cellml_services Namespace Reference

AnnoTools provide supplementary annotation services to users of the CellML API, built on top of the user data facilities in the core API. More...

Classes
interface	StringAnnotation
	A string annotation. More...
interface	ObjectAnnotation
	An object annotation. More...
interface	AnnotationSet
	A set of finite-lifetime annotations. More...
interface	AnnotationToolService
	A service which allows other types of annotation utility objects to be created. More...
interface	ComputationTarget
interface	ComputationTargetIterator
interface	CodeInformation
interface	CodeGenerator
interface	CustomCodeInformation
interface	CustomGenerator
interface	IDACodeInformation
interface	IDACodeGenerator
interface	CodeGeneratorBootstrap
interface	LanguageDictionary
	Language dictionary for a specific service, eg MaLaES Tags or CCGS Patterns. More...
interface	DictionaryGenerator
interface	CeLEDSBootstrap
interface	CodeExporter
	Interface for exporting model to a programming language. More...
interface	CeLEDSExporterBootstrap
interface	ValidationService
	This is the base interface for CellML validation services. More...
interface	ModelTransformationService
	This is the base interface for CellML services which transform models from one form to another. More...
interface	ConnectedVariableSet
interface	CeVAS
interface	CeVASBootstrap
interface	IntegrationProgressObserver
interface	CellMLIntegrationRun
interface	ODESolverRun
interface	DAESolverRun
interface	CellMLCompiledModel
interface	ODESolverCompiledModel
interface	DAESolverCompiledModel
interface	CellMLIntegrationService
interface	BaseUnit
interface	UserBaseUnit
interface	BaseUnitInstance
	A reference to a base unit, optionally with a multiplier, offset, and exponent set. More...
interface	CanonicalUnitRepresentation
	The canonical representation of a units definition, as the product of powers of base units (perhaps with multiplicative factors, and optionally an offset if there is a single base unit). More...
interface	CUSES
	The primary interface to units processing services for a model. More...
interface	CUSESBootstrap
interface	DegreeVariable
	A source variable annotated by a degree. More...
interface	DegreeVariableIterator
	An interface allowing for iteration of variables by degree. More...
interface	MaLaESResult
	An interface allowing transformation results to be described. More...
interface	MaLaESTransform
	A MaLaES transformer, which takes MathML inputs, and produces programming language outputs. More...
interface	MaLaESBootstrap
	The bootstrap interface that can be used as a MaLaES transformer factory. More...
interface	TeLICeMResult
interface	TeLICeMModelResult
interface	TeLICeMMathResult
interface	TeLICeMService
interface	CellMLValidityError
	Represents a specific problem which causes a given document not to be a valid CellML model. More...
interface	CellMLRepresentationValidityError
	A validity error about the underlying structure used to represent the CellML model. More...
interface	CellMLSemanticValidityError
	A validity error at the semantic layer (used when the representation is valid, but there is some contradiction inherent in what is being represented. More...
interface	CellMLValidityErrorSet
	A list of CellML validity errors. More...
interface	VACSService
	The 'validation against CellML Specification Service' (VACSS) bootstrap interface. More...

Typedefs
typedef sequence< double >	DoubleSeq

Enumerations
enum	VariableEvaluationType {   VARIABLE_OF_INTEGRATION, CONSTANT, STATE_VARIABLE, ALGEBRAIC,   FLOATING, LOCALLY_BOUND, PSEUDOSTATE_VARIABLE }
enum	ModelConstraintLevel { UNDERCONSTRAINED, UNSUITABLY_CONSTRAINED, OVERCONSTRAINED, CORRECTLY_CONSTRAINED }
enum	ODEIntegrationStepType {   RUNGE_KUTTA_2_3, RUNGE_KUTTA_4, RUNGE_KUTTA_FEHLBERG_4_5, RUNGE_KUTTA_CASH_KARP_4_5,   RUNGE_KUTTA_PRINCE_DORMAND_8_9, RUNGE_KUTTA_IMPLICIT_2, RUNGE_KUTTA_IMPLICIT_2_SOLVE, RUNGE_KUTTA_IMPLICIT_4,   BULIRSCH_STOER_IMPLICIT_BD, GEAR_1, GEAR_2, ADAMS_MOULTON_1_12,   BDF_IMPLICIT_1_5_SOLVE }

Detailed Description

AnnoTools provide supplementary annotation services to users of the CellML API, built on top of the user data facilities in the core API.

The VACSS (validation against CellML specification service) provides services which allow models to be validated to check that they comply with the CellML specifications.

TeLICeMS (TeLICeM Service) is a serivce for processing CellML Models represented in the TeLICeM (*Te*xt-based *L*anguage for the *I*nput of *Ce*llML *M*odels) format.

