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

## A

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`.
ACTION_ADD - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
  Transformation action "add"
ACTION_CONTRACT - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
  Transformation action "contract"
ACTION_DELETE - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
  Transformation action "delete"
ACTION_EXTEND - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
  Transformation action "extend"
ACTION_IDENT - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
  Transformation action "ident"
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_RENAME - Static variable in class uk.ac.ic.doc.automed.reps.Transformation
  Transformation action "rename"
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.gui.IntegrateDialog
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.ArgumentsDialog
actionPerformed(ActionEvent) - Method in class uk.ac.ic.doc.automed.gui.ArgPane
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(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.
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.
addCommand(String, Class, String) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
  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.
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
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
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
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
addPrefix(String, String) - Static method in class uk.ac.ic.doc.automed.Util
  Adds the prefix to the beginning of each line in message
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.DataSourceRepository
addVertex(HDMElement) - Method in class uk.ac.ic.doc.automed.reps.HDMEdge
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.
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.
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.
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.
Arc - class uk.ac.ic.doc.automed.gui.Arc.
Arc() - Constructor for class uk.ac.ic.doc.automed.gui.Arc
areRelativesMaximal() - Method in class uk.ac.ic.doc.automed.reps.Network
ARG_ACTION_IN_PRIMITIVE - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for action
ARG_ARGSEQUENCES_IN_FOREACH - Static variable in class uk.ac.ic.doc.automed.reps.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.reps.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.reps.CompositeTransformation
  Position in the INVOCATION_STATEMENT for the argument sequnce ID
ARG_CID_IN_NEWOBJECT - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the NEW_OBJECT_STATEMENT for CID(Construct ID)
ARG_CONSTRAINTS_IN_PRIMITIVE - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for constraints
ARG_FROMOBJ_IN_PRIMITIVE - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for FromObject OBID
ARG_FROMSCHEMA_IN_CONTRACT - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the CONTRACT_STATEMENT for the initial schema ID
ARG_FROMSCHEMA_IN_PRIMITIVE - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for FromSchema SID
ARG_FUNCTION_IN_PRIMITIVE - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for function
ARG_ISTEMP_IN_NEWOBJECT - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the NEW_OBJECT_STATEMENT for IsTemp
ARG_OBID_IN_NEWOBJECT - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the NEW_OBJECT_STATEMENT for OBID(Object ID)
ARG_OBJECT_IN_CONTRACT - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the CONTRACT_STATEMENT for object ID
ARG_RETURNED_ARGS_START_IN_FOREACH - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the FOREACH_STATEMENT where the returned argument sequences start
ARG_SCHEMA_IN_FOREACH - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the FOREACH_STATEMENT for current schema SID
ARG_SCHEME_IN_NEWOBJECT - Static variable in class uk.ac.ic.doc.automed.reps.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.reps.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.reps.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.reps.CompositeTransformation
  Position in the NEW_OBJECT_STATEMENT for SID(Schema ID)
ARG_SUBENTITIES_IN_EXTGENSCHEME - Static variable in class uk.ac.ic.doc.automed.reps.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.reps.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for ToObject OBID
ARG_TOSCHEMA_IN_CONTRACT - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the CONTRACT_STATEMENT for the final schema ID
ARG_TOSCHEMA_IN_PRIMITIVE - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the PRIMITIVE_TRANSFORMATION_STATEMENT for ToSchema SID
ARG_TRANS_IN_FOREACH - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Position in the FOREACH_STATEMENT for template transformation ID
ARG_TRANSFORMATION_IN_INVOCATION - Static variable in class uk.ac.ic.doc.automed.reps.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.reps.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
AT_LEAST_ONE - Static variable in class uk.ac.ic.doc.automed.editor.CommandLineDriver
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.
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.
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.

## 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.
Box - class uk.ac.ic.doc.automed.gui.Box.
Box() - Constructor for class uk.ac.ic.doc.automed.gui.Box

## C

caseCommand(String) - Static method in class uk.ac.ic.doc.automed.Util
  converts the argument into lower case with the first letter in uppercase
checkEditable() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Checks whether a schema is editable.
cidExists(int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
  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.
clear() - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Removes all of the statements from this ModelingProgram.
clearAccessMethods() - Static method in class uk.ac.ic.doc.automed.reps.AccessMethod
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.
close() - Method in class uk.ac.ic.doc.automed.editor.Gui
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
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
compareTo(Object) - Method in class uk.ac.ic.doc.automed.reps.Transformation
compareTo(Object) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
CompositeTransformation - class uk.ac.ic.doc.automed.reps.CompositeTransformation.
  The CompositeTransformation class.
CompositeTransformation(String, String, boolean) - Constructor for class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Constructs a new CompositeTransformation without any argument definitions nor program.
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
Construct - class uk.ac.ic.doc.automed.reps.Construct.
  The Construct class
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`.
ConstructAny - Static variable in class uk.ac.ic.doc.automed.reps.Construct
ConstructArray - Static variable in class uk.ac.ic.doc.automed.reps.Construct
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.
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(String) - Method in class uk.ac.ic.doc.automed.reps.Network
  Returns whether or not the network contains the named schema
CONTRACT_STATEMENT - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Statement to contract an object
copySchemaObject(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Deprecated. contents of intentional schemas will no longer be stored in the STR. The materialization code does not use this method. This method is called when the contents of an intentional schema are being materialized. The temporary copy of the object has the same OBID as the original, it just exists in the new SID as well as the original (via the objectSchema table).
createAccessMethod(int, String, int, String, String) - 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
  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.reps.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.reps.TemplateArgumentSequence
  Constructs a new TemplateArgument and adds it to this TemplateArgumentSequence.
createArgument(int, String) - Method in class uk.ac.ic.doc.automed.reps.RuntimeArgumentSequence
  Constructs a new RuntimeArgument and adds it to this RuntimeArgumentSequence.
createArgument(int, TemplateArgument) - Method in class uk.ac.ic.doc.automed.reps.TemplateArgumentSequence
  Constructs a new TemplateArgument and adds it to this TemplateArgumentSequence.
createArgument(int, TemplateArgumentSequence, int) - Method in class uk.ac.ic.doc.automed.reps.TemplateArgumentSequence
  Constructs a new TemplateArgument and adds it to this TemplateArgumentSequence.
createArgumentDefinition(int, String, boolean) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Defines an argument for this CompositeTransformation.
createArgumentDefinition(int, String, String, String) - Method in class uk.ac.ic.doc.automed.reps.Statement
  Defines an argument for this Statement.
createArgumentDefinition(int, String, String, String, boolean) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Defines an argument for this CompositeTransformation.
createArgumentSequence(Vector) - Method in class uk.ac.ic.doc.automed.gui.SchemaTool
createBox() - Static method in class uk.ac.ic.doc.automed.gui.SchemaManager
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, 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.ModelDefinitionsRepository
  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
  Deprecated. See the addXxxScheme() methods Creates a new `ConstructScheme` for the construct.
createConstructScheme(int, int, int, boolean, int, int, int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
  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.
createDefaultSchema(Vector) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Creates a new schema and appends it to the STR.
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.
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.
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.reps.CompositeTransformation
  Creates a new sequence of arguments and adds a new argument to the sequence
createIdentTransformations(Schema, Schema, String, String) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates an IDENT transformation.
createIntSchema(String) - Static method in class uk.ac.ic.doc.automed.STR
  Adds an intentional schema to the STR.
  Returns an integer that specifies the schema identifier (SID) assigned to the new schema.
createLine() - Static method in class uk.ac.ic.doc.automed.gui.SchemaManager
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(String) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
  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.
createObjectScheme(int, int) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Creates the scheme for a schema object and appends it to the STR.
createPrimitiveTransformation(int) - Method in class uk.ac.ic.doc.automed.reps.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.
createReturnedArgumentsDefinition(TemplateArgumentSequence) - Method in class uk.ac.ic.doc.automed.reps.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) - Static method in class uk.ac.ic.doc.automed.STR
  Adds a new schema to the STR.
createSchema(String, boolean, boolean, boolean, boolean) - 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(int, Vector) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Creates a new schema object and appends it to the STR.
createSchemaObject(Schema, Construct, Object[]) - Static method in class uk.ac.ic.doc.automed.reps.SchemaObject
  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.
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.reps.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.

