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* @file SpeciesType.h
* @brief Definitions of SpeciesType and ListOfSpeciesType.
* @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 (C) 2009-2013 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
*
* Copyright (C) 2006-2008 by the California Institute of Technology,
* Pasadena, CA, USA
*
* Copyright (C) 2002-2005 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. Japan Science and Technology Agency, Japan
*
* 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
* @sbmlbrief{core} A <em>species type</em> in SBML Level 2.
*
* 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.
*
* SBML Level 2 Versions 2–4 provide an explicit
* SpeciesType class of object to enable Species objects of the same type
* to be related together. SpeciesType 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 Level 2 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 SBML Level 1 nor in Level 3.
*
* @see Species
* @see ListOfSpeciesTypes
* @see CompartmentType
* @see ListOfCompartmentTypes
*
* <!---------------------------------------------------------------------- -->
* @class ListOfSpeciesTypes
* @sbmlbrief{core} A list of SpeciesType objects.
*
* @copydetails doc_what_is_listof
*/
#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
*
* @copydetails doc_throw_exception_lv
*
* @copydetails doc_note_setting_lv
*/
SpeciesType (unsigned int level, unsigned int version);
/**
* Creates a new SpeciesType using the given SBMLNamespaces object
* @p sbmlns.
*
* @copydetails doc_what_are_sbmlnamespaces
*
* It is worth emphasizing that although this constructor does not take
* an identifier argument, in SBML Level 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 SBase::setId(@if java String@endif).
*
* @param sbmlns an SBMLNamespaces object.
*
* @copydetails doc_throw_exception_namespace
*
* @copydetails doc_note_setting_lv
*/
SpeciesType (SBMLNamespaces* sbmlns);
/**
* Destroys this SpeciesType.
*/
virtual ~SpeciesType ();
/**
* Copy constructor; creates a copy of this SpeciesType.
*
* @param orig the object to copy.
*/
SpeciesType(const SpeciesType& orig);
/**
* Assignment operator for SpeciesType.
*
* @param rhs The object whose values are used as the basis of the
* assignment.
*/
SpeciesType& operator=(const SpeciesType& rhs);
/** @cond doxygenLibsbmlInternal */
/**
* 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;
/** @endcond */
/**
* Creates and returns a deep copy of this SpeciesType object.
*
* @return the (deep) copy of this SpeciesType object.
*/
virtual SpeciesType* clone () const;
/**
* Returns the value of the "id" attribute of this SpeciesType.
*
* @return the id of this SpeciesType.
*/
virtual const std::string& getId () const;
/**
* Returns the value of the "name" attribute of this SpeciesType.
*
* @return the name of this SpeciesType.
*/
virtual const std::string& getName () const;
/**
* Predicate returning @c true if this
* SpeciesType's "id" attribute is set.
*
* @return @c true if the "id" attribute of this SpeciesType is
* set, @c false otherwise.
*/
virtual bool isSetId () const;
/**
* Predicate returning @c true if this
* SpeciesType's "name" attribute is set.
*
* @return @c true if the "name" attribute of this SpeciesType is
* set, @c false otherwise.
*/
virtual bool isSetName () const;
/**
* Sets the value of the "id" attribute of this SpeciesType.
*
* The string @p sid is copied.
*
* @copydetails doc_id_syntax
*
* @param sid the string to use as the identifier of this SpeciesType
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*/
virtual int setId (const std::string& sid);
/**
* Sets the value of the "name" attribute of this SpeciesType.
*
* The string in @p name is copied.
*
* @param name the new name for the SpeciesType
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*/
virtual int setName (const std::string& name);
/**
* Unsets the value of the "name" attribute of this SpeciesType.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int unsetName ();
/**
* Returns the libSBML type code for this SBML object.
*
* @copydetails doc_what_are_typecodes
*
* @return the SBML type code for this object:
* @sbmlconstant{SBML_SPECIES_TYPE, SBMLTypeCode_t} (default).
*
* @copydetails doc_warning_typecodes_not_unique
*
* @see getElementName()
* @see getPackageName()
*/
virtual int 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;
/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to write out their contained
* SBML objects as XML elements. Be sure to call your parents
* implementation of this method as well.
*/
virtual void writeElements (XMLOutputStream& stream) const;
/** @endcond */
/**
* Predicate returning @c true if
* all the required attributes for this SpeciesType object
* have been set.
*
* The required attributes for a SpeciesType object are:
* @li "id"
*
* @return @c true if the required attributes have been set, @c false
* otherwise.
