic.doc.automed.Util
printSQLFeedback(Object, OutputStream, String) - Static method in class uk.ac.ic.doc.automed.Util
printSQLFeedback(Object, Writer, String) - Static method in class uk.ac.ic.doc.automed.Util
printStackTrace() - Method in class uk.ac.ic.doc.automed.RepositoryAccessException
printStackTrace() - Method in class uk.ac.ic.doc.automed.reps.AutoRepException
printStackTrace() - Method in class uk.ac.ic.doc.automed.gui.GUIException
printStackTrace() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateDefinitionException
printTree(TreeNode, int) - Method in class uk.ac.bbk.dcs.automed.graph.Forest
process(ASG) - Method in class uk.ac.bbk.dcs.automed.qproc.FragmentProcessor
  Replaces schemes with wrapper objects in the given ASG
process(Cell) - Method in class uk.ac.bbk.dcs.automed.qproc.FragmentProcessor
  Replaces schemes with wrapper objects in the ASG with root n
processCommands() - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
processCommands(Reader, Writer) - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
processResultSet() - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
production_table() - Method in class uk.ac.bbk.dcs.automed.qproc.EnvParser
  Access to production table.
production_table() - Method in class uk.ac.bbk.dcs.automed.qproc.QParser
  Access to production table.
PROPERTY_AUTOMED_SCHEMA - Static variable in class uk.ac.ic.doc.automed.reps.AccessMethod
  Name to give to a AccessMethod property to hold the name of an AutoMed oriented schema that was produced from the schema associated with this AccessMethod.
PROPERTY_CREATE_TIME - Static variable in class uk.ac.ic.doc.automed.reps.AccessMethod
  Name to give to a AccessMethod property for the time in milliseconds since 1 Jan 1970 that the datasource schema was created in the AutoMed repository.
protectIdentifier(String) - Static method in class uk.ac.ic.doc.automed.reps.Syntax
protectString(String) - Static method in class uk.ac.ic.doc.automed.reps.Syntax
protocol - Variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
Protocol - class uk.ac.ic.doc.automed.reps.Protocol.
  The Protocol class describes a generic method of accessing data sources, such as JDBC or ODBC.
protocolDOM - Static variable in class uk.ac.bbk.dcs.automed.xml.XMLConstants
protocolSAX - Static variable in class uk.ac.bbk.dcs.automed.xml.XMLConstants

## Q

QLexer - class uk.ac.bbk.dcs.automed.qproc.QLexer.
QLexer(InputStream) - Constructor for class uk.ac.bbk.dcs.automed.qproc.QLexer
QLexer(Reader) - Constructor for class uk.ac.bbk.dcs.automed.qproc.QLexer
QParser - class uk.ac.bbk.dcs.automed.qproc.QParser.
  CUP v0.10j generated parser.
QParser() - Constructor for class uk.ac.bbk.dcs.automed.qproc.QParser
  Default constructor.
QParser(Scanner) - Constructor for class uk.ac.bbk.dcs.automed.qproc.QParser
  Constructor which sets the default scanner.
QSym - class uk.ac.bbk.dcs.automed.qproc.QSym.
  CUP generated class containing symbol constants.
QSym() - Constructor for class uk.ac.bbk.dcs.automed.qproc.QSym
query(String, String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.LowLevelWrapperHdm
  The query is given in the form of an string and returned as a Linked List of `EdgeElement`'s
queryList - Variable in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
QueryReformulator - class uk.ac.bbk.dcs.automed.qproc.QueryReformulator.
  The class that goes through an ASG that applies to a global schema and reformulates the ASG so that it applies to all local schemas
QueryReformulator() - Constructor for class uk.ac.bbk.dcs.automed.qproc.QueryReformulator
QueryReformulator(Schema, Schema[]) - Constructor for class uk.ac.bbk.dcs.automed.qproc.QueryReformulator
QueryReformulator(Schema, Schema[], String) - Constructor for class uk.ac.bbk.dcs.automed.qproc.QueryReformulator
  Constructs a QueryReformulator object containing view definitions for the constructs of source in terms of the constructs of targets assuming the appropriate transformation pathways exist.
quitHelp - Static variable in class uk.ac.ic.doc.automed.editor.CommandLineDriver
quitSyntax - Static variable in class uk.ac.ic.doc.automed.editor.CommandLineDriver

## R

r() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns a reference to the right child of the Cell
random(int) - Static method in class uk.ac.ic.doc.automed.matching.Util
RCB - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
RDAB - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
RDAB - Static variable in class uk.ac.bbk.dcs.automed.qproc.FSym
read(InputStream) - Static method in class uk.ac.ic.doc.automed.reps.Schema
read(InputStream) - Static method in class uk.ac.ic.doc.automed.reps.Model
read(InputStream) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
read(InputStream, String) - Static method in class uk.ac.ic.doc.automed.reps.Schema
read(InputStream, String) - Static method in class uk.ac.ic.doc.automed.reps.Model
readConfigFile() - Static method in class uk.ac.ic.doc.automed.DSR
  Reads the current configuration file.
readConfigFile(String) - Static method in class uk.ac.ic.doc.automed.DSR
  Reads the directives for the data sources defined in configFile.
readMetaData() - Method in class uk.ac.ic.doc.automed.wrappers.YattaWrapper
readScheme(Schema, Construct, Syntax.Tokenizer) - Static method in class uk.ac.ic.doc.automed.reps.SchemaObject
readSchemeDefinition(Construct, String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Take a String containing the definition of a scheme of a SchemaObject and create an Object array that would be used in creating the SchemaObject
readSchemeRef(Syntax.Tokenizer) - Static method in class uk.ac.ic.doc.automed.reps.SchemaObject
readSchemeTokens(Syntax.Tokenizer) - Static method in class uk.ac.ic.doc.automed.reps.SchemaObject
reAssignPositions() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
reduce_table() - Method in class uk.ac.bbk.dcs.automed.qproc.EnvParser
  Access to `reduce_goto` table.
reduce_table() - Method in class uk.ac.bbk.dcs.automed.qproc.QParser
  Access to `reduce_goto` table.
reEvaluateRequiredNumberOfElements() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
referenceHasFinalised(int) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
reflectCommandMethods() - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
reformulate(ASG) - Method in class uk.ac.bbk.dcs.automed.qproc.QueryReformulator
  Reformulates the query represented by the ASG g according to the view defintions it has stored.
registerWrapper(Class, Protocol, String, String) - Static method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Register an AutoMedWrapper implementation with the AutoMed system.
REL_BETWEEN_ELEMENTS - Variable in class uk.ac.ic.doc.automed.matching.relationships.Subsumption
REL_BETWEEN_ELEMENTS - Variable in class uk.ac.ic.doc.automed.matching.relationships.Overlapness
REL_BETWEEN_ELEMENTS - Variable in class uk.ac.ic.doc.automed.matching.relationships.Incompatibility
REL_BETWEEN_ELEMENTS - Variable in class uk.ac.ic.doc.automed.matching.relationships.Equivalence
REL_BETWEEN_ELEMENTS - Variable in class uk.ac.ic.doc.automed.matching.relationships.Disjointness
RelationshipConflictException - exception uk.ac.ic.doc.automed.matching.RelationshipConflictException.
RelationshipConflictException() - Constructor for class uk.ac.ic.doc.automed.matching.RelationshipConflictException
RelationshipConflictException(String) - Constructor for class uk.ac.ic.doc.automed.matching.RelationshipConflictException
RelationshipConflictException(String, Throwable) - Constructor for class uk.ac.ic.doc.automed.matching.RelationshipConflictException
RelationshipExtractor - class uk.ac.ic.doc.automed.matching.RelationshipExtractor.
RelationshipExtractor() - Constructor for class uk.ac.ic.doc.automed.matching.RelationshipExtractor
RelationshipExtractorException - exception uk.ac.ic.doc.automed.matching.RelationshipExtractorException.
RelationshipExtractorException() - Constructor for class uk.ac.ic.doc.automed.matching.RelationshipExtractorException
RelationshipExtractorException(String) - Constructor for class uk.ac.ic.doc.automed.matching.RelationshipExtractorException
RelationshipExtractorException(String, Throwable) - Constructor for class uk.ac.ic.doc.automed.matching.RelationshipExtractorException
RelationshipExtractorException(Throwable) - Constructor for class uk.ac.ic.doc.automed.matching.RelationshipExtractorException
RelativeEuclideanClassifier - class uk.ac.ic.doc.automed.matching.modules.RelativeEuclideanClassifier.
RelativeEuclideanClassifier(Cluster[]) - Constructor for class uk.ac.ic.doc.automed.matching.modules.RelativeEuclideanClassifier
reloadComponents() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
reloadModels() - Static method in class uk.ac.ic.doc.automed.reps.Model
  This method empties the cached model data and then reloads it from the MDR as if the class had just been loaded.
reloadSchemas() - Static method in class uk.ac.ic.doc.automed.reps.Schema
remove() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Remove the `SchemaObject` form the repository.
remove() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Removes the Construct from the repository if it is not being used, and removes all the construct's Scheme elements.
remove() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Removes the Schema from the repository.
remove() - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Remove this AccessMethod from the repository.
remove() - Method in class uk.ac.ic.doc.automed.reps.ConstructWithModelingProgram
  Removes this ConstructWithModelingProgram object.
remove() - Method in class uk.ac.ic.doc.automed.reps.Protocol
remove() - Method in class uk.ac.ic.doc.automed.reps.Model
  Removes the Model from the repository.
remove() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Removes this `Transformation` from the repository.
remove() - Method in class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
  Removes this TransformationArgumentDefinition from the TTR.
remove() - Method in class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
  Removes this TemplateArgumentSequence.
remove() - Method in class uk.ac.ic.doc.automed.templates.TemplateArgument
  Removes this TemplateArgument from the TTR.
remove() - Method in class uk.ac.ic.doc.automed.templates.StatementExecution
  Removes this StatementExecution from the TTR.
remove() - Method in class uk.ac.ic.doc.automed.templates.StatementArgumentDefinition
  Removes this StatementArgumentDefinition from the TTSR.
remove() - Method in class uk.ac.ic.doc.automed.templates.Statement
  Removes this Statement
remove() - Method in class uk.ac.ic.doc.automed.templates.RuntimeArgumentSequence
  Removes this RuntimeArgumentSequence.
remove() - Method in class uk.ac.ic.doc.automed.templates.RuntimeArgument
  Removes this RuntimeArgument from the TER.
remove() - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Removes this CompositeTransformation
remove(int) - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Removes the stamement at the specified program counter in this program.
remove(int) - Static method in class uk.ac.ic.doc.automed.reps.Protocol
  Removes the protocol with the given protocol PID.
remove(String) - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Removes the Schema with the given schemaName.
remove(String) - Static method in class uk.ac.ic.doc.automed.reps.Protocol
  Removes the protocol with the given protocolName.
removeAccessMethod(int) - Static method in class uk.ac.ic.doc.automed.STR
  Removes an access method from the STR.
removeAccessMethodBySID(int) - Static method in class uk.ac.ic.doc.automed.STR
  Removes all access methods for the given schema identifier (SID).
removeAccessMethods() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Remove all `AccessMethod`s recorded for this schema.
removeAllItems() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
removeAllSchemes(int) - Static method in class uk.ac.ic.doc.automed.STR
  Removes all the schemes associated with the given schema object.
removeArgument(int) - Method in class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
  Removes a particular argument from this TemplateArgumentSequence.
removeArgument(int) - Method in class uk.ac.ic.doc.automed.templates.RuntimeArgumentSequence
  Removes a particular argument from this RuntimeArgumentSequence.
removeArgument(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Removes a particular position from a sequence of arguments
removeArgument(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Removes a particular position from a sequence of arguments
removeArgumentDefinition(int) - Method in class uk.ac.ic.doc.automed.templates.Statement
  Removes a particular argument definition from this Statements's argument definition list.
removeArgumentDefinition(int) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Removes a particular argument definition from this CompositeTransformation's argument definition list.
removeArguments(int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Removes a particular sequence of arguments
removeArguments(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Removes a particular sequence of arguments
removeArgumentSequences() - Method in class uk.ac.ic.doc.automed.gui.SchemaTool
removeAssociationBySFID(int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Removes all associations for the given ssdformat identifier (SFID).
removeCompositeTransformation(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Removes a composite transformation from the TTR `comp_transformations` table
removeCompositeTransformation(String) - Static method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Removes a CompositeTransformation
removeCompositeTransformationDefinition(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Removes all arguments definitions of a particular composite transformation
removeCompositeTransformationDefinition(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Removes a particular position of a transformation's sequence of arguments
removeCompositeTransformationExecution(int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Removes a template transformation's execution
removeCompositeTransformationExecution(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Removes a particular program counter of a template transformation's execution
removeCompositeTransformationInvocation(int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Removes a composite transformation's invocation
removeCompositeTransformationProgram(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Removes a particular template transformation's program
removeCompositeTransformationProgram(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Removes a particular program counter of a transformation's template program
removeCompositeTransformationReturnedValuesArgumentDefinition(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Removes a composite transformation returned values definition
removeConstruct(int) - Static method in class uk.ac.ic.doc.automed.MDR
  Remove the construct.
removeConstructFromMap(Construct) - Static method in class uk.ac.ic.doc.automed.reps.Construct
  Deprecated. Remove constructs using @link remove() which will also do the job of this method Removes from the HashMap that holds the CID and ref to all Construct objs.
removeConstructFromMap(String) - Method in class uk.ac.ic.doc.automed.reps.Model
