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* @file GeneProductAssociation.h
* @brief Implementation of the GeneProductAssociation class
* @author SBMLTeam
*
* <!--------------------------------------------------------------------------
* 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 GeneProductAssociation
* @sbmlbrief{fbc} Association between gene products and reactions
*
* In Version 2 of the SBML Level 3 @ref fbc (“fbc”)
* package specification, GeneProductAssociation is a class derived from
* SBase used to associate one more genes or gene products with reactions.
* GeneProductAssociation objects are essentially containers, with one such
* container optionally attached as a subelement to a Reaction object in a
* model. The container can contain one of three kinds of objects, all of
* which are subclasses of the libSBML parent class FbcAssociation. (Note
* that this class is named <em>%Association</em> in the “fbc”
* Version 2 specification, but in libSBML is named FbcAssociation to
* avoid a name conflict with an existing class.)
*
* One of the kinds of FbcAssociation subclasses that can appear in a
* GeneProductAssociation is GeneProductRef. This class of objects
* references a GeneProduct declared in a ListOfGeneProducts attached to the
* enclosing Model object. In the “fbc” approach, when more than
* one gene (or gene product) is present in an association, they are written
* as logical expressions using Boolean logical operators <em>and</em> and
* <em>or</em> through the classes (in libSBML) FbcAnd and FbcOr. (In the
* “fbc” Version 2 specification, these are simply named
* <em>And</em> and <em>Or</em>, respectively.) The FbcAnd and FbcOr objects
* in turn can contain either GeneProductRef objects or other FbcAnd and/or
* FbcOr objects.
*
* Here is a concrete example of what the XML representation of a simple
* <em>or</em> relationship might look like:
<pre class="fragment">
<reaction id = "R_ABTA" <span class="regular-text" style="font-weight: normal; font-style: italic; background-color: #ffd; padding-left: 2px; padding-right: 2px">... rest of Reaction declaration elided for this example ...</span>>
<fbc:geneProductAssociation fbc:id="ga_16">
<fbc:or>
<fbc:geneProductRef fbc:geneProduct="g_b2662"/>
<fbc:geneProductRef fbc:geneProduct="g_b1302"/>
</fbc:or>
</fbc:geneProductAssociation>
</reaction>
</pre>
*
* @copydetails doc_note_fbcv2_annotation_replacement
*/
#ifndef GeneProductAssociation_H__
#define GeneProductAssociation_H__
#include <sbml/common/extern.h>
#include <sbml/common/sbmlfwd.h>
#include <sbml/packages/fbc/common/fbcfwd.h>
#ifdef __cplusplus
#include <string>
#include <sbml/SBase.h>
#include <sbml/ListOf.h>
#include <sbml/packages/fbc/extension/FbcExtension.h>
#include <sbml/packages/fbc/sbml/FbcAssociation.h>
LIBSBML_CPP_NAMESPACE_BEGIN
class LIBSBML_EXTERN GeneProductAssociation : public SBase
{
protected:
/** @cond doxygenLibsbmlInternal */
std::string mId;
std::string mName;
FbcAssociation* mAssociation;
/** @endcond */
public:
/**
* Creates a new GeneProductAssociation with the given SBML Level, Version, and
* “fbc” package version.
*
* @param level an unsigned int, the SBML Level to assign to this
* GeneProductAssociation
*
* @param version an unsigned int, the SBML Version to assign to this
* GeneProductAssociation
*
* @param pkgVersion an unsigned int, the SBML “fbc” Version to
* assign to this GeneProductAssociation object
*/
GeneProductAssociation(unsigned int level = FbcExtension::getDefaultLevel(),
unsigned int version = FbcExtension::getDefaultVersion(),
unsigned int pkgVersion = FbcExtension::getDefaultPackageVersion());
/**
* Creates a new GeneProductAssociation with the given FbcPkgNamespaces
* object.
*
* @param fbcns the FbcPkgNamespaces object
*/
GeneProductAssociation(FbcPkgNamespaces* fbcns);
/**
* Copy constructor for GeneProductAssociation.
*
* @param orig; the GeneProductAssociation instance to copy.
*/
GeneProductAssociation(const GeneProductAssociation& orig);
/**
* Assignment operator for GeneProductAssociation.
*
* @param rhs; the object whose values are used as the basis
* of the assignment.
*/
GeneProductAssociation& operator=(const GeneProductAssociation& rhs);
/**
* Creates and returns a deep copy of this GeneProductAssociation object.
*
* @return a (deep) copy of this GeneProductAssociation object.
*/
virtual GeneProductAssociation* clone () const;
/**
* Destructor for GeneProductAssociation.
