/**
 * @file    SpeciesType.h
 * @brief   Definitions of SpeciesType and ListOfSpeciesType.
 * @author  Ben Bornstein
 *
 * $Id: SpeciesType.h 10084 2009-08-22 11:52:43Z ajouraku $
 * $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/branches/rel-4-0-0/src/sbml/SpeciesType.h $
 *
 *<!---------------------------------------------------------------------------
 * This file is part of libSBML.  Please visit http://sbml.org for more
 * information about SBML, and the latest version of libSBML.
 *
 * Copyright 2005-2009 California Institute of Technology.
 * Copyright 2002-2005 California Institute of Technology and
 *                     Japan Science and Technology Corporation.
 * 
 * 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
 *------------------------------------------------------------------------- -->
 *
 * @class SpeciesType
 * @brief LibSBML implementation of %SBML's %SpeciesType construct.
 *
 * The term @em species @em type refers to reacting entities independent of
 * location.  These include simple ions (e.g., protons, calcium), simple
 * molecules (e.g., glucose, ATP), large molecules (e.g., RNA,
 * polysaccharides, and proteins), and others.
 * 
 * SpeciesType structures are included in %SBML to enable Species of the
 * same type to be related together.  It is a conceptual construct; the
 * existence of SpeciesType objects in a model has no effect on the
 * model's numerical interpretation.  Except for the requirement for
 * uniqueness of species/species type combinations located in compartments,
 * simulators and other numerical analysis software may ignore SpeciesType
 * definitions and references to them in a model.
 * 
 * There is no mechanism in %SBML for representing hierarchies of species
 * types.  One SpeciesType object cannot be the subtype of another
 * SpeciesType object; %SBML provides no means of defining such
 * relationships.
 * 
 * As with other major structures in %SBML, SpeciesType has a mandatory
 * attribute, "id", used to give the species type an identifier.  The
 * identifier must be a text string conforming to the identifer syntax
 * permitted in %SBML.  SpeciesType also has an optional "name" attribute,
 * of type @c string.  The "id" and "name" must be used according to the
 * guidelines described in the %SBML specification (e.g., Section 3.3 in
 * the Level 2 Version 4 specification).
 *
 * SpeciesType was introduced in SBML Level 2 Version 2.  It is not
 * available in earlier versions of Level 2 nor in any version of Level 1.
 *
 * <!---------------------------------------------------------------------- -->
 *
 * @class ListOfSpeciesTypes.
 * @brief LibSBML implementation of SBML's %ListOfSpeciesTypes construct.
 * 
 * The various ListOf___ classes in %SBML are merely containers used for
 * organizing the main components of an %SBML model.  All are derived from
 * the abstract class SBase, and inherit the various attributes and
 * subelements of SBase, such as "metaid" as and "annotation".  The
 * ListOf___ classes do not add any attributes of their own.
 *
 * The relationship between the lists and the rest of an %SBML model is
 * illustrated by the following (for %SBML Level&nbsp;2 Version&nbsp;4):
 *
 * @image html listof-illustration.jpg "ListOf___ elements in an SBML Model"
 * @image latex listof-illustration.jpg "ListOf___ elements in an SBML Model"
 *
 * Readers may wonder about the motivations for using the ListOf___
 * containers.  A simpler approach in XML might be to place the components
 * all directly at the top level of the model definition.  We chose instead
 * to group them within XML elements named after ListOf<em>Classname</em>,
 * in part because we believe this helps organize the components and makes
 * visual reading of models in XML easier.  More importantly, the fact that
 * the container classes are derived from SBase means that software tools
 * can add information about the lists themselves into each list
 * container's "annotation".
 *
 * @see ListOfFunctionDefinitions
 * @see ListOfUnitDefinitions
 * @see ListOfCompartmentTypes
 * @see ListOfSpeciesTypes
 * @see ListOfCompartments
 * @see ListOfSpecies
 * @see ListOfParameters
 * @see ListOfInitialAssignments
 * @see ListOfRules
 * @see ListOfConstraints
 * @see ListOfReactions
 * @see ListOfEvents
 */