  THIS METHOD DOESN'T DO ANYTHING AT THE MOMENT Sets the content of a particular position of the model's constructs list.
removeConstructModelingProgram(int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Removes a particular construct's modeling program
removeConstructModelingProgram(int, int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Removes a particular program counter of a constrcut's modeling program
removeConstructScheme(int, int) - Static method in class uk.ac.ic.doc.automed.MDR
  Remove the construct.
removeCurrentNode(DefaultMutableTreeNode) - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree
  Remove the currently selected node.
removeDuplicates(ModifiedArray) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.SortDistinct
removeDuplicates(SchemaElementPair[]) - Method in class uk.ac.ic.doc.automed.matching.Integrator
removeDuplicates(SchemaElementPairRelationship[]) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
removeExecutionTrace(int, Vector) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Removes the trace of a composite transformation's executionfrom the TER.
removeFromScope(TemplateCompilerSimulator.ITEM) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
removeHighlights(JTextComponent) - Method in class uk.ac.ic.doc.automed.editor.PatternWritingTool
  /* Methods to highlight text in the textarea /
removeItem(InputItem) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
removeLayoutComponent(Component) - Method in class uk.ac.ic.doc.automed.editor.PinBoardLayout
removeMethod(int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Removes the method from the SMR `methods` table.
removeMethodArgument(int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Removes all arguments of a particular method
removeMethodArgument(int, int) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Removes a particular position of a methods's arguments
removeModel(int) - Static method in class uk.ac.ic.doc.automed.MDR
  Remove the modelling language.
removeModel(String) - Static method in class uk.ac.ic.doc.automed.reps.Model
  Removes the Model with the given modelName.
removeModelingProgram() - Method in class uk.ac.ic.doc.automed.reps.ConstructWithModelingProgram
  Remove the ModelingProgram from this Construct.
removeNetworkChangeListener(NetworkChangeListener) - Method in class uk.ac.ic.doc.automed.reps.Network
removeNetworksListener(NetworksListener) - Static method in class uk.ac.ic.doc.automed.reps.Network
removePattern(int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Removes a pattern from the SSMDR.
removeProtocol(int) - Static method in class uk.ac.ic.doc.automed.STR
  Removes the name of a protocol from the STR.
removeReturnedArgumentsDefinition() - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Removes the definitions of this transformation's returned arguments.
removeRuntimeArgumentSequence(int) - Static method in class uk.ac.ic.doc.automed.templates.RuntimeArgumentSequence
  Removes a RuntimeArgumentSequence.
removeSchema(int) - Static method in class uk.ac.ic.doc.automed.STR
  Removes a schema from the STR.
removeSchemaChangeListener(SchemaChangeListener) - Method in class uk.ac.ic.doc.automed.reps.Schema
removeSchemaObject(int) - Static method in class uk.ac.ic.doc.automed.STR
  Removes a schema object from the STR.
removeSchemaObject(SchemaObject, SchemaObject[]) - Method in class uk.ac.ic.doc.automed.matching.SQLIntegrator
removeSchemaObjects() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Removes all schema objects that belong to the schema, i.e., the schema's `SchemaObject` list is emptied.
removeSchemasListener(SchemasListener) - Static method in class uk.ac.ic.doc.automed.reps.Schema
removeScheme(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Removes a particular position of an object's scheme from the STR.
removeSSDFormat(int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Removes a ssd format from the SSMDR.
removeStatement(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Removes the statement from the TTSR `statements` table.
removeStatement(String) - Static method in class uk.ac.ic.doc.automed.templates.Statement
  Removes a Statement
removeStatementDefinition(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Removes all arguments definitions of a particular statement
removeStatementDefinition(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Removes a particular position of a statement's sequence of arguments
removeStatementExecution(int) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Removes a particular statement execution from this CompositeTransformations's template program
removeTemplateArgumentSequence(int) - Static method in class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
  Removes a TemplateArgumentSequence.
removeTransformation(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Removes a transformation from the STR.
removeTransformation(String, String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Removes the transformation between two given schemas.
removeVertex(HDMElement) - Method in class uk.ac.ic.doc.automed.reps.HDMEdge
RemovingStatement - class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement.
RemovingStatement() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
rename - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
RENAME(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT
RENAME(TemplateCompilerSimulator.NAME) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT
RenameStatement - class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement.
RenameStatement() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
repaint() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
repaint(Graphics, boolean) - Method in class uk.ac.ic.doc.automed.gui.SchemaManager
repair(boolean) - Static method in class uk.ac.ic.doc.automed.STR
  Perform some operators to repair the STR repository after it has become corrupt.
replace(String, String) - Static method in class uk.ac.ic.doc.automed.Util
  Returns a new string resulting from replacing all occurences of `substring` in string `s` with `\` followed by `substring`.
replaceAllSchemaRefs(ASG, Schema) - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  Replaces all references to Schemas within g by references to s.
replaceNullSchemaRefs(ASG, Schema) - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  Replaces all references to a null Schema object in g with references to s.
reportClick() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
reportDragging() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
ReportException - class uk.ac.ic.doc.automed.editor.ReportException.
  A Window to display a Java Exception.
ReportException() - Constructor for class uk.ac.ic.doc.automed.editor.ReportException
reportException(Exception) - Static method in class uk.ac.ic.doc.automed.editor.GUITool
reportException(String, Exception) - Static method in class uk.ac.ic.doc.automed.editor.GUITool
ReportException(String, Exception) - Constructor for class uk.ac.ic.doc.automed.editor.ReportException
RepositoryAccessException - exception uk.ac.ic.doc.automed.RepositoryAccessException.
  The class of exceptions generated when executing updates and queries to TTSR, TTR, TER, SMR.
RepositoryAccessException(String) - Constructor for class uk.ac.ic.doc.automed.RepositoryAccessException
RepositoryAccessException(String, Exception) - Constructor for class uk.ac.ic.doc.automed.RepositoryAccessException
representsComprehension() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if the Cell is the root of an ASG representing a comprehension
representsGenerator() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if the Cell is the root of an ASG representing a generator
representsList() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if the Cell is the root of an ASG representing a list
representsPair() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if tag is "Tuple2"
representsSingleton() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
representsTuple() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns true if the Cell is the root of an ASG representing a Tuple
requestCancel() - Method in class uk.ac.ic.doc.automed.templates.gui.TemplateInputDialogue
requestFinish() - Method in class uk.ac.ic.doc.automed.templates.gui.TemplateInputDialogue
requestNext() - Method in class uk.ac.ic.doc.automed.templates.gui.TemplateInputDialogue
requestPrevious() - Method in class uk.ac.ic.doc.automed.templates.gui.TemplateInputDialogue
ReservedTokens - class uk.ac.bbk.dcs.automed.qproc.ReservedTokens.
ReservedTokens() - Constructor for class uk.ac.bbk.dcs.automed.qproc.ReservedTokens
resetArgumentSequence(TemplateArgumentSequence) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
reSetToolbars() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
resolveDisjoints() - Method in class uk.ac.ic.doc.automed.matching.SQLIntegrator
resolveNamingConflicts() - Method in class uk.ac.ic.doc.automed.matching.SQLIntegrator
resolveNamingConflicts() - Method in class uk.ac.ic.doc.automed.matching.Integrator
resolveOverlaps() - Method in class uk.ac.ic.doc.automed.matching.SQLIntegrator
resolveStructuralConflicts() - Method in class uk.ac.ic.doc.automed.matching.SQLIntegrator
resolveStructuralConflicts() - Method in class uk.ac.ic.doc.automed.matching.Integrator
resolveSubsumptions() - Method in class uk.ac.ic.doc.automed.matching.SQLIntegrator
resultingObject() - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
resultingSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement
resultingSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.SchemeListStatement
resultingSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement
resultingSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatement
resultingSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
resultingSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
resultingSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
resultingSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
resultingSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
resultList - Static variable in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
resultSetToArray(ResultSet) - Static method in class uk.ac.ic.doc.automed.Util
retract() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Removes the SchemaObject from the repository, and all other objects which depend upon it.
retract() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Removes the Construct from the repository, and all other objects which depend upon it.
retract() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Removes the Schema from the repository, together with any `SchemaObject`s left in the schema, and any `Transformation`s that link to this schema.
retract() - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Remove this AccessMethod, and any other classes that are dependent upon its existance.
retract() - Method in class uk.ac.ic.doc.automed.reps.Model
  Removes the Model from the repository, together with all associated information --- in particular all Constructs belonging to the model are removed, and hence all SchemaObjects, and hence all Transformations on those objects.
retract() - Method in class uk.ac.ic.doc.automed.reps.Transformation
retract(String) - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Removes any Schema with the given name from the repository, together with any `SchemaObject`s left in the schema, and any `Transformation`s that link to this schema.
retract(String) - Static method in class uk.ac.ic.doc.automed.ssd.SSDFormat
retract(String) - Static method in class uk.ac.ic.doc.automed.ssd.Pattern
returnGraph() - Method in class uk.ac.bbk.dcs.automed.qproc.functions.ModifiedArray
returnInternalSeperators(String) - Static method in class uk.ac.bbk.dcs.automed.hdmstore.Edge
  If commas that are not at the 'top level' have been removed, replace them e.g.
returnInternalSpaces(String) - Static method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStoreCmd
  Changeback any seperators within an edge thats a span to spaces
returnMAP - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
returnTag(String) - Method in class uk.ac.bbk.dcs.automed.qproc.ReservedTokens
reverseKeywords - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
reverseRelationshipPair(SchemaElementPairRelationship) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
reverseRelationshipPairs(SchemaElementPairRelationship[]) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
rewind() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedResult
Rhombus - class uk.ac.ic.doc.automed.gui.Rhombus.
Rhombus() - Constructor for class uk.ac.ic.doc.automed.gui.Rhombus
RIGHT_ARROW_ICON - Static variable in class uk.ac.ic.doc.automed.templates.gui.Accessories
rightBrace - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
rightBracket - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
rollback() - Method in class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement
rollback() - Method in class uk.ac.ic.doc.automed.templates.wrapper.SchemeListStatement
rollback() - Method in class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement
rollback() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatement
rollback() - Method in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
rollback() - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
rollback() - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
rollback() - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
rollback() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
rollback(CompositeTransformation) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
rollbackSTR(Vector) - Static method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Removes the trace of a composite transformation's execution for the STR.
root() - Method in class uk.ac.bbk.dcs.automed.qproc.ASG
  Returns the root of the ASG
rootNode - Variable in class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree
RRB - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
RRB - Static variable in class uk.ac.bbk.dcs.automed.qproc.FSym
RSB - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
Rule - interface uk.ac.bbk.dcs.automed.qproc.optimise.Rule.
Run - class uk.ac.ic.doc.automed.templates.gui.Run.
run() - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
Run() - Constructor for class uk.ac.ic.doc.automed.templates.gui.Run
RuntimeArgument - class uk.ac.ic.doc.automed.templates.RuntimeArgument.
  The class to create run-time (during a template composite transformation's execution) arguments
RuntimeArgument(int, int, String) - Constructor for class uk.ac.ic.doc.automed.templates.RuntimeArgument
  Constructs a new RuntimeArgument storing the specified value.
RuntimeArgument(int, String) - Constructor for class uk.ac.ic.doc.automed.templates.RuntimeArgument
  Constructs a new RuntimeArgument storing the specified value and creates a new sequence of arguments.
RuntimeArgumentSequence - class uk.ac.ic.doc.automed.templates.RuntimeArgumentSequence.
  The class to create run-time (during a template composite transformation's execution) argument sequences
RuntimeArgumentSequence() - Constructor for class uk.ac.ic.doc.automed.templates.RuntimeArgumentSequence
  Constructs a new RuntimeArgumentSequence without any RuntimeArgument objects