## D

DataSourceRepository - class uk.ac.ic.doc.automed.DataSourceRepository.
  Reads data source definitions from a configuration file and provides methods to get a `Connection` for a data souce.
DataSourceRepositoryException - exception uk.ac.ic.doc.automed.DataSourceRepositoryException.
  The class of exceptions generated by `DataSourceRepository`.
DataSourceRepositoryException(String) - Constructor for class uk.ac.ic.doc.automed.DataSourceRepositoryException
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
DELETE - Static variable in class uk.ac.ic.doc.automed.IntegrityException
  Exception caused by an operation doing some sort of deletion from the repository.
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).
dispatchCommand(String) - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
dispatchCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
  Invokes the method registered for the command args[0] with `#addCommand(String, Class)`.
doCreateCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
doCreatedbCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
  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.DataSourceRepository
doDisplayCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
doDropdbCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
doExitCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
doGetCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
doGetCurrentModelCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.Editor
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.DataSourceRepository
doHelpCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
doIsCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
doListSchemaCommand(String[]) - Method in class uk.ac.ic.doc.automed.editor.Editor
doPopulatedbCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
doPrintCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
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.DataSourceRepository
doRemoveCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
doSetCommand(String[]) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
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
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
duplicateTransformation(Schema) - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Creates a duplicate of the transformation.

## E

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
equals(Object) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
equals(Object) - Method in class uk.ac.ic.doc.automed.reps.Construct
executeContractStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector, Vector) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Executes a `contract` statement.
executeExtGenSchemeStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector, Vector) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Executes a `extend_gen_scheme` statement.
executeForEachStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector, Vector) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Executes a `foreach` statement.
executeInvocationStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector, Vector) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Executes a `transformation_invocation` statement.
executeNewObjectStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector, Vector) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Executes a `new_object` statement.
executePrimitiveTransformationStatement(int, int, int, String[], HashMap, int, String[], String[], Vector, Vector, Vector) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Executes a `primitive_transformation` statement.
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.DataSourceRepository
executeStatement(String, String, boolean, Set) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
executeStatements(String, String, boolean) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
executeStatements(String, String, boolean, Set) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
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(int, int, String[], HashMap, int, String[], String[], Vector, Vector, Vector) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Main method which executes a composite transformation.
exists(int) - Static method in class uk.ac.ic.doc.automed.reps.Model
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.reps.Schema
  Returns true is the named schema exists
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
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.
EXTGENSCHEME_STATEMENT - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Statement to extend an ER generalization's scheme

## F

findAllPaths(String, String) - Static method in class uk.ac.ic.doc.automed.reps.TransformationPathway
findAllPathsToSchema(String) - Static method in class uk.ac.ic.doc.automed.reps.TransformationPathway
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).
findFile(String) - Static method in class uk.ac.ic.doc.automed.Util
findFileURL(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.
findPathFromClosestExtSchema(String) - Static method in class uk.ac.ic.doc.automed.reps.TransformationPathway
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.
findShortestPath(Schema, Schema) - Static method in class uk.ac.ic.doc.automed.reps.TransformationPathway
  Find the shortest path containing the fewest number of steps between two schemas.
findShortestPath(String, String) - Static method in class uk.ac.ic.doc.automed.reps.TransformationPathway
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.
FOREACH_STATEMENT - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Statement to iterate on lists