#ifndef SpeciesType_h
#define SpeciesType_h


#include <sbml/common/extern.h>
#include <sbml/common/sbmlfwd.h>


#ifdef __cplusplus


#include <string>

#include <sbml/SBase.h>
#include <sbml/ListOf.h>

LIBSBML_CPP_NAMESPACE_BEGIN

class SBMLVisitor;


class LIBSBML_EXTERN SpeciesType : public SBase
{
public:

  /**
   * Creates a new SpeciesType using the given SBML @p level and @p version
   * values.
   *
   * @param level an unsigned int, the SBML Level to assign to this SpeciesType
   *
   * @param version an unsigned int, the SBML Version to assign to this
   * SpeciesType
   * 
   * @note Once a SpeciesType has been added to an SBMLDocument, the @p level,
   * @p version for the document @em override those used
   * to create the SpeciesType.  Despite this, the ability to supply the values
   * at creation time is an important aid to creating valid SBML.  Knowledge of
   * the intented SBML Level and Version determine whether it is valid to
   * assign a particular value to an attribute, or whether it is valid to add
   * an object to an existing SBMLDocument.
   */
  SpeciesType (unsigned int level, unsigned int version);


  /**
   * Creates a new SpeciesType using the given SBMLNamespaces object
   * @p sbmlns.
   *
   * The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
   * information.  It is used to communicate the SBML Level, Version, and
   * (in Level&nbsp;3) packages used in addition to SBML Level&nbsp; Core.
   * A common approach to using this class constructor is to create an
   * SBMLNamespaces object somewhere in a program, once, then pass it to
   * object constructors such as this one when needed.
   *
   * It is worth emphasizing that although this constructor does not take
   * an identifier argument, in SBML Level&nbsp;2 and beyond, the "id"
   * (identifier) attribute of a SpeciesType object is required to have a value.
   * Thus, callers are cautioned to assign a value after calling this
   * constructor.  Setting the identifier can be accomplished using the
   * method @if clike SBase::setId() @endif@if java SBase::setId(String id) @endif.
   *
   * @param sbmlns an SBMLNamespaces object.
   *
   * @note Once a SpeciesType has been added to an SBMLDocument, the @p level,
   * @p version and @p xmlns namespaces for the document @em override those used
   * to create the SpeciesType.  Despite this, the ability to supply the values
   * at creation time is an important aid to creating valid SBML.  Knowledge of
   * the intented SBML Level and Version determine whether it is valid to
   * assign a particular value to an attribute, or whether it is valid to add
   * an object to an existing SBMLDocument.
   */
  SpeciesType (SBMLNamespaces* sbmlns);


  /**
   * Destroys this SpeciesType.
   */
  virtual ~SpeciesType ();


  /**
  * Copy constructor; creates a copy of this SpeciesType.
  */
  SpeciesType(const SpeciesType& orig);


  /**
   * Assignment operator for SpeciesType.
   */
  SpeciesType& operator=(const SpeciesType& orig);


  /**
   * Accepts the given SBMLVisitor for this instance of SpeciesType.
   *
   * @param v the SBMLVisitor instance to be used.
   *
   * @return the result of calling <code>v.visit()</code>, which indicates
   * whether the Visitor would like to visit the next SpeciesType in
   * the list of compartment types.
   */
  virtual bool accept (SBMLVisitor& v) const;


  /**
   * Creates and returns a deep copy of this SpeciesType.
   * 
   * @return a (deep) copy of this SpeciesType.
   */
  virtual SpeciesType* clone () const;


  /**
   * Returns the value of the "id" attribute of this SpeciesType.
   * 
   * @return the id of this SpeciesType.
   */
  const std::string& getId () const;


  /**
   * Returns the value of the "name" attribute of this SpeciesType.
   * 
   * @return the name of this SpeciesType.
   */
  const std::string& getName () const;


  /**
   * Predicate returning @c true or @c false depending on whether this
   * SpeciesType's "id" attribute has been set.
   *
   * @htmlinclude libsbml-comment-set-methods.html
   * 
   * @return @c true if the "id" attribute of this SpeciesType has been
   * set, @c false otherwise.
   */
  bool isSetId () const;