## S

s - Variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
safeNextToken() - Method in class uk.ac.ic.doc.automed.reps.Syntax.Tokenizer
safeSQLString(String) - Static method in class uk.ac.ic.doc.automed.Util
  Provide a version of a string that is safe to use in JDBC update statements.
sameScheme(SchemaObject) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Determines whether or not the scheme is the same as that of the given `SchemaObject`.
saveDegrees(String) - Method in class uk.ac.ic.doc.automed.matching.modules.AbstractModule
saveObjectPosition() - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
savePosition() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
saxDriver - Static variable in class uk.ac.bbk.dcs.automed.xml.XMLConstants
SAXWrapper - class uk.ac.bbk.dcs.automed.xml.wrappers.SAXWrapper.
  A lower level wrapper that conforms to the XMLWrapper class.
SAXWrapper(AccessMethod, String) - Constructor for class uk.ac.bbk.dcs.automed.xml.wrappers.SAXWrapper
SAXWrapperFactory - class uk.ac.bbk.dcs.automed.xml.wrappers.SAXWrapperFactory.
  A lower level wrapper factory for accessing XML files using SAX.
SAXWrapperFactory() - Constructor for class uk.ac.bbk.dcs.automed.xml.wrappers.SAXWrapperFactory
schema - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
Schema - class uk.ac.ic.doc.automed.reps.Schema.
  The Schema class represents a database schema as a set of `SchemaObject`s.
SCHEMA - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TConstants
SCHEMA_ADDED - Static variable in class uk.ac.ic.doc.automed.reps.SchemaChangeEvent
SCHEMA_AWARE - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  A feature option to model SQL schemas.
SCHEMA_MERGING - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
SCHEMA_NAME - Static variable in class uk.ac.ic.doc.automed.TemplateExecutionRepository
SCHEMA_REMOVED - Static variable in class uk.ac.ic.doc.automed.reps.SchemaChangeEvent
schema() - Method in class uk.ac.bbk.dcs.automed.qproc.SchemeInfo
  Returns the schema reference for this SchemeInfo object
schemaAdded(SchemaChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.SchemasListener
schemaAdded(SchemaChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
schemaARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
SchemaCanvas - class uk.ac.ic.doc.automed.gui.SchemaCanvas.
SchemaCanvas(Frame) - Constructor for class uk.ac.ic.doc.automed.gui.SchemaCanvas
SchemaCanvas(Frame, JScrollPane) - Constructor for class uk.ac.ic.doc.automed.gui.SchemaCanvas
SchemaChangeEvent - class uk.ac.ic.doc.automed.reps.SchemaChangeEvent.
SchemaChangeEvent(int, Positionable) - Constructor for class uk.ac.ic.doc.automed.reps.SchemaChangeEvent
SchemaChangeListener - interface uk.ac.ic.doc.automed.reps.SchemaChangeListener.
schemaDoc - Variable in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
SchemaElement - class uk.ac.ic.doc.automed.matching.SchemaElement.
SchemaElement(int, SchemaObject, boolean) - Constructor for class uk.ac.ic.doc.automed.matching.SchemaElement
SchemaElementPair - class uk.ac.ic.doc.automed.matching.SchemaElementPair.
SchemaElementPair(SchemaElement, SchemaElement) - Constructor for class uk.ac.ic.doc.automed.matching.SchemaElementPair
SchemaElementPairRelationship - class uk.ac.ic.doc.automed.matching.SchemaElementPairRelationship.
SchemaElementPairRelationship(SchemaElement, SchemaElement, SemanticRelationship) - Constructor for class uk.ac.ic.doc.automed.matching.SchemaElementPairRelationship
SchemaFrame - class uk.ac.ic.doc.automed.templates.gui.SchemaFrame.
SchemaFrame() - Constructor for class uk.ac.ic.doc.automed.templates.gui.SchemaFrame
SchemaManager - class uk.ac.ic.doc.automed.gui.SchemaManager.
SchemaManager(GraphicCanvas) - Constructor for class uk.ac.ic.doc.automed.gui.SchemaManager
SchemaMapGenerator - class uk.ac.ic.doc.automed.reps.SchemaMapGenerator.
SchemaMapGenerator() - Constructor for class uk.ac.ic.doc.automed.reps.SchemaMapGenerator
SchemaMatchingSQLWrapperFactory - class uk.ac.ic.doc.automed.wrappers.SchemaMatchingSQLWrapperFactory.
  An AutoMed high wrapper factory for creating `SQLWrapper` instances.
SchemaMatchingSQLWrapperFactory() - Constructor for class uk.ac.ic.doc.automed.wrappers.SchemaMatchingSQLWrapperFactory
  Constructor.
SchemaModelingRepository - class uk.ac.ic.doc.automed.SchemaModelingRepository.
SchemaModelingRepository() - Constructor for class uk.ac.ic.doc.automed.SchemaModelingRepository
SchemaModelingRepositoryException - exception uk.ac.ic.doc.automed.SchemaModelingRepositoryException.
  The class of exceptions generated by `TemplateTransformationSyntaxRepository`.
SchemaModelingRepositoryException(String) - Constructor for class uk.ac.ic.doc.automed.SchemaModelingRepositoryException
schemaName(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Given an HDM store name return the name of the schema it stores data for
SchemaObject - class uk.ac.ic.doc.automed.reps.SchemaObject.
  The SchemaObject class
SchemaPanel - class uk.ac.ic.doc.automed.templates.gui.SchemaPanel.
SchemaPanel() - Constructor for class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
SchemaPanel(Schema) - Constructor for class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
SchemaPanel(Schema, Component) - Constructor for class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
schemaPanelScroller - Variable in class uk.ac.ic.doc.automed.templates.gui.SchemaFrame
schemaRemoved(SchemaChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.SchemasListener
schemaRemoved(SchemaChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.SchemaChangeListener
schemaRemoved(SchemaChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
SchemasListener - interface uk.ac.ic.doc.automed.reps.SchemasListener.
SchemasNotIdenticalException - exception uk.ac.ic.doc.automed.reps.SchemasNotIdenticalException.
  This exception is generated when an attempt to join to transformation pathways via createIdentTransformation() fails due to the schemas' object schemes being different.
SchemasNotIdenticalException(Schema, Schema, SchemaObject[], SchemaObject[]) - Constructor for class uk.ac.ic.doc.automed.reps.SchemasNotIdenticalException
SchemaTool - class uk.ac.ic.doc.automed.gui.SchemaTool.
SchemaTool() - Constructor for class uk.ac.ic.doc.automed.gui.SchemaTool
SchemaTransformationRepository - class uk.ac.ic.doc.automed.SchemaTransformationRepository.
  Deprecated. Old name for the STR
SchemaTransformationRepository() - Constructor for class uk.ac.ic.doc.automed.SchemaTransformationRepository
  Deprecated.
SchemaTransformationRepositoryException - exception uk.ac.ic.doc.automed.SchemaTransformationRepositoryException.
  Old name for STRException
SchemaTransformationRepositoryException(String) - Constructor for class uk.ac.ic.doc.automed.SchemaTransformationRepositoryException
schemaUIDDoc - Variable in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
scheme - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
scheme - Static variable in class uk.ac.bbk.dcs.automed.qproc.Cell
scheme - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
Scheme - class uk.ac.ic.doc.automed.reps.Scheme.
  The Scheme class is used to described each element of the scheme of `SchemaObject`.
SCHEME_HDM_TYPE_C - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. HDM type of construct scheme - constraints
SCHEME_HDM_TYPE_MAXIMUM - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated.
SCHEME_HDM_TYPE_MINIMUM - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated.
SCHEME_HDM_TYPE_N1 - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. HDM type of construct scheme - new node at position 1
SCHEME_HDM_TYPE_N2 - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. HDM type of construct scheme - new node at position 2
SCHEME_HDM_TYPE_P1 - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. HDM type of construct scheme - pre-existing node at position 1
SCHEME_HDM_TYPE_P2 - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. HDM type of construct scheme - pre-existing node at position 2
SCHEME_LIST() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT
SCHEME_LIST(TemplateCompilerSimulator.OBJECT) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
SCHEME_TYPE_ALTERNATION - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Scheme type of construct scheme
SCHEME_TYPE_CONSTRUCT - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Scheme type of construct scheme
SCHEME_TYPE_MAXIMUM - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated.
SCHEME_TYPE_MINIMUM - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated.
SCHEME_TYPE_NAME - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Scheme type of construct scheme
SCHEME_TYPE_SEQUENCE - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Scheme type of construct scheme
scheme() - Method in class uk.ac.bbk.dcs.automed.qproc.SchemeInfo
  Returns the scheme for this SchemeInfo object as a string
Scheme(SchemaObject, int, SchemaObject, boolean, int, boolean) - Constructor for class uk.ac.ic.doc.automed.reps.Scheme
  Creates a new scheme for a schema object.
SchemeInfo - class uk.ac.bbk.dcs.automed.qproc.SchemeInfo.
  Class containing a scheme and the reference to the schema the scheme belongs to.
SchemeInfo(Schema, String) - Constructor for class uk.ac.bbk.dcs.automed.qproc.SchemeInfo
SchemeInfo(String) - Constructor for class uk.ac.bbk.dcs.automed.qproc.SchemeInfo
SchemeInfo(String, String) - Constructor for class uk.ac.bbk.dcs.automed.qproc.SchemeInfo
SchemeInstances - class uk.ac.ic.doc.automed.wrappers.SchemeInstances.
  Provides a representation of the data associated with a scheme in an AutoMed Schema.
SchemeInstances() - Constructor for class uk.ac.ic.doc.automed.wrappers.SchemeInstances
SCHEMELIST_STATEMENT - Static variable in class uk.ac.ic.doc.automed.templates.CompositeTransformation
SchemeListStatement - class uk.ac.ic.doc.automed.templates.wrapper.SchemeListStatement.
SchemeListStatement() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.SchemeListStatement
schemeObjects - Variable in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
schemePosnARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
SchemeQuery - class uk.ac.ic.doc.automed.wrappers.SchemeQuery.
  A generic representation of query expressions as trees, where each SchemeQuery has an operator type, and 0 or more fields that have a field type
SchemeQuery() - Constructor for class uk.ac.ic.doc.automed.wrappers.SchemeQuery
Second - class uk.ac.bbk.dcs.automed.qproc.functions.Second.
SECOND - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedTime
  Granularity of one minute
Second() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Second
SELECT - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
  The SQL SELECT operator; the first field should contain a SQLQuery with a FROM operator, and the remaining fields should be relation attribute identifiers
selectionModes - Variable in class uk.ac.ic.doc.automed.editor.UserActionClass
selectNewAutoMedWrapper(String, String, Protocol, String, String) - Static method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Using the url and driver information, try to select an appropriate type of AutoMedWrapper to create.
selectNewAutoMedWrapper(String, String, Protocol, String, String, String, AutoMedWrapperFactory) - Static method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Using the url and driver information, try to select an appropriate type of AutoMedWrapper to create.
selectPairs(ArrayList, ArrayList) - Method in class uk.ac.ic.doc.automed.matching.Integrator
selectPairs(ArrayList, SchemaElement[], int) - Method in class uk.ac.ic.doc.automed.matching.Integrator
self - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TStatement
SemanticException - exception uk.ac.ic.doc.automed.editor.SemanticException.
SemanticException(String, int) - Constructor for class uk.ac.ic.doc.automed.editor.SemanticException
SemanticRelationship - class uk.ac.ic.doc.automed.matching.relationships.SemanticRelationship.
SemanticRelationship() - Constructor for class uk.ac.ic.doc.automed.matching.relationships.SemanticRelationship
SemiColon - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
sequence - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
sequencesARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
sequencesArgSeq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
sequencesMAP - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
SET_ICON - Static variable in class uk.ac.ic.doc.automed.templates.gui.Accessories
set_l(Cell) - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Sets the reference to the left child of the Cell to n
set_r(Cell) - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Sets the reference to the left child of the Cell to n
set(int, ModelingStatement) - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Replaces the statement at the specified program counter in this program with the specified statement.
set(int, Pattern) - Method in class uk.ac.ic.doc.automed.matching.modules.Vectors
setAccessMethodAWFFeatures(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the AutoMedWrapperFactory featrures of a particular access method.
setAccessMethodDBDriver(int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the database driver of a particular access method.
setAccessMethodPassword(int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the password of a particular access method.
setAccessMethodPID(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the protocol identifier (PID) of a particular access method.
setAccessMethodProperty(int, String, String) - Static method in class uk.ac.ic.doc.automed.STR
setAccessMethodSID(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the schema identifier (SID) of a particular access method.
setAccessMethodURL(int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the URL of a particular access method.
setAccessMethodUsername(int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the username of a particular access method.
setAccessMethodWrapper(int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the wrapper of a particular access method.
setAddMissingNodes(boolean) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  If you try to add an instance of an edge then all the nodes and edges that are spans of the new edge must already exist in the database.
setArcDrawable(String) - Method in class uk.ac.ic.doc.automed.reps.Construct
  Sets the name of the class used to draw the arc of this `Construct` in any diagram containing it.
setArcHeight(int) - Method in class uk.ac.ic.doc.automed.gui.Box
setArcWidth(int) - Method in class uk.ac.ic.doc.automed.gui.Box
setArgConstruct(Construct) - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Sets the `Construct` in the `ConstructScheme`.
setArgument(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
setArgument(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.ITEM
setArgument(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRAINTS
setArgument(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.FUNCTION
setArgument(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
setArgument(TemplateArgumentSequence) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
setArgumentsArgIdRef(int, int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets an argument's `arg_id_ref` field
setArgumentsArgPosRef(int, int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets an argument's `arg_pos_ref` field
setArgumentSequence(TemplateArgumentSequence) - Method in class uk.ac.ic.doc.automed.templates.StatementExecution
  Sets the TemplateArgumentSequence of this StatementExecution
setArgumentsValue(int, int, String) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Sets an argument's `value` field
setArgumentsValue(int, int, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets an argument's `value` field
setAtomicPairRelationships(SchemaElementPairRelationship[]) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
setAttribute(int, AutoMedType) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTuple
  Set the value of a certain field
setAutoMedWrapperFactoryFeatures(int) - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Sets the password used for connecting to the database.
setBackgroundColor(Color) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
setBackgroundColor(Color) - Method in class uk.ac.ic.doc.automed.reps.Construct
  Set the default background colour to be used from drawing `SchemaObject`s of this `Construct`.
setBackgroundColor(Color) - Method in class uk.ac.ic.doc.automed.reps.Network
setBackgroundColor(Color) - Method in class uk.ac.ic.doc.automed.reps.Schema
setBackgroundColor(Color) - Method in class uk.ac.ic.doc.automed.reps.Model
  Set the default background colour to be used from drawing `SchemaObject`s of this `Model`.
setBackgroundColor(Color) - Method in interface uk.ac.ic.doc.automed.editor.Positionable
setBackwardDegree(double) - Method in class uk.ac.ic.doc.automed.matching.BidirectionalDegree
setBgColour(String) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setBgColour(String) - Method in class uk.ac.ic.doc.automed.gui.Box
setBgColour(String) - Method in class uk.ac.ic.doc.automed.gui.Arc
setBidirectionalDegrees(Hashtable, Hashtable) - Method in class uk.ac.ic.doc.automed.matching.modules.AbstractModule
setBlock(TStatement[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
setChildren(HashSet) - Method in class uk.ac.bbk.dcs.automed.graph.TreeNode
  Sets the children of the node.
setClassName(int, String) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Sets the class name of the method specified by `meth_id`
setCloseSchemeBracket(String) - Static method in class uk.ac.ic.doc.automed.STR
  Set the `String`that is used to close a scheme name, such as "<<person>>" or "<<person,name>>" By default it is set to ">>".``
setCommandClass(Class) - Static method in class uk.ac.ic.doc.automed.DSR
setCommandHelp(String[][]) - Static method in class uk.ac.ic.doc.automed.DSR
setCompiler(TemplateCompilerSimulator) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.ITEM
setCompositeTransformationDefinitionDescription(int, int, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets a particular transformation's argument definition (the `description` field).
setCompositeTransformationDefinitionFieldName(int, int, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets a particular transformation's argument definition (the `field_name` field).
setCompositeTransformationDefinitionIsReturnedValue(int, int, boolean) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets a particular transformation's argument type.
setCompositeTransformationDefinitionTableName(int, int, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets a particular transformation's argument definition (the `table_name` field).
setCompositeTransformationDescription(int, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets the description of the composite transformation specified by `trans_id`
setCompositeTransformationExecutionArgId(int, int, int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Sets the sequence of arguments identifier in a specific program counter in the composite transformation's execution
setCompositeTransformationExecutionStId(int, int, int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Sets the statement identifier in a specific program counter in the composite transformation's execution
setCompositeTransformationName(int, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets the name of the composite transformation specified by `trans_id`
setCompositeTransformationPreservesEquivalence(int, boolean) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets the `preserves equivalence` field of the composite transformation specified by `trans_id`
setCompositeTransformationProgramArgId(int, int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets the sequence of arguments ID in a specific program counter in the composite transformation's template program
setCompositeTransformationProgramStId(int, int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets the statement identifier in a specific program counter in the specified composite transformation's template program
setCompositeTransformationReturnedValuesDefinitionArgId(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets the sequence of arguments ID that defines the transformation's returned values.
setConcatenationOp(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
setConfigFileName(String) - Static method in class uk.ac.ic.doc.automed.DSR
  Sets the name of the file used for data source defintiions, this resets any data cached in the MDR or STR and invalidates all objects returned by them prior to this call.
setConstraintDefinition(String, String) - Method in class uk.ac.ic.doc.automed.reps.Construct
  Set the definition of a constraint used within this `Construct`.
setConstraints(HDMConstraint[]) - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
setConstraints(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
setConstraints(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
setConstraints(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
setConstraints(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
setConstruct(Construct) - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
setConstructClass(int) - Method in class uk.ac.ic.doc.automed.reps.Construct
  Sets the class of the construct.
setConstructClass(int, int) - Static method in class uk.ac.ic.doc.automed.MDR
setConstructConstraint(int, String, String) - Static method in class uk.ac.ic.doc.automed.MDR
setConstructMID(int, int) - Static method in class uk.ac.ic.doc.automed.MDR
  Changes the modelling language that a construct belongs to
setConstructModelingProgramMethod(int, int, String) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Sets the method in a specific program counter in the specified construct's modeling program
setConstructName(int, String) - Static method in class uk.ac.ic.doc.automed.MDR