## G

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.
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.
getAccessMethodPID(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the protocol identifier (PID) of the specified access method.
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.
getActionFrom(Schema) - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the action of the transformation.
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.
getAllCompositeTransformations() - Static method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Returns an array of all CompositeTransformation objects.
getAllNetworks() - Static method in class uk.ac.ic.doc.automed.reps.Network
  Returns an array of all networks in the repository.
getAllNodes() - Method in class uk.ac.ic.doc.automed.reps.Network
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, int, int) - 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, int, int) - 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
getArgConstruct() - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Returns the `Construct` type of the `ConstructScheme`.
getArgumentAt(int) - Method in class uk.ac.ic.doc.automed.reps.TemplateArgumentSequence
  Returns a particular TemplateArgument in this TemplateArgumentSequence.
getArgumentAt(int) - Method in class uk.ac.ic.doc.automed.reps.RuntimeArgumentSequence
  Returns a particular RuntimeArgument in this RuntimeArgumentSequence.
getArgumentDefinitionAt(int) - Method in class uk.ac.ic.doc.automed.reps.Statement
  Returns a particular StatementArgumentDefinition in the Statements's argument definition list.
getArgumentDefinitionAt(int) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Returns a particular TransformationArgumentDefinition in the CompositeTransformations's argument definition list.
getArgumentDefinitions() - Method in class uk.ac.ic.doc.automed.reps.Statement
  Returns an array of all the StatementArgumentDefinition objects of this Statement.
getArgumentDefinitions() - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Returns an array of all the TransformationArgumentDefinition objects in this CompositeTransformation.
getArgumentDefinitions(boolean) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Returns an array of TransformationArgumentDefinition objects.
getArgumentDefinitionsForStatement(int) - Static method in class uk.ac.ic.doc.automed.reps.StatementArgumentDefinition
  Returns all the StatementArgumentDefinition objects of the specified statement.
getArgumentDefinitionsForTransformation(int) - Static method in class uk.ac.ic.doc.automed.reps.TransformationArgumentDefinition
  Returns all the TransformationArgumentDefinition objects of the specified transformation.
getArguments() - Method in class uk.ac.ic.doc.automed.reps.TemplateArgumentSequence
  Returns an array of all the TemplateArguments in this TemplateArgumentSequence.
getArguments() - Method in class uk.ac.ic.doc.automed.reps.RuntimeArgumentSequence
  Returns an array of all the RuntimeArguments in this RuntimeArgumentSequence.
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.
getArgumentsArgIdList() - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a list of identifiers of all the sequences of arguments
getArgumentsArgIdList() - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  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.TemplateTransformationRepository
  Returns a particular's sequence of arguments list of positions.
getArgumentsArgPosList(int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  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.reps.StatementExecution
  Returns the TemplateArgumentSequence of this StatementExecution.
getArgumentsForSequence(int) - Static method in class uk.ac.ic.doc.automed.reps.TemplateArgument
  Returns all the TemplateArgument objects of the specified sequence of arguments.
getArgumentsForSequence(int) - Static method in class uk.ac.ic.doc.automed.reps.RuntimeArgument
  Returns all RuntimeArgument objects of the specified sequence of arguments.
getArgumentsValue(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular argument's `value` field
getArgumentsValue(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns a particular argument's `value` field
getArgumentsValueList(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Returns a particular's sequence of arguments list of values.
getArgumentsValueList(int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Returns a particular's sequence of arguments list of `value` fields.
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
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
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.
getCID() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Returns the construct identifier (CID) of the construct.
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>>".
getColumnNames(ResultSet) - Static method in class uk.ac.ic.doc.automed.Util
getColumnTypes(ResultSet) - Static method in class uk.ac.ic.doc.automed.Util
getCommandClass() - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
getCommonSchema(Transformation) - Method in class uk.ac.ic.doc.automed.reps.Transformation
getCompositeTransformation(int) - Static method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Returns a reference to a CompositeTransformation.
getCompositeTransformation(String) - Static method in class uk.ac.ic.doc.automed.reps.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).
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).
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).
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.
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.reps.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
getConfigFileName() - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
  Returns the name of the file used for data source definitions.
getConstraint() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the constraint associated with the transformation.
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(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.ModelDefinitionsRepository
getConstructClassString(int) - Static method in class uk.ac.ic.doc.automed.reps.Construct
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.ModelDefinitionsRepository
  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.ModelDefinitionsRepository
getConstructNames(int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
  Gets a list of all construct names for a modelling language
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.ModelDefinitionsRepository
  Get the CIDs of all constructs for a modelling language
getConstructSchemeArgCID(int, int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
getConstructSchemeCount(int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
  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.ModelDefinitionsRepository
getConstructSchemeLowerBound(int, int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
getConstructSchemeType(int, int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
getConstructSchemeUpperBound(int, int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
getConstructType() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getConstructType() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getCurrentModelSyntax - Static variable in class uk.ac.ic.doc.automed.editor.Editor
getDataSourceConnection(String) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
  Gets a connection to the named data souce.
getDataSourceConnection(String, String, String) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
  Gets a connection to the named data souce.
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.TemplateTransformationRepository
  Returns the name of the repository in the local database.
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.SchemaModelingRepository
  Returns the name of the repository in the local database.
getDataSourceName() - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
  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.
getDataSourceProperty(String, String) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
  Returns the named property for the named data source as defined in the configuration file.
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.DataSourceRepository
getDefaultUserName() - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
getDescription() - Method in class uk.ac.ic.doc.automed.reps.TransformationArgumentDefinition
  Returns the description of this TransformationArgumentDefinition.
getDescription() - Method in class uk.ac.ic.doc.automed.reps.StatementArgumentDefinition
  Returns the description of this StatementArgumentDefinition.
getDescription() - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Returns the description of this CompositeTransformation.
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
getElements() - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
getEntityEdgePosition(Point) - Method in class uk.ac.ic.doc.automed.gui.Rhombus
getExpression() - Method in class uk.ac.ic.doc.automed.reps.HDMConstraint
getExtend(boolean) - Method in class uk.ac.ic.doc.automed.gui.SchemaManager
getFieldName() - Method in class uk.ac.ic.doc.automed.reps.TransformationArgumentDefinition
  Returns the fieldname of this TransformationArgumentDefinition.
getFieldName() - Method in class uk.ac.ic.doc.automed.reps.StatementArgumentDefinition
  Returns the fieldname of this StatementArgumentDefinition.
getFromOBID() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the schema object identifier (OBID) of the input of the transformaiton (fromObject).
getFromObjectsUnmatched() - Method in class uk.ac.ic.doc.automed.reps.SchemasNotIdenticalException
getFromSchema() - Method in class uk.ac.ic.doc.automed.reps.SchemasNotIdenticalException
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.
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
getGraphicObject(SchemaObject) - Method in class uk.ac.ic.doc.automed.gui.SchemaManager
getGraphics() - Method in class uk.ac.ic.doc.automed.gui.SchemaManager
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
getIconHeight() - Method in class uk.ac.ic.doc.automed.gui.ArrowIcon
getIconWidth() - Method in class uk.ac.ic.doc.automed.gui.ArrowIcon
getInsertableSQLValue(Object, int) - Static method in class uk.ac.ic.doc.automed.Util
getIsReturnedValue() - Method in class uk.ac.ic.doc.automed.reps.TransformationArgumentDefinition
  Returns the type of this TransformationArgumentDefinition.
getLeafs() - Method in class uk.ac.ic.doc.automed.reps.Network
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
getMDR_DataSourceName() - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
  Deprecated, use getDataSourceName instead
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
getModel() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Return the `Model` to which this Construct belongs
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.
getModelByName(String) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
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(int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
getModelNames() - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
  Gets a list of all modelling language names in the MDR
getModels() - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
  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.Network
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.ic.doc.automed.reps.Statement
  Returns the name of this Statement.
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.Construct
  Returns the name of the construct.
getName() - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Returns the name of this CompositeTransformation.