  /**
   * Predicate returning @c true or @c false depending on whether this
   * SpeciesType's "name" attribute has been set.
   *
   * @htmlinclude libsbml-comment-set-methods.html
   * 
   * @return @c true if the "name" attribute of this SpeciesType has been
   * set, @c false otherwise.
   */
  bool isSetName () const;


  /**
   * Sets the value of the "id" attribute of this SpeciesType.
   *
   * The string @p sid is copied.  Note that SBML has strict requirements
   * for the syntax of identifiers.  The following is summary of the
   * definition of the SBML 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 SBML 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 SBML model.  Please consult the
   * SBML specifications for the exact formulations.
   *
   * @htmlinclude libsbml-comment-set-methods.html
   *
   * @param sid the string to use as the identifier of this SpeciesType
   *
   * @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 LIBSBML_OPERATION_SUCCESS
   * @li LIBSBML_INVALID_ATTRIBUTE_VALUE
   */
  int setId (const std::string& sid);


  /**
   * Sets the value of the "name" attribute of this SpeciesType.
   *
   * The string in @p name is copied.
   *
   * @htmlinclude libsbml-comment-set-methods.html
   *
   * @param name the new name for the SpeciesType
   *
   * @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 LIBSBML_OPERATION_SUCCESS
   * @li LIBSBML_INVALID_ATTRIBUTE_VALUE
   */
  int setName (const std::string& name);


  /**
   * Unsets the value of the "name" attribute of this SpeciesType.
   *
   * @htmlinclude libsbml-comment-set-methods.html
   *
   * @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 LIBSBML_OPERATION_SUCCESS
   * @li LIBSBML_OPERATION_FAILED
   */
  int unsetName ();


  /**
   * Returns the libSBML type code for this %SBML object.
   * 
   * @if clike LibSBML attaches an identifying code to every
   * kind of SBML object.  These are known as <em>SBML type codes</em>.
   * The set of possible type codes is defined in the enumeration
   * #SBMLTypeCode_t.  The names of the type codes all begin with the
   * characters @c SBML_. @endif@if java LibSBML attaches an
   * identifying code to every kind of SBML object.  These are known as
   * <em>SBML type codes</em>.  In other languages, the set of type codes
   * is stored in an enumeration; in the Java language interface for
   * libSBML, the type codes are defined as static integer constants in
   * interface class {@link libsbmlConstants}.  The names of the type codes
   * all begin with the characters @c SBML_. @endif
   *
   * @return the SBML type code for this object, or @c SBML_UNKNOWN (default).
   *
   * @see getElementName()
   */
  virtual SBMLTypeCode_t getTypeCode () const;


  /**
   * Returns the XML element name of this object, which for
   * SpeciesType, is always @c "compartmentType".
   * 
   * @return the name of this element, i.e., @c "compartmentType".
   */
  virtual const std::string& getElementName () const;


  /**
   * Predicate returning @c true or @c false depending on whether
   * all the required attributes for this SpeciesType object
   * have been set.
   *
   * @note The required attributes for a SpeciesType object are:
   * id
   *
   * @return a boolean value indicating whether all the required
   * attributes for this object have been defined.
   */
  virtual bool hasRequiredAttributes() const ;


protected:
  /** @cond doxygen-libsbml-internal */

  /* this is a constructor that takes no arguments and 
   * only exists because the validator code needs it
   */
  SpeciesType ();


  /**
   * Subclasses should override this method to read values from the given
   * XMLAttributes set into their specific fields.  Be sure to call your
   * parents implementation of this method as well.
   *
   * @param attributes the XMLAttributes to use.
   */
  virtual void readAttributes (const XMLAttributes& attributes);


  /**
   * Subclasses should override this method to write their XML attributes
   * to the XMLOutputStream.  Be sure to call your parents implementation
   * of this method as well.
   *
   * @param stream the XMLOutputStream to use.
   */
  virtual void writeAttributes (XMLOutputStream& stream) const;

  std::string  mId;
  std::string  mName;

  /* 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;
  friend class L1CompatibilityValidator;
  friend class L2v1CompatibilityValidator;
  friend class L2v2CompatibilityValidator;
  friend class L2v3CompatibilityValidator;
  friend class L2v4CompatibilityValidator;
  friend class MathMLConsistencyValidator;
  friend class ModelingPracticeValidator;
  friend class OverdeterminedValidator;
  friend class SBOConsistencyValidator;
  friend class UnitConsistencyValidator;