setConstructProperty(int, int, String, Integer, String) - Static method in class uk.ac.ic.doc.automed.MDR
setConstructRoot(int, boolean) - Static method in class uk.ac.ic.doc.automed.MDR
setConstructSchemeArgCID(int, int, int) - Static method in class uk.ac.ic.doc.automed.MDR
setConstructSchemeHDMType(int, int, int) - Static method in class uk.ac.ic.doc.automed.MDR
setConstructSchemeKey(int, int, boolean) - Static method in class uk.ac.ic.doc.automed.MDR
setConstructSchemeLowerBound(int, int, int) - Static method in class uk.ac.ic.doc.automed.MDR
setConstructSchemeType(int, int, int) - Static method in class uk.ac.ic.doc.automed.MDR
setConstructSchemeUpperBound(int, int, int) - Static method in class uk.ac.ic.doc.automed.MDR
setConstructType(Construct) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Sets the construct type of the schema object.
setData(Object) - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Sets the Cell's data
setDataSource(boolean) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Sets whether or not the schema represents an external data source.
setDataSourceName(String) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Sets the name of the repository in the local database.
setDataSourceName(String) - Static method in class uk.ac.ic.doc.automed.MDR
  Sets the name of the repository in the local database.
setDataSourceName(String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets the name of the repository in the local database.
setDataSourceName(String) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Sets the name of the repository in the local database.
setDataSourceName(String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Sets the name of the repository in the local database.
setDataSourceName(String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the name of the Schema Transformation Repository in the local database.
setDataSourceName(String) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Sets the name of the SemiStructured MetaData Repository in the local database.
setDataType(int) - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
setDatatype(String, String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  The meta data for an HDM store is contained in the associated AutoMed schema except for the data type of the nodes in the schema which are set with this method (initially they default to String)
setDBDriver(String) - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Sets the database driver used for connecting to the database.
setDebugLevel(int) - Static method in class uk.ac.ic.doc.automed.STR
  Control the printing of debug information printed on the command line
setDebugLevel(int) - Static method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Set the debug level for all AutoMed wrappers.
setDefaultDataSource(String) - Static method in class uk.ac.ic.doc.automed.DSR
setDefaultModel() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
setDefaultUserName(String) - Static method in class uk.ac.ic.doc.automed.DSR
setDescription(String) - Method in class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
  Sets the description of this TransformationArgumentDefinition .
setDescription(String) - Method in class uk.ac.ic.doc.automed.templates.StatementArgumentDefinition
  Sets the description of this StatementArgumentDefinition.
setDescription(String) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Sets this CompositeTransformation's description.
setDescription(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
  Sets the description of the template transformation.
setDescription(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
setDialogueManager(TemplateInputDialogue) - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
setDialogueManager(TemplateInputDialogue) - Method in interface uk.ac.ic.doc.automed.templates.gui.InteractiveSchemaDisplay
setDialogueManager(TemplateInputDialogue) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
setEdges(HDMEdge[]) - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
setElements(HDMElement[]) - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
setElements(Map) - Method in class uk.ac.ic.doc.automed.editor.EditorPanel
setEnable(boolean) - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
setEndAggregation(boolean) - Method in class uk.ac.ic.doc.automed.gui.Line
setEndAngle(int) - Method in class uk.ac.ic.doc.automed.gui.Arc
setEndArrow(boolean) - Method in class uk.ac.ic.doc.automed.gui.Line
setEnvironment(Environment) - Method in class uk.ac.bbk.dcs.automed.qproc.Evaluator
setExistenceModule(AbstractModule) - Method in class uk.ac.ic.doc.automed.matching.DegreeCombinator
setExpression(String) - Method in class uk.ac.ic.doc.automed.reps.HDMConstraint
setExtDB(boolean) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Sets whether or not the schema represents an extentional database.
setExtend(int) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setExtSchema(boolean) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Sets whether or not the schema is an extentional schema.
setFeatures(int) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Allows certain features of the `Model` used for `Schema`s generated by this wrapper factory.
setFeatures(int) - Method in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  Allows certain features of the SQL92 data model to be represented in the AutoMed repository.
setFeatures(int[]) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Allows certain features of the `Model` used for `Schema`s generated by this wrapper factory.
setFgColour(String) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setFgColour(String) - Method in class uk.ac.ic.doc.automed.gui.Line
setFgColour(String) - Method in class uk.ac.ic.doc.automed.gui.Box
setFgColour(String) - Method in class uk.ac.ic.doc.automed.gui.Arc
setField(int, Object) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
  Return a field in the query node.
setFieldName(String) - Method in class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
  Sets the fieldname of this TransformationArgumentDefinition .
setFieldName(String) - Method in class uk.ac.ic.doc.automed.templates.StatementArgumentDefinition
  Sets the fieldname of this StatementArgumentDefinition.
setFocus(Point) - Method in class uk.ac.ic.doc.automed.gui.SchemaManager
setFontColour(String) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setFontColour(String) - Method in class uk.ac.ic.doc.automed.gui.Line
setFontColour(String) - Method in class uk.ac.ic.doc.automed.gui.Box
setFontColour(String) - Method in class uk.ac.ic.doc.automed.gui.Arc
setFontName(String) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setFontName(String) - Method in class uk.ac.ic.doc.automed.gui.Line
setFontName(String) - Method in class uk.ac.ic.doc.automed.gui.Box
setFontName(String) - Method in class uk.ac.ic.doc.automed.gui.Arc
setFontSize(int) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setFontSize(int) - Method in class uk.ac.ic.doc.automed.gui.Line
setFontSize(int) - Method in class uk.ac.ic.doc.automed.gui.Box
setFontSize(int) - Method in class uk.ac.ic.doc.automed.gui.Arc
setFontStyle(int) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setFontStyle(int) - Method in class uk.ac.ic.doc.automed.gui.Line
setFontStyle(int) - Method in class uk.ac.ic.doc.automed.gui.Box
setFontStyle(int) - Method in class uk.ac.ic.doc.automed.gui.Arc
setForeachTemplateSchema() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
setForegroundColor(Color) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
setForegroundColor(Color) - Method in class uk.ac.ic.doc.automed.reps.Construct
  Set the default foreground colour to be used from drawing `SchemaObject`s of this `Construct`.
setForegroundColor(Color) - Method in class uk.ac.ic.doc.automed.reps.Network
setForegroundColor(Color) - Method in class uk.ac.ic.doc.automed.reps.Schema
setForegroundColor(Color) - Method in class uk.ac.ic.doc.automed.reps.Model
  Set the default foreground colour to be used from drawing `SchemaObject`s of this `Model`.
setForegroundColor(Color) - Method in interface uk.ac.ic.doc.automed.editor.Positionable
setForwardDegree(double) - Method in class uk.ac.ic.doc.automed.matching.BidirectionalDegree
setFromSchema(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement
setFromSchema(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.SchemeListStatement
setFromSchema(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement
setFromSchema(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatement
setFromSchema(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
setFromSchema(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
setFromSchema(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
setFromSchema(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
setFromSchema(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
setFunction(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
setFunction(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
setFunction(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
setFunction(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
setGraphicManager(GraphicManager) - Method in class uk.ac.ic.doc.automed.gui.SchemaCanvas
setGraphics(Graphics) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setGraphics(Graphics) - Method in class uk.ac.ic.doc.automed.gui.Line
setGraphics(Graphics) - Method in class uk.ac.ic.doc.automed.gui.Box
setGraphics(Graphics) - Method in class uk.ac.ic.doc.automed.gui.Arc
setHdmStore(HdmStore) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapper
  Set the HdmStore that this wrapper will use
setHDMType(int) - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Sets the HDM type of the `ConstructScheme`.
setHeight(int) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setHeight(int) - Method in class uk.ac.ic.doc.automed.gui.Box
setHeight(int) - Method in class uk.ac.ic.doc.automed.gui.Arc
setHighlight(boolean) - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
setIndex(int) - Method in class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement
setInput(int, TType) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
setInput(String, String, Construct) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
setInput(String, String, Construct, int) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
setInput(String, String, Construct, TTemplateArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
setInput(String, String, int) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
setInput(String, String, int, int) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
setInput(String, String, int, TTemplateArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
setInstances(ArrayList) - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
setIsReturnedValue(boolean) - Method in class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
  Sets the isReturnedValue type of this TransformationArgumentDefinition.
setIterator(String, TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
setKey(boolean) - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Sets whether or not the current scheme position is part the key of the whole scheme.
setLabel(String) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
setLabel(String) - Method in class uk.ac.ic.doc.automed.reps.Network
setLabel(String) - Method in class uk.ac.ic.doc.automed.reps.Schema
setLabel(String) - Method in interface uk.ac.ic.doc.automed.editor.Positionable
setLabelPosition(int, int) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
setLabelPosition(int, int) - Method in class uk.ac.ic.doc.automed.reps.Network
setLabelPosition(int, int) - Method in class uk.ac.ic.doc.automed.reps.Schema
setLabelPosition(int, int) - Method in interface uk.ac.ic.doc.automed.editor.Positionable
setLabelXPos(int) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
setLabelXPos(int) - Method in class uk.ac.ic.doc.automed.reps.Network
setLabelXPos(int) - Method in class uk.ac.ic.doc.automed.reps.Schema
setLabelXPos(int) - Method in interface uk.ac.ic.doc.automed.editor.Positionable
setLabelYPos(int) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
setLabelYPos(int) - Method in class uk.ac.ic.doc.automed.reps.Network
setLabelYPos(int) - Method in class uk.ac.ic.doc.automed.reps.Schema
setLabelYPos(int) - Method in interface uk.ac.ic.doc.automed.editor.Positionable
setLayout(String) - Method in class uk.ac.ic.doc.automed.gui.Box
setLayoutAxis(String) - Method in class uk.ac.ic.doc.automed.gui.Box
setList(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement
setList(TArgument[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement
setListData(Object[]) - Method in class uk.ac.ic.doc.automed.gui.LoadDialog
setListData(Object[]) - Method in class uk.ac.ic.doc.automed.templates.gui.LoadDialog
setLocation(Point) - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
setLower(int) - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Sets the lower bound indicating the minimum occurence of the `ConstructScheme`.
setMDR_DataSourceName(String) - Static method in class uk.ac.ic.doc.automed.MDR
  Deprecated. use `setDataSourceName()` instead
setMethodArgumentsType(int, int, String) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Sets a particular method's argument type.
setMethodName(int, String) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
  Sets the name of the method specified by `meth_id`
setModel(Model) - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
  Sets the model of the template transformation.
setModelBaseName(String) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  Each implementing class gives a name for the `Model`s that will be generated for `Schema`s.
setModelingProgram(ModelingProgram) - Method in class uk.ac.ic.doc.automed.reps.ConstructWithModelingProgram
  Defines the graphical representation of this Construct.
setModelName(int, String) - Static method in class uk.ac.ic.doc.automed.MDR
setName(String) - Method in class uk.ac.ic.doc.automed.reps.HDMElement
setName(String) - Method in class uk.ac.ic.doc.automed.reps.Construct
  Sets the name of the construct to the given string.
setName(String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Set the name of a Schema.
setName(String) - Method in class uk.ac.ic.doc.automed.reps.Protocol
  Sets the name of the protocol to the given string.
setName(String) - Method in class uk.ac.ic.doc.automed.reps.Model
  Sets the model's name.
setName(String) - Method in class uk.ac.ic.doc.automed.templates.Statement
  Sets this Statement's name.
setName(String) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Sets this CompositeTransformation's name.
setName(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
  Sets the name of the template transformation.
setName(String) - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
setNameDimensions() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
setNewName(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
setNewName(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
setNewScope() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
setNodeLabels(Map) - Method in class uk.ac.ic.doc.automed.matching.modules.MapDisplay
  This method is called from within the constructor to initialize the form.
setNodes(HDMNode[]) - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
setNonAtomicPairRelationships(SchemaElementPairRelationship[]) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
setNumberInstancesModule(AbstractModule) - Method in class uk.ac.ic.doc.automed.matching.DegreeCombinator
setObject(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.SchemeListStatement
setObjectToRename(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
setObserver(Component) - Method in class uk.ac.ic.doc.automed.templates.gui.SchemaPanel
setObserver(Component) - Method in interface uk.ac.ic.doc.automed.templates.gui.InteractiveSchemaDisplay
setObserver(Component) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
setOpenCloseSchemeBracket(String, String) - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Set the `String`s that is used to open and close a scheme name, such as the "<<" and ">>" in "<<person>>" or "<<person,name>>".``
setOpenSchemeBracket(String) - Static method in class uk.ac.ic.doc.automed.STR
  Set the `String`that is used to open a scheme name, such as "<<person>>" or "<<person,name>>".``
setOption(String, String) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
  Make an option setting.
setOutput(int, TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
setOutput(String, String, TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
setOutputList(String, TStatementArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
setParent(SchemaPanel) - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
setParent(TreeNode) - Method in class uk.ac.bbk.dcs.automed.graph.TreeNode
  Sets the parent node.
setPassword(String) - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Sets the password used for connecting to the database.
setPatternToSchemaObject(SSDPattern, SchemaObject, int) - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
setPatternValue(int, String) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Sets the value of the pattern.
setPoint1(Point) - Method in class uk.ac.ic.doc.automed.gui.Line
setPoint2(Point) - Method in class uk.ac.ic.doc.automed.gui.Line
setPosition(int) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
setPosition(int, int) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
setPosition(int, int) - Method in class uk.ac.ic.doc.automed.reps.Network
setPosition(int, int) - Method in class uk.ac.ic.doc.automed.reps.Schema
setPosition(int, int) - Method in interface uk.ac.ic.doc.automed.editor.Positionable
setPrecisionModule(AbstractModule) - Method in class uk.ac.ic.doc.automed.matching.DegreeCombinator
setPreservesEquivalence(boolean) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Sets whether this CompositeTransformation preserves schema equivalence.
setProperty(String, String) - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Sets a property associated with this AccessMethod.
setProtocol(Protocol) - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Sets the protocol used for connecting to the database.
setProtocolName(int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the name of the protocol specified by the given protocol identifier (PID).
setRecord(CompositeTransformationRecord) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformationRecord
setReference(int) - Method in class uk.ac.ic.doc.automed.templates.TemplateArgument
  Sets the TemplateArgument to refer to the transformation's arguments.
setReference(TemplateArgument) - Method in class uk.ac.ic.doc.automed.templates.TemplateArgument
  Sets this TemplateArgument to refer to another TemplateArgument.
setReference(TemplateArgumentSequence, int) - Method in class uk.ac.ic.doc.automed.templates.TemplateArgument
  Sets this TemplateArgument to refer to the specified position in the specified TemplateArgumentSequence.
setReferencedArguments() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
setReferencedArguments(Vector) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
setRelationship(SemanticRelationship) - Method in class uk.ac.ic.doc.automed.matching.SchemaElementPairRelationship
setRelationships(SchemaElementPairRelationship[]) - Method in class uk.ac.ic.doc.automed.matching.Integrator
setRemovedObject(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
setReturnedArgumentsDefinition(TemplateArgumentSequence) - Method in class uk.ac.ic.doc.automed.templates.CompositeTransformation
  Sets the arguments that store returned values after the transformation's invocation.
setRoot(boolean) - Method in class uk.ac.ic.doc.automed.reps.Construct
  Sets whether or not the construct is a construct type of its underlying data model.
setRounded(boolean) - Method in class uk.ac.ic.doc.automed.gui.Box
setSchema(int, int) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Sets the SID for the ssd format.
setSchema(Schema) - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Sets the schema that represents the database to which the access method connects.
setSchema(Schema) - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
setSchema(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapper
  Set the value of the schema that this wrapper is for
setSchema(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
setSchemaBackgroundColor(int, int) - Static method in class uk.ac.ic.doc.automed.STR
setSchemaDataSource(int, boolean) - Static method in class uk.ac.ic.doc.automed.STR
  Sets whether or not a schema is a data source.
setSchemaExtDB(int, boolean) - Static method in class uk.ac.ic.doc.automed.STR
  Sets whether or not a schema is an extentional database.
setSchemaExtSchema(int, boolean) - Static method in class uk.ac.ic.doc.automed.STR
  Sets whether or not a schema is an extentional schema.
setSchemaForegroundColor(int, int) - Static method in class uk.ac.ic.doc.automed.STR
setSchemaLabelPos(int, int, int) - Static method in class uk.ac.ic.doc.automed.STR
setSchemaName(int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the name of schema.
setSchemaObjectBackgroundColor(int, int) - Static method in class uk.ac.ic.doc.automed.STR
setSchemaObjectCID(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the construct identifier (CID) of the schema object.
setSchemaObjectForegroundColor(int, int) - Static method in class uk.ac.ic.doc.automed.STR
setSchemaObjectLabelPos(int, int, int) - Static method in class uk.ac.ic.doc.automed.STR
setSchemaObjectPos(int, int, int) - Static method in class uk.ac.ic.doc.automed.STR
setSchemaObjectSID(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the schema identifier (SID) to which a particular schema object belongs.
setSchemaObjectTextColor(int, int) - Static method in class uk.ac.ic.doc.automed.STR