*/
virtual ~GeneProductAssociation();
/**
* Returns the value of the "id" attribute of this GeneProductAssociation.
*
* @return the value of the "id" attribute of this GeneProductAssociation
* as a string.
*/
virtual const std::string& getId() const;
/**
* Returns the value of the "name" attribute of this GeneProductAssociation.
*
* @return the value of the "name" attribute of this GeneProductAssociation
* as a string.
*/
virtual const std::string& getName() const;
/**
* Returns the "association" element of this GeneProductAssociation.
*
* @return the "association" element of this GeneProductAssociation.
*/
virtual const FbcAssociation* getAssociation() const;
/**
* Returns the "association" element of this GeneProductAssociation.
*
* @return the "association" element of this GeneProductAssociation.
*/
virtual FbcAssociation* getAssociation();
/**
* Creates a new "association" and sets it for this GeneProductAssociation.
*
* @return the
*/
virtual FbcAnd* createAnd();
/**
* Creates a new "association" and sets it for this GeneProductAssociation.
*/
virtual FbcOr* createOr();
/**
* Creates a new "association" and sets it for this GeneProductAssociation.
*/
virtual GeneProductRef* createGeneProductRef();
/**
* Predicate returning @c true if this GeneProductAssociation's "id"
* attribute is set.
*
* @return @c true if this GeneProductAssociation's "id" attribute has been set,
* otherwise @c false is returned.
*/
virtual bool isSetId() const;
/**
* Predicate returning @c true if this GeneProductAssociation's "name"
* attribute is set.
*
* @return @c true if this GeneProductAssociation's "name" attribute has been set,
* otherwise @c false is returned.
*/
virtual bool isSetName() const;
/**
* Predicate returning @c true if this GeneProductAssociation's
* "association" element is set.
*
* @return @c true if this GeneProductAssociation's "association" element has been set,
* otherwise @c false is returned.
*/
virtual bool isSetAssociation() const;
/**
* Sets the value of the "id" attribute of this GeneProductAssociation.
*
* @param id; const std::string& value of the "id" attribute to be set
*
* @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 @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*/
virtual int setId(const std::string& id);
/**
* Sets the value of the "name" attribute of this GeneProductAssociation.
*
* @param name; const std::string& value of the "name" attribute to be set
*
* @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 @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*/
virtual int setName(const std::string& name);
/**
* Sets the "association" element of this GeneProductAssociation.
*
* @param association; FbcAssociation* to be set.
*
* @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 @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*/
virtual int setAssociation(FbcAssociation* association);
/**
* Sets the "association" element of this GeneProductAssociation.
*
* @param association; string representation of the association to be set
*
* @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 @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*/
virtual int setAssociation(const std::string& association);
/**
* Unsets the value of the "id" attribute of this GeneProductAssociation.
*
* @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 @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int unsetId();
/**
* Unsets the value of the "name" attribute of this GeneProductAssociation.
*
* @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 @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int unsetName();
/**
* Unsets the "association" element of this GeneProductAssociation.
*
* @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 @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int unsetAssociation();
/**
* Returns a List of all child SBase objects, including those nested to an
* arbitrary depth.
*
* @return a List* of pointers to all child objects.
*/
virtual List* getAllElements(ElementFilter * filter = NULL);
/**
* Returns the XML element name of this object.
*
* For GeneProductAssociation, the XML element name is always @c "geneProductAssociation".
*
* @return the name of this element, i.e. @c "geneProductAssociation".
*/
virtual const std::string& getElementName () const;
/**
* Returns the libSBML type code for this SBML object.
*
* @copydetails doc_what_are_typecodes
*
* @return the SBML type code for this object:
* @sbmlconstant{SBML_FBC_GENEPRODUCTASSOCIATION, SBMLTypeCode_t} (default).
*
* @copydetails doc_warning_typecodes_not_unique
*
* @see getElementName()
* @see getPackageName()
*/
virtual int getTypeCode () const;
/**
* Predicate returning @c true if all the required attributes for this
* GeneProductAssociation object have been set.
*
* @note The required attributes for a GeneProductAssociation object are:
* @li "association"
*
* @return a boolean value indicating whether all the required
* attributes for this object have been defined.
*/
virtual bool hasRequiredAttributes() const;
/**
* Predicate returning @c true if all the required elements for this
* GeneProductAssociation object have been set.
*
* @note The required elements for a GeneProductAssociation object are:
* @li "association"
*
* @return a boolean value indicating whether all the required
* elements for this object have been defined.