*/
virtual bool hasRequiredAttributes() const ;
protected:
/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to get the list of
* expected attributes.
* This function is invoked from corresponding readAttributes()
* function.
*/
virtual void addExpectedAttributes(ExpectedAttributes& attributes);
/**
* 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,
const ExpectedAttributes& expectedAttributes);
void readL2Attributes (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 */
};
class LIBSBML_EXTERN ListOfSpeciesTypes : public ListOf
{
public:
/**
* Creates a new ListOfSpeciesTypes object.
*
* The object is constructed such that it is valid for the given SBML
* Level and Version combination.
*
* @param level the SBML Level
*
* @param version the Version within the SBML Level
*
* @copydetails doc_throw_exception_lv
*
* @copydetails doc_note_setting_lv
*/
ListOfSpeciesTypes (unsigned int level, unsigned int version);
/**
* Creates a new ListOfSpeciesTypes object.
*
* The object is constructed such that it is valid for the SBML Level and
* Version combination determined by the SBMLNamespaces object in @p
* sbmlns.
*
* @param sbmlns an SBMLNamespaces object that is used to determine the
* characteristics of the ListOfSpeciesTypes object to be created.
*
* @copydetails doc_throw_exception_namespace
*
* @copydetails doc_note_setting_lv
*/
ListOfSpeciesTypes (SBMLNamespaces* sbmlns);
/**
* Creates and returns a deep copy of this ListOfSpeciesTypes object.
*
* @return the (deep) copy of this ListOfSpeciesTypes object.
*/
virtual ListOfSpeciesTypes* clone () const;
/**
* Returns the libSBML type code for the objects contained in this ListOf
* (i.e., SpeciesType objects, if the list is non-empty).
*
* @copydetails doc_what_are_typecodes
*
* @return the SBML type code for objects contained in this list:
* @sbmlconstant{SBML_SPECIES_TYPE, SBMLTypeCode_t} (default).
*
* @see getElementName()
* @see getPackageName()
*/
virtual int 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 @p sid or @c 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 @p sid or @c 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 doxygenLibsbmlInternal */
/**
* 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 */
protected:
/** @cond doxygenLibsbmlInternal */
/**
* 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 */
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#ifndef SWIG
LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
/**
* Creates a new SpeciesType_t structure using the given SBML @p level
* and @p version values.
*
* @param level an unsigned int, the SBML Level to assign to this
* SpeciesType_t
*
* @param version an unsigned int, the SBML Version to assign to this
* SpeciesType_t
*
* @return a pointer to the newly created SpeciesType_t structure.
*
* @note Once a SpeciesType_t has been added to an SBMLDocument_t, the @p
* level and @p version for the document @em override those used to create
* the SpeciesType_t. Despite this, the ability to supply the values at
* creation time is an important aid to creating valid SBML. Knowledge of
* the intended SBML Level and Version determine whether it is valid to
* assign a particular value to an attribute, or whether it is valid to add
* a structure to an existing SBMLDocument_t.
*
* @memberof SpeciesType_t
*/
LIBSBML_EXTERN
SpeciesType_t *
SpeciesType_create (unsigned int level, unsigned int version);
/**
* Creates a new SpeciesType_t structure using the given
* SBMLNamespaces_t structure.
*
* @param sbmlns SBMLNamespaces_t, a pointer to an SBMLNamespaces_t structure
* to assign to this SpeciesType_t
*
* @return a pointer to the newly created SpeciesType_t structure.
*
* @note Once a SpeciesType_t has been added to an SBMLDocument_t, the
* @p sbmlns namespaces for the document @em override those used to create
* the SpeciesType_t. Despite this, the ability to supply the values at creation
* time is an important aid to creating valid SBML. Knowledge of the intended
* SBML Level and Version determine whether it is valid to assign a particular
* value to an attribute, or whether it is valid to add a structure to an existing
* SBMLDocument_t.
*
* @memberof SpeciesType_t
*/
LIBSBML_EXTERN
SpeciesType_t *
SpeciesType_createWithNS (SBMLNamespaces_t *sbmlns);
/**
* Frees the given SpeciesType_t structure.
*
* @param st the SpeciesType_t structure to be freed.
*
* @memberof SpeciesType_t
*/
LIBSBML_EXTERN
void
SpeciesType_free (SpeciesType_t *st);
/**
* Creates a deep copy of the given SpeciesType_t structure
*
* @param st the SpeciesType_t structure to be copied
*
* @return a (deep) copy of this SpeciesType_t structure.