setSchemaObjectValue(int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the name/value of the schema object.
setSchemaPos(int, int, int) - Static method in class uk.ac.ic.doc.automed.STR
setSchemas(Schema[]) - Method in class uk.ac.ic.doc.automed.matching.SQLRelationshipExtractor
setSchemas(Schema[]) - Method in class uk.ac.ic.doc.automed.matching.RelationshipExtractor
setSchemas(Schema[]) - Method in class uk.ac.ic.doc.automed.matching.SQLIntegrator
setSchemas(Schema[]) - Method in class uk.ac.ic.doc.automed.matching.Integrator
setSchemaSubnetSID(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the subnet SID of a schema.
setSchemaTextColor(int, int) - Static method in class uk.ac.ic.doc.automed.STR
setScheme(Object[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
setSchemeObjects() - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
setSchemeSOBID(int, int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the referenced schema object in a specific position of the scheme of a schema object.
setSchemeType(int) - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Sets the scheme type of the `ConstructScheme`.
setScrollPane(JScrollPane) - Method in class uk.ac.ic.doc.automed.gui.SchemaCanvas
setSectionDebugLevel(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Set the level of debug info output to the console for a numbered section of code.
setShape(SchemaShape) - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
setShapeLocation(Point) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setShapeLocation(Point) - Method in class uk.ac.ic.doc.automed.gui.Box
setShapeLocation(Point) - Method in class uk.ac.ic.doc.automed.gui.Arc
setSimilarityDegree(double) - Method in class uk.ac.ic.doc.automed.matching.modules.SimilarCluster
setSmartQuoting(boolean) - Static method in class uk.ac.ic.doc.automed.reps.Syntax
setSSDFormatName(int, String) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Sets the name of ssd format.
setSSDPattern(SSDPattern) - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
setSSMDR_DataSourceName(String) - Static method in class uk.ac.ic.doc.automed.SSMDR
  Deprecated. use setDataSourceName()
setStartAggregation(boolean) - Method in class uk.ac.ic.doc.automed.gui.Line
setStartAngle(int) - Method in class uk.ac.ic.doc.automed.gui.Arc
setStartArrow(boolean) - Method in class uk.ac.ic.doc.automed.gui.Line
setStatement(Statement) - Method in class uk.ac.ic.doc.automed.templates.StatementExecution
  Sets the Statement of this StatementExecution.
setStatementDefinitionDescription(int, int, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Sets a particular statement's argument definition (the `description` field).
setStatementDefinitionFieldName(int, int, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Sets a particular statement's argument definition (the `field_name` field).
setStatementDefinitionTableName(int, int, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Sets a particular statement's argument definition (the `table_name` field).
setStatementName(int, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
  Sets the name of the statement specified by `st_id`
setStatementSequence(TStatement[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
setSTR_DataSourceName(String) - Static method in class uk.ac.ic.doc.automed.STR
  Deprecated. use setDataSourceName()
setString(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
setStyle(String) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setStyle(String) - Method in class uk.ac.ic.doc.automed.gui.Line
setStyle(String) - Method in class uk.ac.ic.doc.automed.gui.Box
setStyle(String) - Method in class uk.ac.ic.doc.automed.gui.Arc
setTableName(String) - Method in class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
  Sets the tablename of this TransformationArgumentDefinition .
setTableName(String) - Method in class uk.ac.ic.doc.automed.templates.StatementArgumentDefinition
  Sets the tablename of this StatementArgumentDefinition.
setText(String) - Method in class uk.ac.ic.doc.automed.editor.DrawVertex
  Set the text that will be used in this {link @Drawable}, and record its width and heigh in `textBounds`.
setText(String) - Method in class uk.ac.ic.doc.automed.gui.ToolTip
  Sets the text to be displayed by this ToolTip.
setText(String) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setText(String) - Method in class uk.ac.ic.doc.automed.gui.Line
setText(String) - Method in class uk.ac.ic.doc.automed.gui.Box
setText(String) - Method in class uk.ac.ic.doc.automed.gui.Arc
setTextColor(Color) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
setTextColor(Color) - Method in class uk.ac.ic.doc.automed.reps.Construct
  Set the default text colour to be used from drawing `SchemaObject`s of this `Construct`.
setTextColor(Color) - Method in class uk.ac.ic.doc.automed.reps.Network
setTextColor(Color) - Method in class uk.ac.ic.doc.automed.reps.Schema
setTextColor(Color) - Method in class uk.ac.ic.doc.automed.reps.Model
  Set the default text colour to be used from drawing `SchemaObject`s of this `Model`.
setTextColor(Color) - Method in interface uk.ac.ic.doc.automed.editor.Positionable
setTextLocation(String) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setTextLocation(String) - Method in class uk.ac.ic.doc.automed.gui.Line
setTextLocation(String) - Method in class uk.ac.ic.doc.automed.gui.Box
setTextLocation(String) - Method in class uk.ac.ic.doc.automed.gui.Arc
setTranAction(int, int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the action of a transformation between two schemas.
setTranConstraint(int, int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the constraint of a transformation between two schemas.
setTranFromObject(int, int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the object identifier (OBID) of the schema object to be transformed in a transformation
setTranFunction(int, int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the function of a transformation between two schemas.
setTranToObject(int, int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the object identifier (OBID) of the schema object as a result of a transformation.
setType(TType) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
setType(TType) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
setType(TType) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
setTypeInstance(int) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
setTypeInstance(int) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
setTypeInstance(int) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TArgument
SetUnion - class uk.ac.bbk.dcs.automed.qproc.functions.SetUnion.
SetUnion() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.SetUnion
setUpper(int) - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Sets the upper bound indicating the maximum occurence of the `ConstructScheme`.
setURL(String) - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Sets the URL of the database to which the access method connects.
setUsername(String) - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Sets the username used for connecting to the database.
setValue(String) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Sets the name/value of the schema object.
setValue(String) - Method in class uk.ac.ic.doc.automed.templates.TemplateArgument
  Sets the value of this TemplateArgument.
setValue(String) - Method in class uk.ac.ic.doc.automed.templates.RuntimeArgument
  Sets the value of this RuntimeArgument.
setValue(String) - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
setValue(String[]) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
setValue(TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
setVariable(String, TArgument) - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
setVertexDrawable(String) - Method in class uk.ac.ic.doc.automed.reps.Construct
  Sets the name of the class used to draw the vertex of this `Construct` in any diagram containing it.
setWidth(int) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
setWidth(int) - Method in class uk.ac.ic.doc.automed.gui.Box
setWidth(int) - Method in class uk.ac.ic.doc.automed.gui.Arc
setWrapper(String) - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Sets the wrapper asscociated with this.
setXPos(int) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
setXPos(int) - Method in class uk.ac.ic.doc.automed.reps.Network
setXPos(int) - Method in class uk.ac.ic.doc.automed.reps.Schema
setXPos(int) - Method in interface uk.ac.ic.doc.automed.editor.Positionable
setXPos(int) - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
setYPos(int) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
setYPos(int) - Method in class uk.ac.ic.doc.automed.reps.Network
setYPos(int) - Method in class uk.ac.ic.doc.automed.reps.Schema
setYPos(int) - Method in interface uk.ac.ic.doc.automed.editor.Positionable
setYPos(int) - Method in class uk.ac.ic.doc.automed.templates.gui.DrawingObject
show() - Method in class uk.ac.ic.doc.automed.gui.ToolTip
showDialog() - Method in class uk.ac.ic.doc.automed.gui.LoadDialog
showDialog() - Method in class uk.ac.ic.doc.automed.templates.gui.LoadDialog
SimilarCluster - class uk.ac.ic.doc.automed.matching.modules.SimilarCluster.
SimilarCluster(Cluster, double) - Constructor for class uk.ac.ic.doc.automed.matching.modules.SimilarCluster
SimilarSchemaElementPair - class uk.ac.ic.doc.automed.matching.SimilarSchemaElementPair.
SimilarSchemaElementPair(SchemaElementPair, BidirectionalDegree) - Constructor for class uk.ac.ic.doc.automed.matching.SimilarSchemaElementPair
SimilarSchemaElementPair(SchemaElement, SchemaElement, BidirectionalDegree) - Constructor for class uk.ac.ic.doc.automed.matching.SimilarSchemaElementPair
Single - class uk.ac.bbk.dcs.automed.qproc.functions.Single.
SINGLE - Static variable in class uk.ac.ic.doc.automed.editor.UserActionClass
SINGLE - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TConstants
SINGLE_ICON - Static variable in class uk.ac.ic.doc.automed.templates.gui.Accessories
Single() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Single
singleton() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns the root of an ASG representing an empty list
singletonsARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
singletonsArgSeq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
singletonsMAP - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
size() - Method in class uk.ac.ic.doc.automed.reps.Pathway
  Returns the number of `Schema`s in the pathway.
size() - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Returns the number of statements in this program.
size() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTuple
size() - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraph
size() - Method in class uk.ac.ic.doc.automed.tml.TempPathway
SIZEOF(TemplateCompilerSimulator.LIST) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
Sort - class uk.ac.bbk.dcs.automed.qproc.functions.Sort.
Sort() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Sort
sort(ModifiedArray) - Static method in class uk.ac.bbk.dcs.automed.qproc.functions.Utilities
SortDistinct - class uk.ac.bbk.dcs.automed.qproc.functions.SortDistinct.
SortDistinct() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.SortDistinct
SOURCE_PREFIX - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapperFactory
  String prefixed to AutoMed oriented Model names in order to obtain source oriented Model names.
source() - Method in class uk.ac.bbk.dcs.automed.qproc.QueryReformulator
  Returns the global schema
Span - class uk.ac.bbk.dcs.automed.hdmstore.Span.
  A Span represents one element in a HDM edge.
special - Static variable in class uk.ac.bbk.dcs.automed.qproc.Cell
SQL_MODEL_FOREIGN_KEY - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
SQL_MODEL_INDEX - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
SQL_MODEL_PRIMARY_KEY - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
SQL_MODEL_TABLE - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
  The name of the `Construct` used to represent SQL tables.
SQLIntegrator - class uk.ac.ic.doc.automed.matching.SQLIntegrator.
SQLIntegrator() - Constructor for class uk.ac.ic.doc.automed.matching.SQLIntegrator
SQLQuery - class uk.ac.ic.doc.automed.wrappers.SQLQuery.
  An SQLQuery expression tree that can be generated by the high level wrapper `SQLWrapper` and used by a low level wrapper as the basis for generating SQL queries on a relational database.
SQLQuery(AutoMedQueryToken, Object[]) - Constructor for class uk.ac.ic.doc.automed.wrappers.SQLQuery
SQLRelationshipExtractor - class uk.ac.ic.doc.automed.matching.SQLRelationshipExtractor.
SQLRelationshipExtractor() - Constructor for class uk.ac.ic.doc.automed.matching.SQLRelationshipExtractor
SQLResult - class uk.ac.ic.doc.automed.wrappers.SQLResult.
  Provides a representation of the data associated with a scheme in an AutoMed Schema.
SQLResult(int) - Constructor for class uk.ac.ic.doc.automed.wrappers.SQLResult
  return the instance of the scheme which the cursor currently points at, as an ArrayList of Objects.
SQLTranslator - class uk.ac.bbk.dcs.automed.wrappers.SQLTranslator.
SQLTranslator() - Constructor for class uk.ac.bbk.dcs.automed.wrappers.SQLTranslator
SQLWrapper - class uk.ac.ic.doc.automed.wrappers.SQLWrapper.
  An AutoMed high wrapper for connecting to SQL databases that have a JBDC driver.
SQLWrapper() - Constructor for class uk.ac.ic.doc.automed.wrappers.SQLWrapper
SQLWrapperFactory - class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory.
  An AutoMed high wrapper factory for creating `SQLWrapper` instances.
SQLWrapperFactory() - Constructor for class uk.ac.ic.doc.automed.wrappers.SQLWrapperFactory
SSDFormat - class uk.ac.ic.doc.automed.ssd.SSDFormat.
  The SSDFormat class represents a format of a particular semistructured datasource as a set of `SSDPattern`s.
SSDFormat(String) - Constructor for class uk.ac.ic.doc.automed.ssd.SSDFormat
SSDFunctionTable - class uk.ac.ic.doc.automed.wrappers.SSDFunctionTable.
SSDFunctionTable() - Constructor for class uk.ac.ic.doc.automed.wrappers.SSDFunctionTable
SSDPattern - class uk.ac.ic.doc.automed.ssd.SSDPattern.
  The SSDPattern class represents a pattern used in a particular `SSDFormat`.
SSDPattern(int) - Constructor for class uk.ac.ic.doc.automed.ssd.SSDPattern
SSDPattern(Pattern) - Constructor for class uk.ac.ic.doc.automed.ssd.SSDPattern
SSMDR - class uk.ac.ic.doc.automed.SSMDR.
  The SSMD library<<
SSMDR_DataSourceName - Static variable in class uk.ac.ic.doc.automed.SSMDR
SSMDR() - Constructor for class uk.ac.ic.doc.automed.SSMDR
SSMDRException - exception uk.ac.ic.doc.automed.SSMDRException.
  The class of exceptions generated by `SSMD`.
SSMDRException(String) - Constructor for class uk.ac.ic.doc.automed.SSMDRException
  Creates a SSMDException.
StandardFoldFunctionTable - class uk.ac.bbk.dcs.automed.qproc.optimise.StandardFoldFunctionTable.
StandardFoldFunctionTable() - Constructor for class uk.ac.bbk.dcs.automed.qproc.optimise.StandardFoldFunctionTable
StandardFunctionTable - class uk.ac.bbk.dcs.automed.qproc.StandardFunctionTable.
  Class that creates a FunctionTable containing all currently implemented functions.
StandardFunctionTable() - Constructor for class uk.ac.bbk.dcs.automed.qproc.StandardFunctionTable
standardStroke - Static variable in class uk.ac.ic.doc.automed.editor.DrawVertex
standardStroke - Static variable in class uk.ac.ic.doc.automed.editor.DrawArc
start_production() - Method in class uk.ac.bbk.dcs.automed.qproc.EnvParser
  Indicates start production.
start_production() - Method in class uk.ac.bbk.dcs.automed.qproc.QParser
  Indicates start production.
start_state() - Method in class uk.ac.bbk.dcs.automed.qproc.EnvParser
  Indicates start state.
start_state() - Method in class uk.ac.bbk.dcs.automed.qproc.QParser
  Indicates start state.
START() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
START() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
startDocument() - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLDSSSAX
STARTED - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
startElement(String, String, String, Attributes) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLDSSSAX
state - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
Statement - class uk.ac.ic.doc.automed.templates.Statement.
  The class to create statements that can be used in a template transformation's program.
Statement(String) - Constructor for class uk.ac.ic.doc.automed.templates.Statement
  Constructs a new Statement without any StatementArgumentDefinition objects.
statementArgSeq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement
statementArgSeq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.SchemeListStatement
statementArgSeq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement
statementArgSeq - Variable in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
StatementArgumentDefinition - class uk.ac.ic.doc.automed.templates.StatementArgumentDefinition.
  The class used to define a statement's arguments.
StatementArgumentDefinition(int, int, String, String, String) - Constructor for class uk.ac.ic.doc.automed.templates.StatementArgumentDefinition
  Constructs a new StatementArgumentDefinition.
statementExecuted - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
statementExecuted - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
StatementExecution - class uk.ac.ic.doc.automed.templates.StatementExecution.
  The class used to define a template transformation's program.
StatementExecution(int, int, Statement, TemplateArgumentSequence) - Constructor for class uk.ac.ic.doc.automed.templates.StatementExecution
  Constructs a new StatementExecution.
statementType - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TStatement
StatisticsModule - class uk.ac.ic.doc.automed.matching.modules.StatisticsModule.
StatisticsModule(ArrayList, ArrayList) - Constructor for class uk.ac.ic.doc.automed.matching.modules.StatisticsModule
stmArg - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
stopped() - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
STR - class uk.ac.ic.doc.automed.STR.
  The STR library.
STR_DataSourceName - Static variable in class uk.ac.ic.doc.automed.STR
STR() - Constructor for class uk.ac.ic.doc.automed.STR
STRException - exception uk.ac.ic.doc.automed.STRException.
  The class of exceptions generated by `STR`.
STRException(String) - Constructor for class uk.ac.ic.doc.automed.STRException
  Creates a STRException.
string - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
STRING - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
STRING - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedType
  Type to represent an arbitrary length string in the unicode character set.
STRING - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TConstants
STRING_TOKEN - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
stringSafe(String) - Static method in class uk.ac.ic.doc.automed.reps.Syntax
stringToObject(String, Class) - Static method in class uk.ac.ic.doc.automed.Util
stripUIDs(Document) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  This method takes as input an XML document in DOM format, duplicates it, then strips the uids from the duplicated DOM.
STRMethodTest - class uk.ac.ic.doc.automed.STRMethodTest.
STRMethodTest() - Constructor for class uk.ac.ic.doc.automed.STRMethodTest
StrToken - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
SubBag - class uk.ac.bbk.dcs.automed.qproc.functions.SubBag.
SubBag() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.SubBag
Subset - class uk.ac.ic.doc.automed.matching.relationships.Subset.
Subsumption - class uk.ac.ic.doc.automed.matching.relationships.Subsumption.
Subsumption() - Constructor for class uk.ac.ic.doc.automed.matching.relationships.Subsumption
subsumptions - Variable in class uk.ac.ic.doc.automed.matching.Integrator
subtract(AutoMedFloat) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedFloat
  Return the difference of two AutoMedFloats.
subtract(AutoMedInteger) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedInteger
  Return the difference of two AutoMedIntegers.
Sum - class uk.ac.bbk.dcs.automed.qproc.functions.Sum.
Sum() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Sum
SUPER_TYPE - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TConstants
Superset - class uk.ac.ic.doc.automed.matching.relationships.Superset.
sval - Variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
swap(int, int) - Method in class uk.ac.bbk.dcs.automed.qproc.functions.ModifiedArray
SYMBOL_TOKEN - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
symbolHeight - Variable in class uk.ac.ic.doc.automed.editor.DrawVertex
symbolWidth - Variable in class uk.ac.ic.doc.automed.editor.DrawVertex
syncWithRepository() - Static method in class uk.ac.ic.doc.automed.reps.Transformation
Syntax - class uk.ac.ic.doc.automed.reps.Syntax.
Syntax - class uk.ac.ic.doc.automed.editor.Syntax.
Syntax.Token - class uk.ac.ic.doc.automed.reps.Syntax.Token.
Syntax.Tokenizer - class uk.ac.ic.doc.automed.reps.Syntax.Tokenizer.
Syntax.Tokenizer(Reader) - Constructor for class uk.ac.ic.doc.automed.reps.Syntax.Tokenizer
Syntax() - Constructor for class uk.ac.ic.doc.automed.reps.Syntax
Syntax() - Constructor for class uk.ac.ic.doc.automed.editor.Syntax
SyntaxException - exception uk.ac.ic.doc.automed.reps.SyntaxException.
SyntaxException - exception uk.ac.ic.doc.automed.editor.SyntaxException.
SyntaxException(String) - Constructor for class uk.ac.ic.doc.automed.reps.SyntaxException
SyntaxException(String, Exception) - Constructor for class uk.ac.ic.doc.automed.reps.SyntaxException
SyntaxException(String, int) - Constructor for class uk.ac.ic.doc.automed.editor.SyntaxException
SyntaxException(String, int, String, String) - Constructor for class uk.ac.ic.doc.automed.reps.SyntaxException
SYSTEM - Static variable in class uk.ac.ic.doc.automed.editor.UserActionClass
sysvariable - Static variable in class uk.ac.bbk.dcs.automed.qproc.Cell
SysVarToken - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym

## T

TABLE - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
tables - Variable in class uk.ac.ic.doc.automed.matching.SQLRelationshipExtractor
tag() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns the Cell's tag
targets() - Method in class uk.ac.bbk.dcs.automed.qproc.QueryReformulator
  Returns the array of local schemas
TArgument - class uk.ac.ic.doc.automed.templates.wrapper.TArgument.
TArgument() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TArgument
TConstants - class uk.ac.ic.doc.automed.templates.wrapper.TConstants.
TConstants() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TConstants
TemplateArgument - class uk.ac.ic.doc.automed.templates.TemplateArgument.
  The class to create compile-time arguments (arguments used in template transformation's definitions)
TemplateArgument(int, int) - Constructor for class uk.ac.ic.doc.automed.templates.TemplateArgument
  Constructs a new TemplateArgument that refers to a composite transformation's arguments and creates a new sequence of arguments.
TemplateArgument(int, int, int) - Constructor for class uk.ac.ic.doc.automed.templates.TemplateArgument
  Constructs a new TemplateArgument that refers to a composite transformation's arguments.
TemplateArgument(int, int, String) - Constructor for class uk.ac.ic.doc.automed.templates.TemplateArgument
  Constructs a new TemplateArgument storing the specified value.
TemplateArgument(int, int, TemplateArgument) - Constructor for class uk.ac.ic.doc.automed.templates.TemplateArgument
  Constructs a new TemplateArgument that refers to another TemplateArgument
TemplateArgument(int, int, TemplateArgumentSequence, int) - Constructor for class uk.ac.ic.doc.automed.templates.TemplateArgument
  Constructs a new TemplateArgument that refers to another argument
TemplateArgument(int, String) - Constructor for class uk.ac.ic.doc.automed.templates.TemplateArgument
  Constructs a new TemplateArgument storing the specified value and creates a new sequence of arguments.
TemplateArgument(int, TemplateArgument) - Constructor for class uk.ac.ic.doc.automed.templates.TemplateArgument
  Constructs a new TemplateArgument that refers to another TemplateArgument and creates a new argument sequence
TemplateArgument(int, TemplateArgumentSequence, int) - Constructor for class uk.ac.ic.doc.automed.templates.TemplateArgument
  Constructs a new TemplateArgument that refers to another argument and creates a new argument sequence
TemplateArgumentSequence - class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence.
  The class to create compile-time argument sequences (sequences used in template transformation's definitions)
TemplateArgumentSequence() - Constructor for class uk.ac.ic.doc.automed.templates.TemplateArgumentSequence
  Constructs a new TemplateArgumentSequence without any TemplateArgument objects.
TemplateCompilerSimulator - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.
TemplateCompilerSimulator.CONSTRAINTS - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRAINTS.
TemplateCompilerSimulator.CONSTRAINTS() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRAINTS
TemplateCompilerSimulator.CONSTRAINTS(String) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRAINTS
TemplateCompilerSimulator.CONSTRAINTS(TArgument) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRAINTS
TemplateCompilerSimulator.CONSTRAINTSLIST - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRAINTSLIST.
TemplateCompilerSimulator.CONSTRAINTSLIST(TArgument) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRAINTSLIST
TemplateCompilerSimulator.CONSTRUCT - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRUCT.
TemplateCompilerSimulator.CONSTRUCT() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRUCT
TemplateCompilerSimulator.FUNCTION - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.FUNCTION.
TemplateCompilerSimulator.FUNCTION() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.FUNCTION
TemplateCompilerSimulator.FUNCTION(String) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.FUNCTION
TemplateCompilerSimulator.FUNCTION(TArgument) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.FUNCTION
TemplateCompilerSimulator.FUNCTIONLIST - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.FUNCTIONLIST.
TemplateCompilerSimulator.FUNCTIONLIST(TArgument) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.FUNCTIONLIST
TemplateCompilerSimulator.ITEM - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.ITEM.
TemplateCompilerSimulator.ITEM() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.ITEM
TemplateCompilerSimulator.ITEM(TArgument) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.ITEM
TemplateCompilerSimulator.LIST - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.LIST.
TemplateCompilerSimulator.LIST() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.LIST
TemplateCompilerSimulator.LIST(TArgument) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.LIST
TemplateCompilerSimulator.NAME - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.NAME.
TemplateCompilerSimulator.NAME(TArgument) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.NAME
TemplateCompilerSimulator.NAMELIST - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.NAMELIST.
TemplateCompilerSimulator.NAMELIST(TArgument) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.NAMELIST
TemplateCompilerSimulator.OBJECT - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT.
TemplateCompilerSimulator.OBJECT(TArgument) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECT
TemplateCompilerSimulator.OBJECTLIST - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECTLIST.
TemplateCompilerSimulator.OBJECTLIST(TArgument) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.OBJECTLIST
TemplateCompilerSimulator.SCHEME - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.SCHEME.
TemplateCompilerSimulator.SCHEME() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.SCHEME
TemplateCompilerSimulator.STRING - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.STRING.
TemplateCompilerSimulator.STRING() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.STRING
TemplateCompilerSimulator.STRING(TArgument) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.STRING
TemplateCompilerSimulator.STRINGLIST - class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.STRINGLIST.
TemplateCompilerSimulator.STRINGLIST(TArgument) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.STRINGLIST
TemplateCompilerSimulator() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TemplateCompilerSimulator(AutoMedWrapperFactory) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TemplateDefinitionException - exception uk.ac.ic.doc.automed.templates.wrapper.TemplateDefinitionException.
TemplateDefinitionException(String) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateDefinitionException
TemplateDefinitionException(String, Exception) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TemplateDefinitionException
templateDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
templateDescription() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TemplateDialogueLauncher - class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher.
TemplateDialogueLauncher(Frame) - Constructor for class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
TemplateExecutionRepository - class uk.ac.ic.doc.automed.TemplateExecutionRepository.
  Manipulate the Template Execution Repository and supply the methods to invoke template transformations
TemplateExecutionRepository() - Constructor for class uk.ac.ic.doc.automed.TemplateExecutionRepository
TemplateExecutionRepositoryException - exception uk.ac.ic.doc.automed.TemplateExecutionRepositoryException.
  The class of exceptions generated by `TemplateExecutionRepository`.
TemplateExecutionRepositoryException(String) - Constructor for class uk.ac.ic.doc.automed.TemplateExecutionRepositoryException
TemplateInputDialogue - class uk.ac.ic.doc.automed.templates.gui.TemplateInputDialogue.
TemplateInputDialogue(int, int, InteractiveSchemaDisplay, TemplateFrame) - Constructor for class uk.ac.ic.doc.automed.templates.gui.TemplateInputDialogue
templateName() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefaultTemplate
templateName() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
  Return the name used to identify the template transformation that will be compiled by an implementation of this class.
templateStatements - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TemplateTransformationRepository - class uk.ac.ic.doc.automed.TemplateTransformationRepository.
  Manipulate the Template Transformation Repository, built template transformations.
TemplateTransformationRepository() - Constructor for class uk.ac.ic.doc.automed.TemplateTransformationRepository
TemplateTransformationRepositoryException - exception uk.ac.ic.doc.automed.TemplateTransformationRepositoryException.
  The class of exceptions generated by `TemplateTransformationRepository`.
TemplateTransformationRepositoryException(String) - Constructor for class uk.ac.ic.doc.automed.TemplateTransformationRepositoryException
TemplateTransformationRepositoryExtension - class uk.ac.ic.doc.automed.TemplateTransformationRepositoryExtension.
TemplateTransformationRepositoryExtension() - Constructor for class uk.ac.ic.doc.automed.TemplateTransformationRepositoryExtension
TemplateTransformationSyntaxRepository - class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository.
  Manipulate the Template Transformation Syntax Repository, create new statements.
TemplateTransformationSyntaxRepository() - Constructor for class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
TemplateTransformationSyntaxRepositoryException - exception uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepositoryException.
  The class of exceptions generated by `TemplateTransformationSyntaxRepository`.
TemplateTransformationSyntaxRepositoryException(String) - Constructor for class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepositoryException
temporaryForeachOutputVariables - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TempPathway - class uk.ac.ic.doc.automed.tml.TempPathway.
  This class represents a temporary pathway used solely for the purpose of pathway optimisation.
TempTML - class uk.ac.ic.doc.automed.tml.TempTML.
  This class represents a temporary `TML` in a `TempPathway`.
testIdenticalSchemas(Schema, Schema) - Method in class uk.ac.ic.doc.automed.tml.TempPathway
text - Variable in class uk.ac.ic.doc.automed.editor.DrawVertex
Text - Static variable in class uk.ac.bbk.dcs.automed.qproc.EnvSym
text() - Method in class uk.ac.bbk.dcs.automed.qproc.Cell
  Returns the string representation of the object contained in the Cell
textFieldCompleted(InputItem, String) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
textHeight - Variable in class uk.ac.ic.doc.automed.editor.DrawVertex
textWidth - Variable in class uk.ac.ic.doc.automed.editor.DrawVertex
thickness - Static variable in class uk.ac.ic.doc.automed.editor.DrawVertex
thickness - Static variable in class uk.ac.ic.doc.automed.editor.DrawArc
TIME - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
TIME - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedType
  Type to represent a time (on a particular day)
TIME_TOKEN - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
title(String) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Prints a line of stars, then the input title centered inside a line of stars, then another line of stars.
TML - class uk.ac.ic.doc.automed.tml.TML.
  This class represents a `Transformation` in TML notation.
TML(int, Schema, Schema, SchemaObject, SchemaObject, String, String) - Constructor for class uk.ac.ic.doc.automed.tml.TML
TML(SchemaObject) - Constructor for class uk.ac.ic.doc.automed.tml.TML
TML(TML) - Constructor for class uk.ac.ic.doc.automed.tml.TML
TML(Transformation) - Constructor for class uk.ac.ic.doc.automed.tml.TML
toActionString(int) - Method in class uk.ac.ic.doc.automed.tml.TML
toASG(LinkedList) - Static method in class uk.ac.bbk.dcs.automed.hdmstore.EdgeElement
  Convert a `LinkedList` of edge elements and convert to an `ASG`
toASG(LinkedList, boolean) - Static method in class uk.ac.bbk.dcs.automed.hdmstore.EdgeElement
  Convert a `LinkedList` of edge elements and convert to an `ASG` If is true return elements as a list, otherwise as a tuple (so that the ASG returned is a list of tuples)
toASGList(ArrayList) - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  Generates an ASG list from an ArrayList.
toASGTuple(ArrayList) - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  Generates an ASG tuple from an ArrayList.
toForest(Forest) - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraph
  This method first divides a given graph into subGraphs.
tokenize(String) - Static method in class uk.ac.ic.doc.automed.Util
  Returns the tokens in s (as defined by default StringTokenizer) as an array
toObjectARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
toObjectARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
toObjectARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
ToolTip - class uk.ac.ic.doc.automed.gui.ToolTip.
  Customized ToolTip class.
ToolTip(Frame) - Constructor for class uk.ac.ic.doc.automed.gui.ToolTip
  Creates a new ToolTip.
toPrintString() - Method in class uk.ac.ic.doc.automed.tml.TML
toSchemaARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TStatement
toString() - Method in class uk.ac.ic.doc.automed.reps.Pathway
toString() - Method in class uk.ac.ic.doc.automed.reps.Node
toString() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
toString() - Method in class uk.ac.ic.doc.automed.reps.Network
toString() - Method in class uk.ac.ic.doc.automed.reps.Schema
toString() - Method in class uk.ac.ic.doc.automed.reps.Syntax.Token
toString() - Method in class uk.ac.ic.doc.automed.reps.Transformation
toString() - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
toString() - Method in class uk.ac.bbk.dcs.automed.qproc.SchemeInfo
toString() - Method in class uk.ac.bbk.dcs.automed.qproc.ASG
toString() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTime
  Return a string representation of this AutoMedTime using ISO format.
toString() - Method in class uk.ac.ic.doc.automed.wrappers.SQLQuery
  Convert this SQLQuery into a text equivalent.
toString() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedString
  Return a string representation of this AutoMedString.
toString() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTuple
  Produce a string representation of the AutoMedTuple
toString() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedFloat
  Return a string representation of this AutoMedFloat.
toString() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedInteger
  Return a string representation of this AutoMedInteger.
toString() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedType
  Return a string representation of this AutoMedType.
toString() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedBoolean
  Return a string representation of this AutoMedBoolean.
toString() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedResult
  Produce a string representation of the result set, where {} indicates a set of values, and [] a list of values
toString() - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedQueryToken
toString() - Method in class uk.ac.ic.doc.automed.tml.TML
toString() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
toString() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
toString() - Method in class uk.ac.ic.doc.automed.matching.SimilarSchemaElementPair
toString() - Method in class uk.ac.ic.doc.automed.matching.SchemaElementPairRelationship
toString() - Method in class uk.ac.ic.doc.automed.matching.SchemaElementPair
toString() - Method in class uk.ac.ic.doc.automed.matching.SchemaElement
toString() - Method in class uk.ac.ic.doc.automed.matching.Instance
toString() - Method in class uk.ac.ic.doc.automed.matching.BidirectionalDegree
toString() - Method in class uk.ac.ic.doc.automed.matching.relationships.Subsumption
toString() - Method in class uk.ac.ic.doc.automed.matching.relationships.SemanticRelationship
toString() - Method in class uk.ac.ic.doc.automed.matching.relationships.Overlapness
toString() - Method in class uk.ac.ic.doc.automed.matching.relationships.Incompatibility
toString() - Method in class uk.ac.ic.doc.automed.matching.relationships.Equivalence
toString() - Method in class uk.ac.ic.doc.automed.matching.relationships.Disjointness
toString() - Method in class uk.ac.ic.doc.automed.matching.modules.ElementVectorRepresentation
toString() - Method in class uk.ac.ic.doc.automed.matching.modules.Cluster
toString(StringBuffer) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedTuple
  Produce a string representation of the result set, where {} indicates a set of values, and [] a list of values
toString(StringBuffer) - Method in class uk.ac.ic.doc.automed.wrappers.AutoMedResult
  Produce a string representation of the result set in a StringBuffer.
toTree() - Method in class uk.ac.bbk.dcs.automed.graph.Forest
  This method adds a generic root node to the forest and adds the trees' roots as children to the generic root node.
TRAN_ACTION_ADD - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Transformation action "add"
TRAN_ACTION_CONTRACT - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Transformation action "contract"
TRAN_ACTION_DELETE - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Transformation action "delete"
TRAN_ACTION_EXTEND - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Transformation action "extend"
TRAN_ACTION_IDENT - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Transformation action "ident"
TRAN_ACTION_MAXIMUM - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated.
TRAN_ACTION_MINIMUM - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated.
TRAN_ACTION_RENAME - Static variable in interface uk.ac.ic.doc.automed.Constants
  Deprecated. Transformation action "rename"
TransactSQLWrapper - class uk.ac.ic.doc.automed.wrappers.TransactSQLWrapper.
  A lower level wrapper for the conforming to the AutoMed SQL high level wrapper for TransactSQL SQL databases.
TransactSQLWrapper(AccessMethod, String) - Constructor for class uk.ac.ic.doc.automed.wrappers.TransactSQLWrapper
  Generate a new wrapper instance from information held in the repository about how to access a data source.
TransactSQLWrapperFactory - class uk.ac.ic.doc.automed.wrappers.TransactSQLWrapperFactory.
  A lower level wrapper factory for TransactSQL databases (i.e.
TransactSQLWrapperFactory() - Constructor for class uk.ac.ic.doc.automed.wrappers.TransactSQLWrapperFactory
transARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
transform(boolean, boolean) - Method in class uk.ac.bbk.dcs.automed.xml.XMLTransformer
  Creates the transformation pathway from the source to the target schema.
transformation - Static variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
Transformation - class uk.ac.ic.doc.automed.reps.Transformation.
  The Transformation class describes a single premitive transformation that connects a pair of schemas.
TRANSFORMATION_ADDED - Static variable in class uk.ac.ic.doc.automed.reps.SchemaChangeEvent
TRANSFORMATION_REMOVED - Static variable in class uk.ac.ic.doc.automed.reps.SchemaChangeEvent
Transformation(int, int, int, int, int, String, String, boolean) - Constructor for class uk.ac.ic.doc.automed.reps.Transformation
  Instantiates a transformation.
transformationAdded(SchemaChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.SchemaChangeListener
transformationAdded(SchemaChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
TransformationArgumentDefinition - class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition.
  The class used to define a template transformation's arguments.
TransformationArgumentDefinition(int, int, String, boolean, int, int, int, int) - Constructor for class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
TransformationArgumentDefinition(int, int, String, String, String, boolean) - Constructor for class uk.ac.ic.doc.automed.templates.TransformationArgumentDefinition
  Constructs a new TransformationArgumentDefinition.
transformationRemoved(SchemaChangeEvent) - Method in interface uk.ac.ic.doc.automed.reps.SchemaChangeListener
transformationRemoved(SchemaChangeEvent) - Method in class uk.ac.ic.doc.automed.editor.Gui.EditorFrame
transformationsScroller - Variable in class uk.ac.ic.doc.automed.templates.gui.SchemaFrame
transidExistsInCompositeTransformationExecution(int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns false if the specified transformation is not found in the execution table, true otherwise.
transIds - Variable in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
translateToQueryText(StringBuffer) - Method in class uk.ac.ic.doc.automed.wrappers.SQLQuery
  Insert into a StringBuffer the text equivalent of this SQLQuery.
Translator - class uk.ac.bbk.dcs.automed.wrappers.Translator.
Translator() - Constructor for class uk.ac.bbk.dcs.automed.wrappers.Translator
tree - Variable in class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree
treeModel - Variable in class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree
TreeNode - class uk.ac.bbk.dcs.automed.graph.TreeNode.
  Class that abstracts the node of a tree structure.
TreeNode(String) - Constructor for class uk.ac.bbk.dcs.automed.graph.TreeNode
tryToUpdateArgumentWithInputValues() - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
tryToUpdateArgumentWithInputValues(String[]) - Method in class uk.ac.ic.doc.automed.templates.gui.InputForm
TStatement - class uk.ac.ic.doc.automed.templates.wrapper.TStatement.
TStatement() - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TStatement
TStatementArgument - class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument.
TStatementArgument(TStatement, TemplateArgumentSequence, int) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
TStatementArgument(TType, TStatement, TemplateArgumentSequence, int) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TStatementArgument
TTemplate - class uk.ac.ic.doc.automed.templates.wrapper.TTemplate.
TTemplate(String) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
TTemplate(String, boolean) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
TTemplate(String, String) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
TTemplate(String, String, boolean) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
TTemplateArgument - class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument.
TTemplateArgument(int, String, TStatementArgument) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
TTemplateArgument(int, String, TType, boolean) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TTemplateArgument
TTemplateInputArgument - class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument.
TTemplateInputArgument(int, int) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
TTemplateInputArgumentList - class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList.
TTemplateInputArgumentList(CompositeTransformation) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList
TTemplateInputArgumentList(int) - Constructor for class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList
TUPLE - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedType
  Type to represent a tuple of atomic types
tx - Variable in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalVertex
ty - Variable in class uk.ac.ic.doc.automed.editor.DefaultDrawLinkNodalVertex
type - Variable in class uk.ac.ic.doc.automed.reps.Syntax.Token
TYPE_ALTERNATION - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
  Deprecated. see `Construct.CLASS_ALTERNATION`
TYPE_CONSTRUCT - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
  Scheme type of construct scheme
TYPE_MAXIMUM - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
TYPE_MINIMUM - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
TYPE_NAME - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
  Scheme type of construct scheme
TYPE_SEQUENCE - Static variable in class uk.ac.ic.doc.automed.reps.Scheme
  Deprecated. see `Construct.CLASS_SEQUENCE`
type() - Method in class uk.ac.bbk.dcs.automed.hdmstore.Span
  Get the type
type() - Method in class uk.ac.bbk.dcs.automed.hdmstore.Edge
  Get the edge type
TypeConstraints - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TypeConstraintsList - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TypeFunction - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TypeFunctionList - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TypeItem - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TypeList - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TypeMismatchException - exception uk.ac.ic.doc.automed.reps.TypeMismatchException.
  The class of exceptions generated by the uk.ac.ic.doc.automed.reps package.
TypeMismatchException(String) - Constructor for class uk.ac.ic.doc.automed.reps.TypeMismatchException
TypeName - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TypeNameList - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TypeObject - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TypeObjectList - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TypeString - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
TypeStringList - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator