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
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
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
getNode(Node) - Method in class uk.ac.ic.doc.automed.reps.Network
  Deprecated.
getNode(Schema) - Method in class uk.ac.ic.doc.automed.reps.Network
  Returns the network node representing the supplied schema
getNode(String) - Method in class uk.ac.ic.doc.automed.reps.Network
  Returns the network node representing the named schema
getNodes() - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
getOBID() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Returns the schema object identifier (OBID) of a schema object.
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.
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.
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.
getPc() - Method in class uk.ac.ic.doc.automed.reps.StatementExecution
  Returns the program counter of this StatementExecution.
getPID() - Method in class uk.ac.ic.doc.automed.reps.Protocol
  Returns the protocol identifier (PID).
getPosition() - Method in class uk.ac.ic.doc.automed.reps.TemplateArgument
  Returns the position of this TemplateArgument.
getPosition() - Method in class uk.ac.ic.doc.automed.reps.RuntimeArgument
  Returns the position of this RuntimeArgument.
getPosition() - Method in class uk.ac.ic.doc.automed.reps.TransformationArgumentDefinition
  Returns the position in the transformation's argument definition list of this TransformationArgumentDefinition.
getPosition() - Method in class uk.ac.ic.doc.automed.reps.StatementArgumentDefinition
  Returns the position in the statement's argument definition list of this StatementArgumentDefinition.
getPositionInReferencedArgumentSequence() - Method in class uk.ac.ic.doc.automed.reps.TemplateArgument
  Returns the position in the referenced arguments sequence.
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.
getProtocol() - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Returns the `Protocol` used for connecting to the database.
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(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the name of the given protocol identifier (PID).
getReferencedArgumentSequence() - Method in class uk.ac.ic.doc.automed.reps.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.Transformation
  Returns all the schema objects referenced in a transformation.
getReferencedSchemaObjects() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Returns the set of SchemaObjects that are referenced by this SchemaObject.
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.
getReferringObjects(Schema, SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.Utility
  Returns the SchemaObject objects that include `object` in their schemes.
getRefSchemaObject() - Method in class uk.ac.ic.doc.automed.reps.Scheme
  Returns the `SchemaObject` that this `Scheme` wraps
getReturnedArgumentsDefinition() - Method in class uk.ac.ic.doc.automed.reps.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.reps.RuntimeArgumentSequence
  Returns the reference to the RuntimeArgumentSequence with the given ID.
getRuntimeArgumentSequences() - Static method in class uk.ac.ic.doc.automed.reps.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.SchemaObject
  Returns the schema to which the schema object belongs.
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.AccessMethod
  Returns the schema that represents the database to which the access method connects.
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.
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.
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.
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(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
  Return the `SchemaObject` that has the supplied name in this schema.
getSchemaObjectByName(String) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Return the `SchemaObject` that has the supplied name in this schema.
getSchemaObjectByOBID(int) - Static method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Returns the `SchemaObject` reference that has the given schema object identifier (OBID).
getSchemaObjectCID(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the construct identifier (CID) of the schema object.
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() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Find all `SchemaObjects` that are instances of a particular Construct.
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.
getSchemaObjectValue(int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the name (value) of the schema object.
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.reps.TransformationPathway
  Return as an array the `Schema`s that appear in the `Transformation`s of this TransformationPathway.
getSchemaSIDs() - Static method in class uk.ac.ic.doc.automed.STR
  Returns the schema identifier (SID) of all the schemas found in the STR.
getScheme() - Method in class uk.ac.ic.doc.automed.reps.Construct
  Returns an array of `ConstructScheme` objects representing the scheme of the construct.
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.
getSchemeNames() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getSchemeNames(int, int) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
getSchemeNamesString() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Returns the scheme representation (of type `String`) of the name of all the elements in a schema object's scheme.
getSchemeNamesString(int, int) - 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
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.
getSchemePos(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Returns the position of a referenced schema object in the scheme of a particular schema object.
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
getSequenceId() - Method in class uk.ac.ic.doc.automed.reps.TemplateArgumentSequence
  Returns the sequence ID of this TemplateArgumentSequence.
getSequenceId() - Method in class uk.ac.ic.doc.automed.reps.TemplateArgument
  Returns the sequence identifier of this TemplateArgument.
getSequenceId() - Method in class uk.ac.ic.doc.automed.reps.RuntimeArgumentSequence
  Returns the sequence ID of this RuntimeArgumentSequence.
getSequenceId() - Method in class uk.ac.ic.doc.automed.reps.RuntimeArgument
  Returns the sequence identifier of this RuntimeArgument.
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.
getSimplifiedTransformation(Transformation, Transformation) - Static method in class uk.ac.ic.doc.automed.reps.TransformationOptimiser
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
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.
getSQLType(String) - Static method in class uk.ac.ic.doc.automed.Util
getSQLTypeName(int) - Static method in class uk.ac.ic.doc.automed.Util
getStatement() - Method in class uk.ac.ic.doc.automed.reps.StatementExecution
  Returns the Statement of this StatementExecution.
getStatement(int) - Static method in class uk.ac.ic.doc.automed.reps.Statement
  Returns a reference to a Statement.
getStatement(String) - Static method in class uk.ac.ic.doc.automed.reps.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).
getStatementExecutionAt(int) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Returns a particular StatementExecution in the CompositeTransformations's template program.
getStatementExecutions() - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Returns an array of all the StatementExecution objects in this CompositeTransformation.
getStatementExecutionsForTransformation(int) - Static method in class uk.ac.ic.doc.automed.reps.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.reps.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.reps.StatementArgumentDefinition
  Returns the statement identifier defining which statement this StatementArgumentDefinition belongs to.
getStId() - Method in class uk.ac.ic.doc.automed.reps.Statement
  Returns the ID of this Statement.
getSTR_DataSourceName() - Static method in class uk.ac.ic.doc.automed.STR
  Deprecated. use getDataSourceName()
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.reps.TransformationArgumentDefinition
  Returns the tablename of this TransformationArgumentDefinition.
getTableName() - Method in class uk.ac.ic.doc.automed.reps.StatementArgumentDefinition
  Returns the tablename of this StatementArgumentDefinition.
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.reps.TemplateArgumentSequence
  Returns the reference to the TemplateArgumentSequence with the given ID.
getTemplateArgumentSequences() - Static method in class uk.ac.ic.doc.automed.reps.TemplateArgumentSequence
  Returns an array of all TemplateArgumentSequence objects that have TemplateArgument objects.
getToOBID() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the schema object identifier (OBID) of the output of the transformaiton (toObject).
getToObjectsUnmatched() - Method in class uk.ac.ic.doc.automed.reps.SchemasNotIdenticalException
getToSchema() - Method in class uk.ac.ic.doc.automed.reps.SchemasNotIdenticalException
getToSID() - Method in class uk.ac.ic.doc.automed.reps.Transformation
  Returns the schema identifier (SID) of the resultant schema.
getTran(int) - Method in class uk.ac.ic.doc.automed.reps.TransformationPathway
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
getTransformationObject(int, Schema) - Static method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Instantiates a transformation object.
getTransformations() - Static method in class uk.ac.ic.doc.automed.STR
  Returns a vector representing all transformations in the repository
getTransformations() - Static method in class uk.ac.ic.doc.automed.reps.Transformation
getTransformations() - Method in class uk.ac.ic.doc.automed.reps.TransformationPathway
  Return as an array the `Transformation`s that make up this TransformationPathway.
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.
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.reps.TransformationArgumentDefinition
  Returns the composite transformation identifier defining which transformation this TransformationArgumentDefinition belongs to.
getTransId() - Method in class uk.ac.ic.doc.automed.reps.StatementExecution
  Returns the transformation identifier of the composite transformation this StatementExecution belongs to.
getTransId() - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Returns the ID of this CompositeTransformation.
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.
getUpper() - Method in class uk.ac.ic.doc.automed.reps.ConstructScheme
  Returns the upper bound indicating the maximum occurence of the `ConstructScheme`.
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.TemplateArgument
  Returns this TemplateArgument's value field.
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.reps.RuntimeArgument
  Returns this RuntimeArgument's value field.
getValue() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
getValueForTemplateArgument(int, int, String, String[], HashMap) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Returns the value for a template argument.
getValueForTemplateArgumentPointingToArgId(int, int, String, String[], HashMap, Vector, boolean) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Returns the value for a template argument that points to another argument in the TTR.
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.
getVertices() - Method in class uk.ac.ic.doc.automed.reps.HDMEdge
GraphicSchemaObject - class uk.ac.ic.doc.automed.gui.GraphicSchemaObject.
GraphicSchemaObject(GraphicManager, Schema, SchemaObject) - Constructor for class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
Gui - class uk.ac.ic.doc.automed.editor.Gui.
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