MaLaES (the MathML Language Expression Service) provides facilities for converting from content MathML expressions (in the context of a CellML component or reaction) into expressions in a particular programming language.

CUSES (the CellML Units Simplification and Expansion Service) provides services for processing units in CellML, providing services such as looking up unit names in specific contexts, and reducing units to the simplest form involving only built in and user defined base units.

The CIS, or CellML Integration Service, allows models to be run (integrated).

The CeVAS, or CellML Variable Association Service, provides services which make it easier to work out which variables are the same, and so reduces the complexity of working with models which have mathematics spread across multiple components, possibly imported from multiple documents.

This module contains a description of the CellML supplementary service interfaces in the language-neutral IDL form.

CeLEDS (CellML Language Export Definition Service) provides a service for accessing language export definitions required by components involved in export of CellML models to various programming languages.

The CCGS, or CellML Code Generation Service, provides services which allow code in a procedural language to be generated for an entire CellML model.

These convenience services make it easier to write local annotations of various kinds on different objects.

The CCGS computes the order in which procedural steps should be performed, and uses the MaLaES service to generate expressions in the desired language.

Language definitions are stored in XML files. This interface depends only on MaLaES and can create a MaLaES transform object

Language definitions are stored in XML files. This interface uses CCGS to export code as a string.

Information about the procedural steps being run, such as information on assigned variable indices, is accessible via the CCGS.

It also provides facilities for converting between different but dimensionally compatible units.

The translation into a programming language occurs according to a special language description format called MAL.

It can also be used to process MathML expressions equation using the relevant subset of the TeLICeM format.

Typedef Documentation

typedef sequence<double> cellml_services::DoubleSeq

Definition at line 11 of file CIS.idl.

Enumeration Type Documentation

enum cellml_services::ModelConstraintLevel

Enumerator:

UNDERCONSTRAINED	The model is underconstrained. In this case, all code fragments will be empty strings. The set of targets which cannot be computed can be found because their VariableEvaluationType will be FLOATING. In order to make the model work, it is necessary to add equations or initial conditions which define some of these variables in terms of variables which can be computed.
UNSUITABLY_CONSTRAINED	There were variables which couldn't be found, but there were also equations which could not be used. This normally means that there is a system of equations which would need to be solved. However, in some cases, adding more constraints may allow the model to get past the this and be solved.
OVERCONSTRAINED	The model is overconstrained. The code generator will stop at the point where a redundant equation was found. The redundant equation will be present in flaggedEquations. The evaluation type will show the variables that have already been assigned.
CORRECTLY_CONSTRAINED	The model is correctly constrained. flaggedEquations contains all equations which are evaluated using the Newton-Raphson solver.

Definition at line 70 of file CCGS.idl.

enum cellml_services::ODEIntegrationStepType

Enumerator:

RUNGE_KUTTA_2_3
RUNGE_KUTTA_4
RUNGE_KUTTA_FEHLBERG_4_5
RUNGE_KUTTA_CASH_KARP_4_5
RUNGE_KUTTA_PRINCE_DORMAND_8_9
RUNGE_KUTTA_IMPLICIT_2
RUNGE_KUTTA_IMPLICIT_2_SOLVE
RUNGE_KUTTA_IMPLICIT_4
BULIRSCH_STOER_IMPLICIT_BD
GEAR_1
GEAR_2
ADAMS_MOULTON_1_12
BDF_IMPLICIT_1_5_SOLVE

Definition at line 13 of file CIS.idl.

enum cellml_services::VariableEvaluationType

Enumerator:

VARIABLE_OF_INTEGRATION	The target appears in the MathML as a bvar for a derivative, (i.e. is the variable of integration).
CONSTANT	The target has a specific, immediate value, taken from an initial_value attribute, or computed from other constants. It is possible for both derivatives and non-state variables to be constant.
STATE_VARIABLE	The target is a state variable, that is, it starts at an initial value and evolves according to rates defined in the model. Note that derivatives can be state variables too, for example if you define d^3x/dt3 = t (where t is the variable of integration), then d^3x/dt3 is COMPUTED, while d^2x/dt2, dx/dt, and x are of type STATE_VARIABLE.
ALGEBRAIC	The target is not a state variable, but can be computed from constants, state variables, variable(s) of integration and other 'algebraic' variables.
FLOATING	No way to compute the variable has yet been determined. This can happen if the model is under-constrained or unsuitably constrained, and no constraint would allow the variable to be computed, or if the model is overconstrained and the algorithm stopped before it worked out how to compute this variable.
LOCALLY_BOUND	The variable is used only locally, for example as the bound variable of a definite integral.
PSEUDOSTATE_VARIABLE	IDA-type only: A variable which changes with time, but is not driven by a higher derivative. In non-IDA type code generation, this would be an algebraic variable which makes up part of a system of equations.

Definition at line 15 of file CCGS.idl.