*/
virtual bool hasRequiredElements() 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 doxygenLibsbmlInternal */
/** @cond doxygenLibsbmlInternal */
/**
* Accepts the given SBMLVisitor.
*/
virtual bool accept (SBMLVisitor& v) const;
/** @endcond doxygenLibsbmlInternal */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
*/
virtual void setSBMLDocument (SBMLDocument* d);
/** @endcond doxygenLibsbmlInternal */
/** @cond doxygenLibsbmlInternal */
/**
* Connects to child elements.
*/
virtual void connectToChild ();
/** @endcond doxygenLibsbmlInternal */
/** @cond doxygenLibsbmlInternal */
/**
* Enables/Disables the given package with this element.
*/
virtual void enablePackageInternal(const std::string& pkgURI,
const std::string& pkgPrefix, bool flag);
/** @endcond doxygenLibsbmlInternal */
protected:
/** @cond doxygenLibsbmlInternal */
/**
* return the SBML object corresponding to next XMLToken.
*/
virtual SBase* createObject(XMLInputStream& stream);
/** @endcond doxygenLibsbmlInternal */
/** @cond doxygenLibsbmlInternal */
/**
* Get the list of expected attributes for this element.
*/
virtual void addExpectedAttributes(ExpectedAttributes& attributes);
/** @endcond doxygenLibsbmlInternal */
/** @cond doxygenLibsbmlInternal */
/**
* Read values from the given XMLAttributes set into their specific fields.
*/
virtual void readAttributes (const XMLAttributes& attributes,
const ExpectedAttributes& expectedAttributes);
/** @endcond doxygenLibsbmlInternal */
/** @cond doxygenLibsbmlInternal */
/**
* Write values of XMLAttributes to the output stream.
*/
virtual void writeAttributes (XMLOutputStream& stream) const;
/** @endcond doxygenLibsbmlInternal */
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#ifndef SWIG
LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
/**
* Creates a new GeneProductAssociation_t structure using the given SBML @p level and
* @p version values.
*
* @param level an unsigned int, the SBML level to assign to this
* GeneProductAssociation_t structure.
*
* @param version an unsigned int, the SBML version to assign to this
* GeneProductAssociation_t structure.
*
* @returns the newly-created GeneProductAssociation_t structure, or a null pointer if
* an error occurred during construction.
*
* @copydetails doc_note_setting_lv
*
* @memberof GeneProductAssociation_t
*/
LIBSBML_EXTERN
GeneProductAssociation_t *
GeneProductAssociation_create(unsigned int level, unsigned int version,
unsigned int pkgVersion);
/**
* Frees the given GeneProductAssociation_t structure.
*
* @param gpa the GeneProductAssociation_t structure to be freed.
*
* @memberof GeneProductAssociation_t
*/
LIBSBML_EXTERN
void
GeneProductAssociation_free(GeneProductAssociation_t * gpa);
/**
* Creates a deep copy of the given GeneProductAssociation_t structure.
*
* @param gpa the GeneProductAssociation_t structure to be copied.
*
* @returns a (deep) copy of the given GeneProductAssociation_t structure, or a null
* pointer if a failure occurred.
*
* @memberof GeneProductAssociation_t
*/
LIBSBML_EXTERN
GeneProductAssociation_t *
GeneProductAssociation_clone(GeneProductAssociation_t * gpa);
/**
* Returns the value of the "id" attribute of the given GeneProductAssociation_t
* structure.
*
* @param gpa the GeneProductAssociation_t structure.
*
* @return the id of this structure.
*
* @member of GeneProductAssociation_t
*/
LIBSBML_EXTERN
const char *
GeneProductAssociation_getId(const GeneProductAssociation_t * gpa);
/**
* Returns the value of the "name" attribute of the given GeneProductAssociation_t
* structure.
*
* @param gpa the GeneProductAssociation_t structure.
*
* @return the name of this structure.
*
* @member of GeneProductAssociation_t
*/
LIBSBML_EXTERN
const char *
GeneProductAssociation_getName(const GeneProductAssociation_t * gpa);
LIBSBML_EXTERN
FbcAssociation_t*
GeneProductAssociation_getAssociation(GeneProductAssociation_t * gpa);
LIBSBML_EXTERN
FbcAnd_t *
GeneProductAssociation_createAnd(GeneProductAssociation_t * gpa);
LIBSBML_EXTERN
FbcOr_t *
GeneProductAssociation_createOr(GeneProductAssociation_t * gpa);
LIBSBML_EXTERN
GeneProductRef_t *
GeneProductAssociation_createGeneProductRef(GeneProductAssociation_t * gpa);
/**
* Predicate returning @c 1 if the given GeneProductAssociation_t structure's
* "id" is set.