## H

handleNonStatementArgument(int, String[], HashMap, Vector, boolean) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Creates an execution argument sequence according to a template argument sequence.
hasObject(SchemaObject) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Determines if the schema contains the given schema object.
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
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
HORIZONTAL_EXT - Static variable in class uk.ac.ic.doc.automed.gui.Rhombus

## I

identifierSafe(String) - Static method in class uk.ac.ic.doc.automed.reps.Syntax
IllegalOperationException - exception uk.ac.ic.doc.automed.reps.IllegalOperationException.
IllegalOperationException(String) - Constructor for class uk.ac.ic.doc.automed.reps.IllegalOperationException
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_ROW - Static variable in class uk.ac.ic.doc.automed.gui.SchemaManager
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.
indexOfTran(Transformation) - Method in class uk.ac.ic.doc.automed.reps.TransformationPathway
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
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
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).
INVOCATION_STATEMENT - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Statement to invoke other template transformations
invoke(RuntimeArgumentSequence) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Invokes this CompositeTransformation with the specified RuntimeArgumentSequence as arguments.
isCached() - Method in class uk.ac.ic.doc.automed.reps.Schema
  Deprecated. the `isCached` field in the schema table of the STR is no longer used. Determines whether or not the schema is cached. If a schema is cached, its contents (schema objects) are materialized and stored temporarily in the STR.
isConstructRoot(int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
isConstructSchemeKey(int, int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
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
isEmpty() - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Tests if this program is empty.
isExecuted() - Method in class uk.ac.ic.doc.automed.reps.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.
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.
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.
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.).
isRedundant(Transformation, Transformation) - Static method in class uk.ac.ic.doc.automed.reps.TransformationOptimiser
isReorderable(TransformationPathway, Transformation, Transformation) - Static method in class uk.ac.ic.doc.automed.reps.TransformationOptimiser
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.
isSchemaCached(int) - Static method in class uk.ac.ic.doc.automed.STR
  Deprecated. the isCached field in the schema table is no longer in use. Determines whether or not the objects of the specified schema are cached.
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.
isSchemaObjectTemp(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Deprecated. the isTemp field in the object table is no longer in use. Determines whether or not the schema object is temporary.
isSimplifiable(Transformation, Transformation) - Static method in class uk.ac.ic.doc.automed.reps.TransformationOptimiser
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`
isTree() - Method in class uk.ac.ic.doc.automed.reps.Network
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.
isWellformed() - Method in class uk.ac.ic.doc.automed.reps.TransformationPathway

## L

Line - class uk.ac.ic.doc.automed.gui.Line.
Line() - Constructor for class uk.ac.ic.doc.automed.gui.Line
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.
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
  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
load(Schema) - Method in class uk.ac.ic.doc.automed.gui.SchemaManager
  Loads the schema specified into this SchemaManager.
LoadDialog - class uk.ac.ic.doc.automed.gui.LoadDialog.
LoadDialog(Frame, String, boolean) - Constructor for class uk.ac.ic.doc.automed.gui.LoadDialog

## M

main(String[]) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepository
main(String[]) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
main(String[]) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
main(String[]) - Static method in class uk.ac.ic.doc.automed.SchemaModelingRepository
main(String[]) - Static method in class uk.ac.ic.doc.automed.STRMethodTest
main(String[]) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
  Executing this class invokes this method which supplies a command line interface to the ModelDefinitionsRepository.
main(String[]) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
  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.STR
main(String[]) - Static method in class uk.ac.ic.doc.automed.reps.SchemaMapGenerator
main(String[]) - Static method in class uk.ac.ic.doc.automed.reps.SchemaEvolutionExample
main(String[]) - Static method in class uk.ac.ic.doc.automed.reps.RepsTest
main(String[]) - Static method in class uk.ac.ic.doc.automed.gui.SchemaTool
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.ic.doc.automed.editor.CommandLineDriver
makeIdentifierSafe(String) - Static method in class uk.ac.ic.doc.automed.reps.Syntax
makeStringSafe(String) - Static method in class uk.ac.ic.doc.automed.reps.Syntax
materialize(Path) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Materialize the contents of an intentional schema via the given path.
MDR_DataSourceName - Static variable in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
Model - class uk.ac.ic.doc.automed.reps.Model.
  The Model class
ModelDefinitionsRepository - class uk.ac.ic.doc.automed.ModelDefinitionsRepository.
  Properties used from the MDR data source
ModelDefinitionsRepository() - Constructor for class uk.ac.ic.doc.automed.ModelDefinitionsRepository
ModelDefinitionsRepositoryException - exception uk.ac.ic.doc.automed.ModelDefinitionsRepositoryException.
  The class of exceptions generated by `ModelDefinitionsRepository`.
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.
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.gui.SchemaCanvas
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.gui.SchemaCanvas
mouseReleased(MouseEvent) - Method in class uk.ac.ic.doc.automed.gui.SchemaCanvas

## N

Network - class uk.ac.ic.doc.automed.reps.Network.
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.
NEW_OBJECT_STATEMENT - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Statement to create new objects
NO_EXT - Static variable in class uk.ac.ic.doc.automed.gui.Rhombus
Node - class uk.ac.ic.doc.automed.reps.Node.
NOT_EQUAL - Static variable in class uk.ac.ic.doc.automed.IntegrityException
  Exception caused by an operation doing some sort comparison where .
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.
numOfTrans() - Method in class uk.ac.ic.doc.automed.reps.TransformationPathway

## O

OBJECT_HDISTANCE - Static variable in class uk.ac.ic.doc.automed.gui.SchemaManager
OBJECT_VDISTANCE - Static variable in class uk.ac.ic.doc.automed.gui.SchemaManager
optimisePathway(TransformationPathway) - Static method in class uk.ac.ic.doc.automed.reps.TransformationOptimiser
OPTIONAL - Static variable in class uk.ac.ic.doc.automed.editor.CommandLineDriver

