/usr/include/sbml/packages/comp/validator/constraints/CompIdBase.h is in libsbml5-dev 5.13.0+dfsg-1.
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* @cond doxygenLibsbmlInternal
*
* @file CompIdBase.h
* @brief Base class for Id constraints
* @author Ben Bornstein
*
* <!--------------------------------------------------------------------------
* This file is part of libSBML. Please visit http://sbml.org for more
* information about SBML, and the latest version of libSBML.
*
* Copyright (C) 2013-2016 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
* 3. University of Heidelberg, Heidelberg, Germany
*
* Copyright 2011-2012 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
*
* This library is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation. A copy of the license agreement is provided
* in the file named "LICENSE.txt" included with this software distribution
* and also available online as http://sbml.org/software/libsbml/license.html
* ---------------------------------------------------------------------- -->*/
#ifndef CompIdBase_h
#define CompIdBase_h
#ifdef __cplusplus
#include <string>
#include <sbml/validator/VConstraint.h>
#include <sbml/packages/comp/common/CompExtensionTypes.h>
LIBSBML_CPP_NAMESPACE_BEGIN
class SBase;
class CompValidator;
/**
* The CompIdBase Constraint is the base class for all SBML id constraints. It
* provides mechanisms for checking only certain subsets of ids within an
* SBML model and tailoring the error messages logged.
*
* To customize:
*
* 1. Override doCheck() to iterate over the SBML objects you are
* interested in and call checkId() for each.
*
* checkId() does the work of extracting the unique identifier
* (whether it be an id or variable name) from the SBML object and
* then delegates to doCheckId().
*
* 2. Override doCheckId() to perform the actual check. If the check
* fails, call logFailure().
*
* 3. Override getMessage() to log error messages. GetMessage() should
* use getPreamble() and getFieldName() when constructing the error
* message.
*
* 4. Override getPreamble() to customize the part of the actual error
* message that remains constant (e.g. the part that doesn't report
* line numbers, SBML object ids and typenames, etc).
*
* 5. Override getFieldName() if you are checking a field that isn't
* called 'id', for instance, the 'variable' field of a Rule.
*
* Finally, if you need the type name of the SBML object that failed,
* e.g. 'Compartment' or 'Species', when constructing an error message,
* call getTypename().
*/
class CompIdBase: public TConstraint<Model>
{
public:
/**
* Creates a new CompIdBase with the given constraint id.
*/
CompIdBase (unsigned int id, CompValidator& v);
/**
* Destroys this Constraint.
*/
virtual ~CompIdBase ();
protected:
/**
* Called by check(). Override this method to define your own subset.
*/
virtual void doCheck (const Model& m) = 0;
/**
* Checks that the id associated with the given object adheres to this
* constraint. If it does not, logFailure is called.
*/
virtual void doCheckId (const std::string& id, const SBase& object) = 0;
/**
* Returns the fieldname to use when logging constraint violations. Subclasses
* are supposed to override this method if "id" is not appropriate.
*
* @return the string "id".
*/
virtual const char* getFieldname ();
/**
* Returns the preamble to use when logging constraint violations.
* An empty string by default, any subclasses
* are supposed to override this method if this is not appropriate.
*
* @return an empty string (the preamble to use when logging constraint violations).
*/
virtual const char* getPreamble ();
/**
* Returns the error message to use when logging constraint violations.
* This method must be overridden by subclasses.
*
* If at all possible please use getPreamble() and getFieldname() when
* constructing error messages. This will help to make your constraint
* easily customizable.
*
* @return the error message to use when logging constraint violations.
*/
virtual const std::string
getMessage (const std::string& id, const SBase& object) = 0;
/* ------------------------------------------------------------ */
/* You should not need to override methods beyond this point. */
/* ------------------------------------------------------------ */
/**
* Checks that all ids for some given subset of the Model adhere to this
* Constraint. Override the doCheck() method to define your own subset.
*/
virtual void check_ (const Model& m, const Model& object);
/*
* These convenience methods simply wrap (delegate to) doCheckId(const
* std::string&, const SBase& object). This is necessary because getId()
* is not (yet) defined on SBase for SBML objects.
*
* For Rules and EventAssignments, it calls getVariable() instead.
*/
void checkId (const Model& x);
void checkId (const Submodel& x);
void checkId (const Port& x);
void checkId (const Deletion& x);
void checkId (const ReplacedElement& x);
void checkId (const ReplacedBy& x);
void checkId (const ModelDefinition& x);
void checkId (const ExternalModelDefinition& x);
void checkId (const FunctionDefinition& x);
void checkId (const UnitDefinition& x);
void checkId (const Compartment& x);
void checkId (const Species& x);
void checkId (const Parameter& x);
void checkId (const Rule& x);
void checkId (const Reaction& x);
void checkId (const Event& x);
void checkId (const EventAssignment& x);
void checkId (const CompartmentType& x);
void checkId (const SpeciesType& x);
void checkId (const SpeciesReference& x);
void checkId (const ModifierSpeciesReference& x);
void checkId (const InitialAssignment& x);
// void checkId (const SBase& x);
/**
* Returns a non-owning character pointer to the typename of the given SBase
* @p object, as constructed from its typecode and package.
*
* @return the typename of the given SBase object.
*/
const char* getTypename (const SBase& object);
/**
* Logs a message that the given @p id (and its corresponding object) have
* failed to satisfy this constraint.
*/
void logIdConflict (const std::string& id, const SBase& object);
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#endif /* CompIdBase_h */
/** @cond doxygenLibsbmlInternal */
|