## U

UIDGetAttNameFromAttUID(String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
UIDGetElementName(Node) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
UIDGetElementName(String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
UIDGetElementNameFromAttUID(String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
UIDGetSchemaUIDFromInstanceUID(Node) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
UIDGetSchemaUIDFromInstanceUID(String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
UIDRemoveSchemaName(Node) - Method in class uk.ac.bbk.dcs.automed.xml.XMLTransformer
UIDRemoveSchemaName(Node) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
UIDRemoveSchemaName(String) - Method in class uk.ac.bbk.dcs.automed.xml.XMLTransformer
UIDRemoveSchemaName(String) - Method in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
uk.ac.bbk.dcs.automed.graph - package uk.ac.bbk.dcs.automed.graph
uk.ac.bbk.dcs.automed.hdmstore - package uk.ac.bbk.dcs.automed.hdmstore
uk.ac.bbk.dcs.automed.qproc - package uk.ac.bbk.dcs.automed.qproc
uk.ac.bbk.dcs.automed.qproc.functions - package uk.ac.bbk.dcs.automed.qproc.functions
uk.ac.bbk.dcs.automed.qproc.optimise - package uk.ac.bbk.dcs.automed.qproc.optimise
uk.ac.bbk.dcs.automed.wrappers - package uk.ac.bbk.dcs.automed.wrappers
uk.ac.bbk.dcs.automed.xml - package uk.ac.bbk.dcs.automed.xml
uk.ac.bbk.dcs.automed.xml.wrappers - package uk.ac.bbk.dcs.automed.xml.wrappers
uk.ac.ic.doc.automed - package uk.ac.ic.doc.automed
uk.ac.ic.doc.automed.editor - package uk.ac.ic.doc.automed.editor
uk.ac.ic.doc.automed.editor.drawables - package uk.ac.ic.doc.automed.editor.drawables
uk.ac.ic.doc.automed.gui - package uk.ac.ic.doc.automed.gui
uk.ac.ic.doc.automed.matching - package uk.ac.ic.doc.automed.matching
uk.ac.ic.doc.automed.matching.modules - package uk.ac.ic.doc.automed.matching.modules
uk.ac.ic.doc.automed.matching.relationships - package uk.ac.ic.doc.automed.matching.relationships
uk.ac.ic.doc.automed.reps - package uk.ac.ic.doc.automed.reps
uk.ac.ic.doc.automed.ssd - package uk.ac.ic.doc.automed.ssd
uk.ac.ic.doc.automed.templates - package uk.ac.ic.doc.automed.templates
uk.ac.ic.doc.automed.templates.gui - package uk.ac.ic.doc.automed.templates.gui
uk.ac.ic.doc.automed.templates.wrapper - package uk.ac.ic.doc.automed.templates.wrapper
uk.ac.ic.doc.automed.tml - package uk.ac.ic.doc.automed.tml
uk.ac.ic.doc.automed.wrappers - package uk.ac.ic.doc.automed.wrappers
uk.ac.ic.doc.automed.wrappers.ssdfunctions - package uk.ac.ic.doc.automed.wrappers.ssdfunctions
UNARY_CLASS - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
UnexpectedTokenException - exception uk.ac.ic.doc.automed.reps.UnexpectedTokenException.
  Deprecated. Use SyntaxException instead
UnexpectedTokenException - exception uk.ac.ic.doc.automed.editor.UnexpectedTokenException.
UnexpectedTokenException(int, int, int, Syntax.Token) - Constructor for class uk.ac.ic.doc.automed.reps.UnexpectedTokenException
  Deprecated.
UnexpectedTokenException(int, int, int, Syntax.Token) - Constructor for class uk.ac.ic.doc.automed.editor.UnexpectedTokenException
UnexpectedTokenException(int, int, Syntax.Token) - Constructor for class uk.ac.ic.doc.automed.reps.UnexpectedTokenException
  Deprecated.
UnexpectedTokenException(int, int, Syntax.Token) - Constructor for class uk.ac.ic.doc.automed.editor.UnexpectedTokenException
UnexpectedTokenException(String) - Constructor for class uk.ac.ic.doc.automed.reps.UnexpectedTokenException
  Deprecated.
unFinalise() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgument
UninstantiatedElementException - exception uk.ac.ic.doc.automed.matching.UninstantiatedElementException.
UninstantiatedElementException() - Constructor for class uk.ac.ic.doc.automed.matching.UninstantiatedElementException
UninstantiatedElementException(String) - Constructor for class uk.ac.ic.doc.automed.matching.UninstantiatedElementException
UninstantiatedException - exception uk.ac.ic.doc.automed.matching.UninstantiatedException.
UninstantiatedException() - Constructor for class uk.ac.ic.doc.automed.matching.UninstantiatedException
UninstantiatedException(String) - Constructor for class uk.ac.ic.doc.automed.matching.UninstantiatedException
UninstantiatedException(String, Throwable) - Constructor for class uk.ac.ic.doc.automed.matching.UninstantiatedException
union(Schema) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Return an `Schema` (`su`) containing the union of `SchemaObject`s in this schema (`s1`) and the schema passed as a parameter (`s2`).
unionByName(Schema) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Return an `SchemaObject` array containing the union by name between this schema (s1) and the schema passed as a parameter (s2).
unvisit() - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraphNode
  Marks the calling node as unvisited
UPDATE - Static variable in class uk.ac.ic.doc.automed.IntegrityException
  Exception caused by an operation doing some sort of update on an exisinting object in the repository.
updateCanvas() - Method in class uk.ac.ic.doc.automed.gui.SchemaCanvas
updateFields() - Method in class uk.ac.ic.doc.automed.editor.PathwayOptimiserTool
updateFields() - Method in class uk.ac.ic.doc.automed.editor.GUITool
updateFields() - Method in class uk.ac.ic.doc.automed.editor.ReportException
updateFields() - Method in class uk.ac.ic.doc.automed.editor.MatchingTool
updateRepository() - Method in class uk.ac.ic.doc.automed.templates.wrapper.CreateListStatement
updateRepository() - Method in class uk.ac.ic.doc.automed.templates.wrapper.SchemeListStatement
updateRepository() - Method in class uk.ac.ic.doc.automed.templates.wrapper.IndexListStatement
updateRepository() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TStatement
updateRepository() - Method in class uk.ac.ic.doc.automed.templates.wrapper.RenameStatement
updateRepository() - Method in class uk.ac.ic.doc.automed.templates.wrapper.RemovingStatement
updateRepository() - Method in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
updateRepository() - Method in class uk.ac.ic.doc.automed.templates.wrapper.ForeachStatement
updateRepository() - Method in class uk.ac.ic.doc.automed.templates.wrapper.DefineStringStatement
updateRepositoryWithRuntimeArguments() - Method in class uk.ac.ic.doc.automed.templates.wrapper.TTemplateInputArgumentList
updateSchemaObjectNameHashMap() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Update this Schema's hashmap of how each `SchemaObject` in the schema is named.
updateSSDPatterns() - Method in class uk.ac.ic.doc.automed.ssd.SSDFormat
upperBound - Static variable in class uk.ac.bbk.dcs.automed.qproc.QueryReformulator
url - Variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
usage() - Static method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStoreCmd
  Show the useage message
use(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmStore
  Use the named HDM store - subsequent calls to this HdmStore will use this store as default
UserAction - class uk.ac.ic.doc.automed.editor.UserAction.
UserAction() - Constructor for class uk.ac.ic.doc.automed.editor.UserAction
UserActionClass - class uk.ac.ic.doc.automed.editor.UserActionClass.
UserActionClass(Action) - Constructor for class uk.ac.ic.doc.automed.editor.UserActionClass
UserActionResult - class uk.ac.ic.doc.automed.editor.UserActionResult.
UserActionResult() - Constructor for class uk.ac.ic.doc.automed.editor.UserActionResult
username - Variable in class uk.ac.ic.doc.automed.wrappers.AutoMedWrapper
userName - Static variable in class uk.ac.ic.doc.automed.MDR
Util - class uk.ac.ic.doc.automed.Util.
Util - class uk.ac.ic.doc.automed.matching.Util.
Util() - Constructor for class uk.ac.ic.doc.automed.Util
Util() - Constructor for class uk.ac.ic.doc.automed.matching.Util
Utilities - class uk.ac.bbk.dcs.automed.qproc.functions.Utilities.
Utilities() - Constructor for class uk.ac.bbk.dcs.automed.qproc.functions.Utilities
Utility - class uk.ac.ic.doc.automed.reps.Utility.
  Class offering utility methods for accessing a SchemaObject's scheme.
Utility() - Constructor for class uk.ac.ic.doc.automed.reps.Utility