## P

paint(Graphics) - Method in class uk.ac.ic.doc.automed.gui.ToolTip
paintComponent(Graphics) - Method in class uk.ac.ic.doc.automed.gui.SchemaCanvas
paintIcon(Component, Graphics, int, int) - Method in class uk.ac.ic.doc.automed.gui.ArrowIcon
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,
preservesEquivalence() - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Returns whether this CompositeTransformation preserves schema equivalence.
PRIMITIVE_TRANSFORMATION_STATEMENT - Static variable in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Statement to execute primitive transformations
print() - Method in class uk.ac.ic.doc.automed.reps.TemplateArgumentSequence
print() - Method in class uk.ac.ic.doc.automed.reps.TemplateArgument
print() - Method in class uk.ac.ic.doc.automed.reps.RuntimeArgumentSequence
print() - Method in class uk.ac.ic.doc.automed.reps.RuntimeArgument
print() - Method in class uk.ac.ic.doc.automed.reps.TransformationArgumentDefinition
print() - Method in class uk.ac.ic.doc.automed.reps.StatementExecution
print() - Method in class uk.ac.ic.doc.automed.reps.StatementArgumentDefinition
print() - Method in class uk.ac.ic.doc.automed.reps.Statement
print() - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
print() - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
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
processCommands() - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
processCommands(Reader, Writer) - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
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 - class uk.ac.ic.doc.automed.reps.Protocol.
  The Protocol class describes a generic method of accessing data sources, such as JDBC or ODBC.

## Q

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

read(InputStream) - Static method in class uk.ac.ic.doc.automed.reps.Transformation
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.Schema
read(InputStream, String) - Static method in class uk.ac.ic.doc.automed.reps.Model
read(InputStream, String) - Static method in class uk.ac.ic.doc.automed.reps.Schema
readConfigFile() - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
  Reads the current configuration file.
readConfigFile(String) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
  Reads the directives for the data sources defined in configFile.
reflectCommandMethods() - Method in class uk.ac.ic.doc.automed.editor.CommandLineDriver
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 ModelDefinitionsRepository 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.Transformation
  Removes this `Transformation` from the repository.
remove() - Method in class uk.ac.ic.doc.automed.reps.TemplateArgumentSequence
  Removes this TemplateArgumentSequence.
remove() - Method in class uk.ac.ic.doc.automed.reps.TemplateArgument
  Removes this TemplateArgument from the TTR.
remove() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
remove() - Method in class uk.ac.ic.doc.automed.reps.Protocol
remove() - Method in class uk.ac.ic.doc.automed.reps.RuntimeArgumentSequence
  Removes this RuntimeArgumentSequence.
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.RuntimeArgument
  Removes this RuntimeArgument from the TER.
remove() - Method in class uk.ac.ic.doc.automed.reps.TransformationArgumentDefinition
  Removes this TransformationArgumentDefinition from the TTR.
remove() - Method in class uk.ac.ic.doc.automed.reps.StatementExecution
  Removes this StatementExecution from the TTR.
remove() - Method in class uk.ac.ic.doc.automed.reps.StatementArgumentDefinition
  Removes this StatementArgumentDefinition from the TTSR.
remove() - Method in class uk.ac.ic.doc.automed.reps.Statement
  Removes this Statement
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.ConstructWithModelingProgram
  Removes this ConstructWithModelingProgram object.
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.CompositeTransformation
  Removes this CompositeTransformation
remove() - Method in class uk.ac.ic.doc.automed.reps.AccessMethod
  Remove this AccessMethod from the repository.
remove(int) - Static method in class uk.ac.ic.doc.automed.reps.Protocol
  Removes the protocol with the given protocol PID.
remove(int) - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Removes the stamement at the specified program counter in this program.
remove(String) - Static method in class uk.ac.ic.doc.automed.reps.Protocol
  Removes the protocol with the given protocolName.
remove(String) - Static method in class uk.ac.ic.doc.automed.reps.Schema
  Removes the Schema with the given schemaName.
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 `AccessMethods` recorded for this schema.
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.reps.TemplateArgumentSequence
  Removes a particular argument from this TemplateArgumentSequence.
removeArgument(int) - Method in class uk.ac.ic.doc.automed.reps.RuntimeArgumentSequence
  Removes a particular argument from this RuntimeArgumentSequence.
removeArgument(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Removes a particular position from a sequence of arguments
removeArgument(int, int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Removes a particular position from a sequence of arguments
removeArgumentDefinition(int) - Method in class uk.ac.ic.doc.automed.reps.Statement
  Removes a particular argument definition from this Statements's argument definition list.
removeArgumentDefinition(int) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Removes a particular argument definition from this CompositeTransformation's argument definition list.
removeArguments(int) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Removes a particular sequence of arguments
removeArguments(int) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Removes a particular sequence of arguments
removeArgumentSequences() - Method in class uk.ac.ic.doc.automed.gui.SchemaTool
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.reps.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.ModelDefinitionsRepository
  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.ModelDefinitionsRepository
  Remove the construct.
removeExecutionTrace(int, Vector) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Removes the trace of a composite transformation's executionfrom the TER.
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.ModelDefinitionsRepository
  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.
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.reps.CompositeTransformation
  Removes the definitions of this transformation's returned arguments.
removeRuntimeArgumentSequence(int) - Static method in class uk.ac.ic.doc.automed.reps.RuntimeArgumentSequence
  Removes a RuntimeArgumentSequence.
removeSchema(int) - Static method in class uk.ac.ic.doc.automed.STR
  Removes a schema from the STR.
removeSchemaObject(int) - Static method in class uk.ac.ic.doc.automed.STR
  Removes a schema object from the STR.
removeSchemaObjectFromMap(SchemaObject) - Static method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Deprecated. use @link remove() to remove SchemaObjects Removes a `SchemaObject` object from the schema object `HashMap`.
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.
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.
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.reps.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.reps.CompositeTransformation
  Removes a particular statement execution from this CompositeTransformations's template program
removeTemplateArgumentSequence(int) - Static method in class uk.ac.ic.doc.automed.reps.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
repaint(Graphics, boolean) - Method in class uk.ac.ic.doc.automed.gui.SchemaManager
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`.
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
RepsTest - class uk.ac.ic.doc.automed.reps.RepsTest.
RepsTest() - Constructor for class uk.ac.ic.doc.automed.reps.RepsTest
resultSetToArray(ResultSet) - Static method in class uk.ac.ic.doc.automed.Util
retract() - Method in class uk.ac.ic.doc.automed.reps.Transformation
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.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.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.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.AccessMethod
  Remove this AccessMethod, and any other classes that are dependent upon its existance.
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.
Rhombus - class uk.ac.ic.doc.automed.gui.Rhombus.
Rhombus() - Constructor for class uk.ac.ic.doc.automed.gui.Rhombus
rollbackSTR(Vector, Vector) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Removes the trace of a composite transformation's execution for the STR.
RuntimeArgument - class uk.ac.ic.doc.automed.reps.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.reps.RuntimeArgument
  Constructs a new RuntimeArgument storing the specified value.
RuntimeArgument(int, String) - Constructor for class uk.ac.ic.doc.automed.reps.RuntimeArgument
  Constructs a new RuntimeArgument storing the specified value and creates a new sequence of arguments.
RuntimeArgumentSequence - class uk.ac.ic.doc.automed.reps.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.reps.RuntimeArgumentSequence
  Constructs a new RuntimeArgumentSequence without any RuntimeArgument objects