  /** @endcond doxygen-libsbml-internal */
};



class LIBSBML_EXTERN ListOfSpeciesTypes : public ListOf
{
public:

  /**
   * Creates and returns a deep copy of this ListOfSpeciesTypes instance.
   *
   * @return a (deep) copy of this ListOfSpeciesTypes.
   */
  virtual ListOfSpeciesTypes* clone () const;


  /**
   * Returns the libSBML type code for this %SBML object.
   *
   * @if clike LibSBML attaches an identifying code to every
   * kind of SBML object.  These are known as <em>SBML type codes</em>.
   * The set of possible type codes is defined in the enumeration
   * #SBMLTypeCode_t.  The names of the type codes all begin with the
   * characters @c SBML_. @endif@if java LibSBML attaches an
   * identifying code to every kind of SBML object.  These are known as
   * <em>SBML type codes</em>.  In other languages, the set of type codes
   * is stored in an enumeration; in the Java language interface for
   * libSBML, the type codes are defined as static integer constants in
   * interface class {@link libsbmlConstants}.  The names of the type codes
   * all begin with the characters @c SBML_. @endif
   *
   * @return the SBML type code for this object, or @c SBML_UNKNOWN (default).
   *
   * @see getElementName()
   */
  virtual SBMLTypeCode_t getTypeCode () const { return SBML_LIST_OF; };


  /**
   * Returns the libSBML type code for the objects contained in this ListOf
   * (i.e., SpeciesType objects, if the list is non-empty).
   *
   * @if clike LibSBML attaches an identifying code to every
   * kind of SBML object.  These are known as <em>SBML type codes</em>.
   * The set of possible type codes is defined in the enumeration
   * #SBMLTypeCode_t.  The names of the type codes all begin with the
   * characters @c SBML_. @endif@if java LibSBML attaches an
   * identifying code to every kind of SBML object.  These are known as
   * <em>SBML type codes</em>.  In other languages, the set of type codes
   * is stored in an enumeration; in the Java language interface for
   * libSBML, the type codes are defined as static integer constants in
   * interface class {@link libsbmlConstants}.  The names of the type codes
   * all begin with the characters @c SBML_. @endif
   * 
   * @return the SBML type code for the objects contained in this ListOf
   * instance, or @c SBML_UNKNOWN (default).
   *
   * @see getElementName()
   */
  virtual SBMLTypeCode_t getItemTypeCode () const;


  /**
   * Returns the XML element name of this object.
   *
   * For ListOfSpeciesTypes, the XML element name is @c
   * "listOfSpeciesTypes".
   * 
   * @return the name of this element, i.e., @c "listOfSpeciesTypes".
   */
  virtual const std::string& getElementName () const;


  /**
   * Get a SpeciesType from the ListOfSpeciesTypes.
   *
   * @param n the index number of the SpeciesType to get.
   * 
   * @return the nth SpeciesType in this ListOfSpeciesTypes.
   *
   * @see size()
   */
  virtual SpeciesType * get(unsigned int n); 


  /**
   * Get a SpeciesType from the ListOfSpeciesTypes.
   *
   * @param n the index number of the SpeciesType to get.
   * 
   * @return the nth SpeciesType in this ListOfSpeciesTypes.
   *
   * @see size()
   */
  virtual const SpeciesType * get(unsigned int n) const; 

  /**
   * Get a SpeciesType from the ListOfSpeciesTypes
   * based on its identifier.
   *
   * @param sid a string representing the identifier 
   * of the SpeciesType to get.
   * 
   * @return SpeciesType in this ListOfSpeciesTypes
   * with the given id or NULL if no such
   * SpeciesType exists.
   *
   * @see get(unsigned int n)
   * @see size()
   */
  virtual SpeciesType* get (const std::string& sid);