## V

VALIDATING - Static variable in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapperFactory
  A feature stating whether the parser of the XML file should validate the file against the accompanying XML Schema/DTD.
validQuery(ASG) - Method in class uk.ac.bbk.dcs.automed.hdmstore.HdmWrapper
  check that the given ASG is a valid query
value - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.CONSTRAINTS
value - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator.FUNCTION
VALUE_CLASS - Static variable in class uk.ac.ic.doc.automed.wrappers.AutoMedQuery
  A class of token that represents an atomic value in an expression
value() - Method in class uk.ac.bbk.dcs.automed.hdmstore.Span
  Get the value
valueARG - Variable in class uk.ac.ic.doc.automed.templates.wrapper.InsertingStatement
valueChanged(ListSelectionEvent) - Method in class uk.ac.ic.doc.automed.gui.SchemaTool
valueChanged(ListSelectionEvent) - Method in class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher
variable - Static variable in class uk.ac.bbk.dcs.automed.qproc.Cell
VARIABLE_PREFIX - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
VARIES_WITH(TemplateCompilerSimulator.NAME) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
VARIES_WITH(TemplateCompilerSimulator.NAMELIST) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
VARIES_WITH(TemplateCompilerSimulator.OBJECT) - Method in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator
VarToken - Static variable in class uk.ac.bbk.dcs.automed.qproc.QSym
VarToken - Static variable in class uk.ac.bbk.dcs.automed.qproc.EnvSym
Vectors - class uk.ac.ic.doc.automed.matching.modules.Vectors.
Vectors(List) - Constructor for class uk.ac.ic.doc.automed.matching.modules.Vectors
VERBOSE - Static variable in class uk.ac.bbk.dcs.automed.hdmstore.Debug
VERTICAL_EXT - Static variable in class uk.ac.ic.doc.automed.gui.Rhombus
viewmap - Variable in class uk.ac.bbk.dcs.automed.qproc.QueryReformulator
visited() - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraphNode
  Marks the calling node as visited.
voidQuery() - Static method in class uk.ac.bbk.dcs.automed.qproc.ASG
  Returns the ASG representation of the query Void.

## W

waffle(String) - Method in class uk.ac.bbk.dcs.automed.hdmstore.Debug
  Write a verbose level message
wasExecuted - Variable in class uk.ac.ic.doc.automed.templates.wrapper.TTemplate
wasVisited() - Method in class uk.ac.bbk.dcs.automed.graph.DirectedGraphNode
weakHeadNF(ASG) - Method in class uk.ac.bbk.dcs.automed.qproc.Evaluator
  Evaluates g to weak head normal form.
weakHeadNF(Cell) - Method in class uk.ac.bbk.dcs.automed.qproc.Evaluator
  Analogous to the above.
WHERE - Static variable in class uk.ac.ic.doc.automed.wrappers.SQLQuery
  The only field should contain a logical operator or a comparison
WHITESPACE_COLLAPSE - Static variable in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapperFactory
  A feature stating that after the processing implied by replace, contiguous sequences of #x20's are collapsed to a single #x20, and leading and trailing #x20's are removed.
WHITESPACE_REPLACE - Static variable in class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapperFactory
  A feature stating that all occurrences of #x9 (tab), #xA (line feed) and #xD (carriage return) are replaced with #x20 (space).
window - Variable in class uk.ac.ic.doc.automed.editor.GUITool
wLayout - Variable in class uk.ac.ic.doc.automed.editor.GUITool
write() - Method in class uk.ac.ic.doc.automed.reps.Pathway
write() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Write to the standard out a text representation of this Schema object, in a form suitable for human interpretation, and suitable for being used as the input to `#read()`
write() - Method in class uk.ac.ic.doc.automed.reps.Transformation
write(OutputStream) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
write(OutputStream) - Method in class uk.ac.ic.doc.automed.reps.Construct
write(OutputStream) - Method in class uk.ac.ic.doc.automed.reps.Schema
write(OutputStream) - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
write(OutputStream) - Method in class uk.ac.ic.doc.automed.reps.Model
write(OutputStream) - Method in class uk.ac.ic.doc.automed.reps.Transformation
write(PrintWriter) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
write(PrintWriter) - Method in class uk.ac.ic.doc.automed.reps.Construct
write(PrintWriter) - Method in class uk.ac.ic.doc.automed.reps.Schema
write(PrintWriter) - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
write(PrintWriter) - Method in class uk.ac.ic.doc.automed.reps.Model
write(PrintWriter) - Method in class uk.ac.ic.doc.automed.reps.Transformation
writeDOM(Document, String) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Serializes the input DOM representation into file "fileName" in path "filePath".
writeDOM(Document, String, String) - Static method in class uk.ac.bbk.dcs.automed.xml.NodeUtility
  Serializes the input DOM representation into file "fileName" in path "filePath".
writeSimilarSchemaElementPairs(String, SimilarSchemaElementPair[]) - Static method in class uk.ac.ic.doc.automed.matching.SimilarSchemaElementPair
writeToRepository() - Method in class uk.ac.ic.doc.automed.tml.TempPathway
writeToRepository(boolean) - Method in class uk.ac.ic.doc.automed.tml.TempPathway
  Write an optimised pathway to the repository
WRITTING_CODE - Static variable in class uk.ac.ic.doc.automed.templates.wrapper.TemplateCompilerSimulator

## X

xInset - Static variable in class uk.ac.ic.doc.automed.editor.DrawVertex
XMLConstants - class uk.ac.bbk.dcs.automed.xml.XMLConstants.
XMLConstants() - Constructor for class uk.ac.bbk.dcs.automed.xml.XMLConstants
XMLDSSDOM - class uk.ac.bbk.dcs.automed.xml.wrappers.XMLDSSDOM.
  The XMLDataSourceSchema class represents the DataSource Schema of an XML file using DOM.
XMLDSSDOM(DOMWrapper, DOMWrapperFactory) - Constructor for class uk.ac.bbk.dcs.automed.xml.wrappers.XMLDSSDOM
XMLDSSSAX - class uk.ac.bbk.dcs.automed.xml.wrappers.XMLDSSSAX.
  The XMLDataSourceSchema class represents the DataSource Schema of an XML file using SAX.
XMLDSSSAX(SAXWrapper, SAXWrapperFactory) - Constructor for class uk.ac.bbk.dcs.automed.xml.wrappers.XMLDSSSAX
XMLException - exception uk.ac.bbk.dcs.automed.xml.XMLException.
  An exception relating to the XML package.
XMLException(String) - Constructor for class uk.ac.bbk.dcs.automed.xml.XMLException
XMLException(String, Exception) - Constructor for class uk.ac.bbk.dcs.automed.xml.XMLException
  Creates an XMLException when it is acting as a wrapper for other Exceptions.
xmlExtension - Static variable in class uk.ac.bbk.dcs.automed.xml.XMLConstants
XMLModel - class uk.ac.bbk.dcs.automed.xml.XMLModel.
  Defines the AutoMed XML Model
XMLModel() - Constructor for class uk.ac.bbk.dcs.automed.xml.XMLModel
  Creates the XML Model in the AutoMed Repository (MDR).
XMLNotFoundException - exception uk.ac.bbk.dcs.automed.xml.XMLNotFoundException.
  An exception relating to something not found in an XML context.
XMLNotFoundException(String) - Constructor for class uk.ac.bbk.dcs.automed.xml.XMLNotFoundException
XMLNotFoundException(String, Exception) - Constructor for class uk.ac.bbk.dcs.automed.xml.XMLNotFoundException
  Creates an XMLNotFoundException when it is acting as a wrapper for other Exceptions.
XMLTransformer - class uk.ac.bbk.dcs.automed.xml.XMLTransformer.
  Class that automatically integrates two AutoMed XML DataSource Schemas.
XMLTransformer(Schema, Document, Schema, Document, boolean) - Constructor for class uk.ac.bbk.dcs.automed.xml.XMLTransformer
XMLWrapper - class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper.
  XMLWrapper class is a wrapper class for the AutoMed Repository.
XMLWrapper() - Constructor for class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapper
XMLWrapperFactory - class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapperFactory.
  XMLWrapperFactory class.
XMLWrapperFactory() - Constructor for class uk.ac.bbk.dcs.automed.xml.wrappers.XMLWrapperFactory
  Creates a new XMLWrapperFactory and sets the model name.
xPos - Variable in class uk.ac.ic.doc.automed.templates.gui.DrawingObject

## Y

YATTA_MODEL_ROOTNODE - Static variable in class uk.ac.ic.doc.automed.wrappers.YattaWrapperFactory
YATTA_MODEL_ROOTORYATTA - Static variable in class uk.ac.ic.doc.automed.wrappers.YattaWrapperFactory
YATTA_MODEL_SEQUENCE - Static variable in class uk.ac.ic.doc.automed.wrappers.YattaWrapperFactory
YATTA_MODEL_YATTANODE - Static variable in class uk.ac.ic.doc.automed.wrappers.YattaWrapperFactory
YattaDrawLinkNodalLink - class uk.ac.ic.doc.automed.editor.drawables.YattaDrawLinkNodalLink.
YattaDrawLinkNodalLink(EditorPanel, Positionable, Positionable[]) - Constructor for class uk.ac.ic.doc.automed.editor.drawables.YattaDrawLinkNodalLink
YattaDrawSequence - class uk.ac.ic.doc.automed.editor.drawables.YattaDrawSequence.
YattaDrawSequence(EditorPanel, Positionable[]) - Constructor for class uk.ac.ic.doc.automed.editor.drawables.YattaDrawSequence
YattaDrawSequence(EditorPanel, Positionable, Positionable[]) - Constructor for class uk.ac.ic.doc.automed.editor.drawables.YattaDrawSequence
YattaQuery - class uk.ac.ic.doc.automed.wrappers.YattaQuery.
YattaQuery(Object[], String) - Constructor for class uk.ac.ic.doc.automed.wrappers.YattaQuery
YattaQueryResult - class uk.ac.ic.doc.automed.wrappers.YattaQueryResult.
YattaQueryResult(int) - Constructor for class uk.ac.ic.doc.automed.wrappers.YattaQueryResult
YattaWrapper - class uk.ac.ic.doc.automed.wrappers.YattaWrapper.
  A YATTA wrapper for semistructured data source.
YattaWrapper(AccessMethod, String) - Constructor for class uk.ac.ic.doc.automed.wrappers.YattaWrapper
YattaWrapperFactory - class uk.ac.ic.doc.automed.wrappers.YattaWrapperFactory.
  A YattaWrapperFactory class able to produce YattaWrapper instances, together with any data (schema, ssdformat, etc.) that the wrapper requires to be present in the repository.
YattaWrapperFactory() - Constructor for class uk.ac.ic.doc.automed.wrappers.YattaWrapperFactory
yInset - Static variable in class uk.ac.ic.doc.automed.editor.DrawVertex
yPos - Variable in class uk.ac.ic.doc.automed.templates.gui.DrawingObject

## _

_action_table - Static variable in class uk.ac.bbk.dcs.automed.qproc.EnvParser
  Parse-action table.
_action_table - Static variable in class uk.ac.bbk.dcs.automed.qproc.QParser
  Parse-action table.
_production_table - Static variable in class uk.ac.bbk.dcs.automed.qproc.EnvParser
  Production table.
_production_table - Static variable in class uk.ac.bbk.dcs.automed.qproc.QParser
  Production table.
_reduce_table - Static variable in class uk.ac.bbk.dcs.automed.qproc.EnvParser
  `reduce_goto` table.
_reduce_table - Static variable in class uk.ac.bbk.dcs.automed.qproc.QParser
  `reduce_goto` table.

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