## S

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`.
Schema - class uk.ac.ic.doc.automed.reps.Schema.
  The Schema class
SCHEMA_NAME - Static variable in class uk.ac.ic.doc.automed.TemplateExecutionRepository
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
SchemaEvolutionExample - class uk.ac.ic.doc.automed.reps.SchemaEvolutionExample.
SchemaEvolutionExample() - Constructor for class uk.ac.ic.doc.automed.reps.SchemaEvolutionExample
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
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
SchemaObject - class uk.ac.ic.doc.automed.reps.SchemaObject.
  The SchemaObject class
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.
  Old name for the STR
SchemaTransformationRepository() - Constructor for class uk.ac.ic.doc.automed.SchemaTransformationRepository
SchemaTransformationRepositoryException - exception uk.ac.ic.doc.automed.SchemaTransformationRepositoryException.
  Old name for STRException
SchemaTransformationRepositoryException(String) - Constructor for class uk.ac.ic.doc.automed.SchemaTransformationRepositoryException
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_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(SchemaObject, int, SchemaObject, boolean) - Constructor for class uk.ac.ic.doc.automed.reps.Scheme
  Creates a new scheme for a schema object.
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.
setAccessMethodDBDriver(int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the database driver 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.
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.
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`.
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.reps.StatementExecution
  Sets the TemplateArgumentSequence of this StatementExecution
setArgumentsValue(int, int, String) - Static method in class uk.ac.ic.doc.automed.TemplateTransformationRepository
  Sets an argument's `value` field
setArgumentsValue(int, int, String) - Static method in class uk.ac.ic.doc.automed.TemplateExecutionRepository
  Sets an argument's `value` field
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
setCached(boolean) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Deprecated. the `isCached` field in the schema table of the STR is no longer used. Sets whether or not the schema is cached. A schema can only be cached if it is an extentional schema.
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.DataSourceRepository
setCommandHelp(String[][]) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
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.
setConfigFileName(String) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
  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.
setConstraints(HDMConstraint[]) - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
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.ModelDefinitionsRepository
setConstructMID(int, int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
  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.ModelDefinitionsRepository
setConstructRoot(int, boolean) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
setConstructSchemeArgCID(int, int, int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
setConstructSchemeHDMType(int, int, int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
setConstructSchemeKey(int, int, boolean) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
setConstructSchemeLowerBound(int, int, int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
setConstructSchemeType(int, int, int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
setConstructSchemeUpperBound(int, int, int) - Static method in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
setConstructType(Construct) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Sets the construct type of the schema object.
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.TemplateTransformationSyntaxRepository
  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.TemplateExecutionRepository
  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.ModelDefinitionsRepository
  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.
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
setDefaultDataSource(String) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
setDefaultUserName(String) - Static method in class uk.ac.ic.doc.automed.DataSourceRepository
setDescription(String) - Method in class uk.ac.ic.doc.automed.reps.TransformationArgumentDefinition
  Sets the description of this TransformationArgumentDefinition .
setDescription(String) - Method in class uk.ac.ic.doc.automed.reps.StatementArgumentDefinition
  Sets the description of this StatementArgumentDefinition.
setDescription(String) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Sets this CompositeTransformation's description.
setEdges(HDMEdge[]) - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
setElements(HDMElement[]) - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
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
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.
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
setFieldName(String) - Method in class uk.ac.ic.doc.automed.reps.TransformationArgumentDefinition
  Sets the fieldname of this TransformationArgumentDefinition .
setFieldName(String) - Method in class uk.ac.ic.doc.automed.reps.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
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
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
setIsReturnedValue(boolean) - Method in class uk.ac.ic.doc.automed.reps.TransformationArgumentDefinition
  Sets the isReturnedValue type of this TransformationArgumentDefinition.
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.
setLayout(String) - Method in class uk.ac.ic.doc.automed.gui.Box
setLayoutAxis(String) - Method in class uk.ac.ic.doc.automed.gui.Box
setListData(Object[]) - Method in class uk.ac.ic.doc.automed.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.ModelDefinitionsRepository
  Deprecated. use setDataSourceName()
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`
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.ModelDefinitionsRepository
setName(String) - Method in class uk.ac.ic.doc.automed.reps.HDMElement
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.reps.Statement
  Sets this Statement's name.
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.Construct
  Sets the name of the construct to the given string.
setName(String) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Sets this CompositeTransformation's name.
setNodes(HDMNode[]) - Method in class uk.ac.ic.doc.automed.reps.HDMNetwork
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>>".``
setPoint1(Point) - Method in class uk.ac.ic.doc.automed.gui.Line
setPoint2(Point) - Method in class uk.ac.ic.doc.automed.gui.Line
setPreservesEquivalence(boolean) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Sets whether this CompositeTransformation preserves schema equivalence.
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).
setReference(int) - Method in class uk.ac.ic.doc.automed.reps.TemplateArgument
  Sets the TemplateArgument to refer to the transformation's arguments.
setReference(TemplateArgument) - Method in class uk.ac.ic.doc.automed.reps.TemplateArgument
  Sets this TemplateArgument to refer to another TemplateArgument.
setReference(TemplateArgumentSequence, int) - Method in class uk.ac.ic.doc.automed.reps.TemplateArgument
  Sets this TemplateArgument to refer to the specified position in the specified TemplateArgumentSequence.
setReturnedArgumentsDefinition(TemplateArgumentSequence) - Method in class uk.ac.ic.doc.automed.reps.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(Schema) - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
  Sets the schema to which the schema object belongs.
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.
setSchemaCached(int, boolean) - Static method in class uk.ac.ic.doc.automed.STR
  Deprecated. the isCached field in the schema table is no longer in use.
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.
setSchemaName(int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the name of schema.
setSchemaObjectCID(int, int) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the construct identifier (CID) of the schema object.
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.
setSchemaObjectValue(int, String) - Static method in class uk.ac.ic.doc.automed.STR
  Sets the name/value of the schema object.
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
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
setSmartQuoting(boolean) - Static method in class uk.ac.ic.doc.automed.reps.Syntax
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.reps.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`
setSTR_DataSourceName(String) - Static method in class uk.ac.ic.doc.automed.STR
  Deprecated. use setDataSourceName()
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.reps.TransformationArgumentDefinition
  Sets the tablename of this TransformationArgumentDefinition .
setTableName(String) - Method in class uk.ac.ic.doc.automed.reps.StatementArgumentDefinition
  Sets the tablename of this StatementArgumentDefinition.
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
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.
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.TemplateArgument
  Sets the value of this TemplateArgument.
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.reps.RuntimeArgument
  Sets the value of this RuntimeArgument.
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
show() - Method in class uk.ac.ic.doc.automed.gui.ToolTip
showDialog() - Method in class uk.ac.ic.doc.automed.gui.LoadDialog
size() - Method in class uk.ac.ic.doc.automed.reps.ModelingProgram
  Returns the number of statements in this program.
Statement - class uk.ac.ic.doc.automed.reps.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.reps.Statement
  Constructs a new Statement without any StatementArgumentDefinition objects.
StatementArgumentDefinition - class uk.ac.ic.doc.automed.reps.StatementArgumentDefinition.
  The class used to define a statement's arguments.
StatementArgumentDefinition(int, int, String, String, String) - Constructor for class uk.ac.ic.doc.automed.reps.StatementArgumentDefinition
  Constructs a new StatementArgumentDefinition.
StatementExecution - class uk.ac.ic.doc.automed.reps.StatementExecution.
  The class used to define a template transformation's program.
StatementExecution(int, int, Statement, TemplateArgumentSequence) - Constructor for class uk.ac.ic.doc.automed.reps.StatementExecution
  Constructs a new StatementExecution.
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.
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
STRMethodTest - class uk.ac.ic.doc.automed.STRMethodTest.
STRMethodTest() - Constructor for class uk.ac.ic.doc.automed.STRMethodTest
syncWithRepository() - Static method in class uk.ac.ic.doc.automed.reps.Transformation
Syntax - class uk.ac.ic.doc.automed.reps.Syntax.
Syntax() - Constructor for class uk.ac.ic.doc.automed.reps.Syntax
SyntaxException - exception uk.ac.ic.doc.automed.reps.SyntaxException.
SyntaxException(String) - Constructor for class uk.ac.ic.doc.automed.reps.SyntaxException