  /**
   * Get a SpeciesType from the ListOfSpeciesTypes
   * based on its identifier.
   *
   * @param sid a string representing the identifier 
   * of the SpeciesType to get.
   * 
   * @return SpeciesType in this ListOfSpeciesTypes
   * with the given id or NULL if no such
   * SpeciesType exists.
   *
   * @see get(unsigned int n)
   * @see size()
   */
  virtual const SpeciesType* get (const std::string& sid) const;


  /**
   * Removes the nth item from this ListOfSpeciesTypes items and returns a pointer to
   * it.
   *
   * The caller owns the returned item and is responsible for deleting it.
   *
   * @param n the index of the item to remove
   *
   * @see size()
   */
  virtual SpeciesType* remove (unsigned int n);


  /**
   * Removes item in this ListOfSpeciesTypes items with the given identifier.
   *
   * The caller owns the returned item and is responsible for deleting it.
   * If none of the items in this list have the identifier @p sid, then @c
   * NULL is returned.
   *
   * @param sid the identifier of the item to remove
   *
   * @return the item removed.  As mentioned above, the caller owns the
   * returned item.
   */
  virtual SpeciesType* remove (const std::string& sid);


  /** @cond doxygen-libsbml-internal */

  /**
   * Get the ordinal position of this element in the containing object
   * (which in this case is the Model object).
   *
   * The ordering of elements in the XML form of %SBML is generally fixed
   * for most components in %SBML.  For example, the
   * ListOfSpeciesTypes in a model (in %SBML Level 2 Version 4) is the
   * third ListOf___.  (However, it differs for different Levels and
   * Versions of SBML, so calling code should not hardwire this number.)
   *
   * @return the ordinal position of the element with respect to its
   * siblings, or @c -1 (default) to indicate the position is not significant.
   */
  virtual int getElementPosition () const;

  /** @endcond doxygen-libsbml-internal */


protected:
  /** @cond doxygen-libsbml-internal */

  /**
   * Create a ListOfSpeciesTypes object corresponding to the next token
   * in the XML input stream.
   * 
   * @return the %SBML object corresponding to next XMLToken in the
   * XMLInputStream, or @c NULL if the token was not recognized.
   */
  virtual SBase* createObject (XMLInputStream& stream);

  /** @endcond doxygen-libsbml-internal */
};

LIBSBML_CPP_NAMESPACE_END

#endif  /* __cplusplus */


#ifndef SWIG

LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS

/*-----------------------------------------------------------------------------
 * See the .cpp file for the documentation of the following functions.
 *---------------------------------------------------------------------------*/


LIBSBML_EXTERN
SpeciesType_t *
SpeciesType_create (unsigned int level, unsigned int version);


LIBSBML_EXTERN
SpeciesType_t *
SpeciesType_createWithNS (SBMLNamespaces_t *sbmlns);


LIBSBML_EXTERN
void
SpeciesType_free (SpeciesType_t *st);


LIBSBML_EXTERN
SpeciesType_t *
SpeciesType_clone (const SpeciesType_t *st);


LIBSBML_EXTERN
const XMLNamespaces_t *
SpeciesType_getNamespaces(SpeciesType_t *c);


LIBSBML_EXTERN
const char *
SpeciesType_getId (const SpeciesType_t *st);


LIBSBML_EXTERN
const char *
SpeciesType_getName (const SpeciesType_t *st);


LIBSBML_EXTERN
int
SpeciesType_isSetId (const SpeciesType_t *st);


LIBSBML_EXTERN
int
SpeciesType_isSetName (const SpeciesType_t *st);


LIBSBML_EXTERN
int
SpeciesType_setId (SpeciesType_t *st, const char *sid);


LIBSBML_EXTERN
int
SpeciesType_setName (SpeciesType_t *st, const char *name);


LIBSBML_EXTERN
int
SpeciesType_unsetName (SpeciesType_t *st);


LIBSBML_EXTERN
SpeciesType_t *
ListOfSpeciesTypes_getById (ListOf_t *lo, const char *sid);


LIBSBML_EXTERN
SpeciesType_t *
ListOfSpeciesTypes_removeById (ListOf_t *lo, const char *sid);


END_C_DECLS
LIBSBML_CPP_NAMESPACE_END

#endif  /* !SWIG */
#endif  /* SpeciesType_h */