*
* @memberof SpeciesType_t
*/
LIBSBML_EXTERN
SpeciesType_t *
SpeciesType_clone (const SpeciesType_t *st);
/**
* Returns a list of XMLNamespaces_t associated with this SpeciesType_t
* structure.
*
* @param st the SpeciesType_t structure
*
* @return pointer to the XMLNamespaces_t structure associated with
* this structure
*
* @memberof SpeciesType_t
*/
LIBSBML_EXTERN
const XMLNamespaces_t *
SpeciesType_getNamespaces(SpeciesType_t *st);
/**
* Takes a SpeciesType_t structure and returns its identifier.
*
* @param st the SpeciesType_t structure whose identifier is sought
*
* @return the identifier of this SpeciesType_t, as a pointer to a string.
*
* @memberof SpeciesType_t
*/
LIBSBML_EXTERN
const char *
SpeciesType_getId (const SpeciesType_t *st);
/**
* Takes a SpeciesType_t structure and returns its name.
*
* @param st the SpeciesType_t whose name is sought.
*
* @return the name of this SpeciesType_t, as a pointer to a string.
*
* @memberof SpeciesType_t
*/
LIBSBML_EXTERN
const char *
SpeciesType_getName (const SpeciesType_t *st);
/**
* Predicate returning @c true or @c false depending on whether the given
* SpeciesType_t structure's identifier is set.
*
* @param st the SpeciesType_t structure to query
*
* @return @c non-zero (true) if the "id" field of the given
* SpeciesType_t is set, zero (false) otherwise.
*
* @memberof SpeciesType_t
*/
LIBSBML_EXTERN
int
SpeciesType_isSetId (const SpeciesType_t *st);
/**
* Predicate returning @c true or @c false depending on whether the given
* SpeciesType_t structure's name is set.
*
* @param st the SpeciesType_t structure to query
*
* @return @c non-zero (true) if the "name" field of the given
* SpeciesType_t is set, zero (false) otherwise.
*
* @memberof SpeciesType_t
*/
LIBSBML_EXTERN
int
SpeciesType_isSetName (const SpeciesType_t *st);
/**
* Assigns the identifier of a SpeciesType_t structure.
*
* This makes a copy of the string passed as the argument @p sid.
*
* @param st the SpeciesType_t structure to set.
* @param sid the string to use as the identifier.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*
* @note Using this function with an id of NULL is equivalent to
* unsetting the "id" attribute.
*
* @memberof SpeciesType_t
*/
LIBSBML_EXTERN
int
SpeciesType_setId (SpeciesType_t *st, const char *sid);
/**
* Assign the name of a SpeciesType_t structure.
*
* This makes a copy of the string passed as the argument @p name.
*
* @param st the SpeciesType_t structure to set.
* @param name the string to use as the name.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*
* @note Using this function with the name set to NULL is equivalent to
* unsetting the "name" attribute.
*
* @memberof SpeciesType_t
*/
LIBSBML_EXTERN
int
SpeciesType_setName (SpeciesType_t *st, const char *name);
/**
* Unsets the name of a SpeciesType_t.
*
* @param st the SpeciesType_t structure whose name is to be unset.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*
* @memberof SpeciesType_t
*/
LIBSBML_EXTERN
int
SpeciesType_unsetName (SpeciesType_t *st);
/**
* Returns the SpeciesType_t structure having a given identifier.
*
* @param lo the ListOfSpeciesTypes_t structure to search.
* @param sid the "id" attribute value being sought.
*
* @return item in the @p lo ListOfSpeciesTypes with the given @p sid or a
* null pointer if no such item exists.
*
* @see ListOf_t
*
* @memberof ListOfSpeciesTypes_t
*/
LIBSBML_EXTERN
SpeciesType_t *
ListOfSpeciesTypes_getById (ListOf_t *lo, const char *sid);
/**
* Removes a SpeciesType_t structure based on its identifier.
*
* The caller owns the returned item and is responsible for deleting it.
*
* @param lo the list of SpeciesType_t structures to search.
* @param sid the "id" attribute value of the structure to remove
*
* @return The SpeciesType_t structure removed, or a null pointer if no such
* item exists in @p lo.
*
* @see ListOf_t
*
* @memberof ListOfSpeciesTypes_t
*/
LIBSBML_EXTERN
SpeciesType_t *
ListOfSpeciesTypes_removeById (ListOf_t *lo, const char *sid);
END_C_DECLS
LIBSBML_CPP_NAMESPACE_END
#endif /* !SWIG */
#endif /* SpeciesType_h */
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