## T

TemplateArgument - class uk.ac.ic.doc.automed.reps.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.reps.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.reps.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.reps.TemplateArgument
  Constructs a new TemplateArgument storing the specified value.
TemplateArgument(int, int, TemplateArgument) - Constructor for class uk.ac.ic.doc.automed.reps.TemplateArgument
  Constructs a new TemplateArgument that refers to another TemplateArgument
TemplateArgument(int, int, TemplateArgumentSequence, int) - Constructor for class uk.ac.ic.doc.automed.reps.TemplateArgument
  Constructs a new TemplateArgument that refers to another argument
TemplateArgument(int, String) - Constructor for class uk.ac.ic.doc.automed.reps.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.reps.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.reps.TemplateArgument
  Constructs a new TemplateArgument that refers to another argument and creates a new argument sequence
TemplateArgumentSequence - class uk.ac.ic.doc.automed.reps.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.reps.TemplateArgumentSequence
  Constructs a new TemplateArgumentSequence without any TemplateArgument objects.
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
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
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
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
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.
toString() - Method in class uk.ac.ic.doc.automed.reps.Node
toString() - Method in class uk.ac.ic.doc.automed.reps.Network
toString() - Method in class uk.ac.ic.doc.automed.reps.Transformation
toString() - Method in class uk.ac.ic.doc.automed.reps.TransformationPathway
toString() - Method in class uk.ac.ic.doc.automed.reps.SchemaObject
toString() - Method in class uk.ac.ic.doc.automed.gui.GraphicSchemaObject
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"
Transformation - class uk.ac.ic.doc.automed.reps.Transformation.
  The Transformation class
Transformation(int, int, int, int, int, String, String, boolean) - Constructor for class uk.ac.ic.doc.automed.reps.Transformation
  Instantiates a transformation.
TransformationArgumentDefinition - class uk.ac.ic.doc.automed.reps.TransformationArgumentDefinition.
  The class used to define a template transformation's arguments.
TransformationArgumentDefinition(int, int, String, String, String, boolean) - Constructor for class uk.ac.ic.doc.automed.reps.TransformationArgumentDefinition
  Constructs a new TransformationArgumentDefinition.
TransformationOptimiser - class uk.ac.ic.doc.automed.reps.TransformationOptimiser.
  This class provides the functionalities to optimise a `TransformationPathway`, by using TML transformation optimisation techniques.
TransformationOptimiser() - Constructor for class uk.ac.ic.doc.automed.reps.TransformationOptimiser
TransformationPathway - class uk.ac.ic.doc.automed.reps.TransformationPathway.
  The TransformationPathway class
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.
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`
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

## U

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.gui - package uk.ac.ic.doc.automed.gui
uk.ac.ic.doc.automed.reps - package uk.ac.ic.doc.automed.reps
UnexpectedTokenException - exception uk.ac.ic.doc.automed.reps.UnexpectedTokenException.
UnexpectedTokenException(int, int, int, Syntax.Token) - Constructor for class uk.ac.ic.doc.automed.reps.UnexpectedTokenException
UnexpectedTokenException(int, int, Syntax.Token) - Constructor for class uk.ac.ic.doc.automed.reps.UnexpectedTokenException
UnexpectedTokenException(String) - Constructor for class uk.ac.ic.doc.automed.reps.UnexpectedTokenException
union(Schema) - Method in class uk.ac.ic.doc.automed.reps.Schema
  Return an `Schema` (`su`) containing the union of `SchemaObjects` 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).
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
updateObjectScheme(int, int, int) - Method in class uk.ac.ic.doc.automed.reps.CompositeTransformation
  Extends a Generalisation's scheme in the STR.
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.
userName - Static variable in class uk.ac.ic.doc.automed.ModelDefinitionsRepository
Util - class uk.ac.ic.doc.automed.Util.
Util() - Constructor for class uk.ac.ic.doc.automed.Util
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

valueChanged(ListSelectionEvent) - Method in class uk.ac.ic.doc.automed.gui.SchemaTool
VERTICAL_EXT - Static variable in class uk.ac.ic.doc.automed.gui.Rhombus

## W

write() - Method in class uk.ac.ic.doc.automed.reps.Transformation
write() - Method in class uk.ac.ic.doc.automed.reps.TransformationPathway
  Write out the series of transformations found in this pathway to the standard output in a human readable form
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(OutputStream) - 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.Model
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.Construct
write(PrintWriter) - 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.Model
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.Construct

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