*
* @param gpa the GeneProductAssociation_t structure.
*
* @return @c 1 if the "id" of this GeneProductAssociation_t structure is
* set, @c 0 otherwise.
*
* @member of GeneProductAssociation_t
*/
LIBSBML_EXTERN
int
GeneProductAssociation_isSetId(const GeneProductAssociation_t * gpa);
/**
* Predicate returning @c 1 if the given GeneProductAssociation_t structure's "name"
* is set.
*
* @param gpa the GeneProductAssociation_t structure.
*
* @return @c 1 if the "name" of this GeneProductAssociation_t structure is
* set, @c 0 otherwise.
*
* @member of GeneProductAssociation_t
*/
LIBSBML_EXTERN
int
GeneProductAssociation_isSetName(const GeneProductAssociation_t * gpa);
/**
* Predicate returning @c 1 if the given GeneProductAssociation_t structure's "association"
* is set.
*
* @param gpa the GeneProductAssociation_t structure.
*
* @return @c 1 if the "association" of this GeneProductAssociation_t structure is
* set, @c 0 otherwise.
*
* @member of GeneProductAssociation_t
*/
LIBSBML_EXTERN
int
GeneProductAssociation_isSetAssociation(const GeneProductAssociation_t * gpa);
/**
* Sets the "id" attribute of the given GeneProductAssociation_t structure.
*
* This function copies the string given in @p string. If the string is
* a null pointer, this function performs GeneProductAssociation_unsetId() instead.
*
* @param gpa the GeneProductAssociation_t structure.
*
* @param id the string to which the structures "id" attribute should be
* set.
*
* @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 @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @note Using this function with a null pointer for @p name is equivalent to
* unsetting the value of the "name" attribute.
*
* @member of GeneProductAssociation_t
*/
LIBSBML_EXTERN
int
GeneProductAssociation_setId(GeneProductAssociation_t * gpa, const char * id);
/**
* Sets the "name" attribute of the given GeneProductAssociation_t structure.
*
* This function copies the string given in @p string. If the string is
* a null pointer, this function performs GeneProductAssociation_unsetName() instead.
*
* @param gpa the GeneProductAssociation_t structure.
*
* @param name the string to which the structures "name" attribute should be
* set.
*
* @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 @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @note Using this function with a null pointer for @p name is equivalent to
* unsetting the value of the "name" attribute.
*
* @member of GeneProductAssociation_t
*/
LIBSBML_EXTERN
int
GeneProductAssociation_setName(GeneProductAssociation_t * gpa, const char * name);
LIBSBML_EXTERN
int
GeneProductAssociation_setAssociation(GeneProductAssociation_t * gpa, FbcAssociation_t* association);
/**
* Unsets the value of the "id" attribute of the given
* GeneProductAssociation_t structure.
*
* @param gpa the GeneProductAssociation_t structure.
*
* @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 @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @member of GeneProductAssociation_t
*/
LIBSBML_EXTERN
int
GeneProductAssociation_unsetId(GeneProductAssociation_t * gpa);
/**
* Unsets the value of the "name" attribute of the given
* GeneProductAssociation_t structure.
*
* @param gpa the GeneProductAssociation_t structure.
*
* @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 @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_OBJECT, OperationReturnValues_t}
*
* @member of GeneProductAssociation_t
*/
LIBSBML_EXTERN
int
GeneProductAssociation_unsetName(GeneProductAssociation_t * gpa);
/**
* Predicate returning @c 1 or *c 0 depending on whether all the required
* attributes of the given GeneProductAssociation_t structure have been set.
*
* @param gpa the GeneProductAssociation_t structure to check.
*
* @return @c 1 if all the required attributes for this
* structure have been defined, @c 0 otherwise.
*
* @member of GeneProductAssociation_t
*/
LIBSBML_EXTERN
int
GeneProductAssociation_hasRequiredAttributes(const GeneProductAssociation_t * gpa);
/**
* Predicate returning @c 1 or *c 0 depending on whether all the required
* sub-elements of the given GeneProductAssociation_t structure have been set.
*
* @param gpa the GeneProductAssociation_t structure to check.
*
* @return @c 1 if all the required sub-elements for this
* structure have been defined, @c 0 otherwise.
*
* @member of GeneProductAssociation_t
*/
LIBSBML_EXTERN
int
GeneProductAssociation_hasRequiredElements(const GeneProductAssociation_t * gpa);
END_C_DECLS
LIBSBML_CPP_NAMESPACE_END
#endif /* !SWIG */
#endif /* GeneProductAssociation_H__ */
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