OntologyTerm.h

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/*
* ****************************************************************************
* This file is part of libNUML.  Please visit http://code.google.com/p/numl/for more
* information about NUML, and the latest version of libNUML. 
* Copyright (c) 2013 The University of Manchester.
* 
* 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://www.gnu.org/licenses/lgpl.html 
* 
* Contributors:
* Joseph O. Dada, The University of Manchester - initial API and implementation
* ****************************************************************************
**/

 
 
#ifndef ONTOLOGYTERM_H_
#define ONTOLOGYTERM_H_
 
#include <numl/common/extern.h>
#include <numl/common/numlfwd.h>
 
 
 
//#include <numl/NUMLVisitor.h>
#include <numl/NMBase.h>
#include <string>
 
#include <numl/NUMLList.h>
 
#ifdef __cplusplus
LIBNUML_CPP_NAMESPACE_BEGIN
 
/*
 *
 */
class LIBNUML_EXTERN OntologyTerm : public NMBase  {
 
public:
    OntologyTerm (unsigned int level, unsigned int version);
 

    OntologyTerm (NUMLNamespaces* numlns);

    virtual bool accept (NUMLVisitor& v) const;
 

    virtual OntologyTerm* clone () const;

    const std::string& getId () const;
 

    const std::string& getTerm () const;

    const std::string& getSourceTermId () const;

    const std::string& getOntologyURI () const;
 
 
    virtual ~OntologyTerm();
 
    /*
     *
     * Sets the value of the "id" attribute of this NUML object.
     *
     * The string @p id is copied.  Note that NUML has strict requirements
     * for the syntax of identifiers.  The following is summary of the
     * definition of the NUML identifier type @c SId (here expressed in an
     * extended form of BNF notation):
     * @code
     *   letter ::= 'a'..'z','A'..'Z'
     *   digit  ::= '0'..'9'
     *   idChar ::= letter | digit | '_'
     *   SId    ::= ( letter | '_' ) idChar*
     * @endcode
     * The equality of NUML identifiers is determined by an exact character
     * sequence match; i.e., comparisons must be performed in a
     * case-sensitive manner.  In addition, there are a few conditions for
     * the uniqueness of identifiers in an NUML model.  Please consult the
     * NUML specifications for the exact formulations.
     *
     * @param id the string to use as the identifier of this object
     *
     * @return integer value indicating success/failure of the
     * function.  @if clike The value is drawn from the
     * enumeration #OperationReturnValues_t. @endif The possible values
     * returned by this function are:
     * @li LIBNUML_OPERATION_SUCCESS
     * @li LIBNUML_INVALID_ATTRIBUTE_VALUE
     */
    int setId (const std::string& sid);
 

    int setTerm (const std::string& term);

    int setSourceTermId(const std::string& sourceTermId);

    int setOntologyURI(const std::string& ontologyURI);

    virtual NUMLTypeCode_t getTypeCode() const;

    virtual const std::string& getElementName() const;

  virtual void readAttributes(const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLAttributes& attributes);
 

  virtual void writeAttributes (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream& stream) const;
 
protected:
 
 
    OntologyTerm();
 
    std::string mId;
    std::string mTerm;
    std::string mSourceTermId;
    std::string mOntologyURI;
 
    //std::vector<ONTOLOGY> mOntologies;
 
 
 
    /* the validator classes need to be friends to access the
     * protected constructor that takes no arguments
     */
    friend class Validator;
    friend class ConsistencyValidator;
    friend class IdentifierConsistencyValidator;
    friend class InternalConsistencyValidator;
 
};
 
//structure for recognised ontologies
struct ONTOLOGY {
    std::string term;
    std::string sourceTermId;
    std::string ontologyURI;
};
class LIBNUML_EXTERN OntologyTerms : public NUMLList
{
public:

    virtual OntologyTerms* clone () const;
 

    virtual NUMLTypeCode_t getTypeCode () const { return NUML_NUMLLIST; };
 

    virtual NUMLTypeCode_t getItemTypeCode () const;
 

    virtual const std::string& getElementName () const;

    virtual OntologyTerm * get(unsigned int n);
 

    virtual const OntologyTerm * get(unsigned int n) const;
 

    virtual OntologyTerm* get (const std::string& sid);
 

    virtual const OntologyTerm* get (const std::string& sid) const;
 

    virtual OntologyTerm* remove (unsigned int n);
 

    virtual OntologyTerm* remove (const std::string& sid);
 
 

    virtual int getElementPosition () const;
 
 
 
 
protected:

  virtual NMBase* createObject (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream& stream);
 
 
};
 
 
LIBNUML_CPP_NAMESPACE_END
 
#endif  /* __cplusplus */
 
#ifndef SWIG
 
LIBNUML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
 
//TODO
 
END_C_DECLS
LIBNUML_CPP_NAMESPACE_END
 
#endif  /* !SWIG   */
 
#endif /* ONTOLOGYTERM_H_ */