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* @file FluxBound.h
* @brief Definition of FluxBound, the SBase derived class of the fbc package.
* @author Frank T. Bergmann
*
*<!---------------------------------------------------------------------------
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* Copyright (C) 2013-2017 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
*
* 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
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*
* @class FluxBound
* @sbmlbrief{fbc} Max or min value for a reaction flux.
*
* The FluxBound class of objects is used in Version 1 of the SBML
* Level 3 @ref fbc (“fbc”) package to express a single
* (in)equality that provides the maximum or minimum value that a reaction
* flux can obtain at steady state. (This same information is encoded
* differently in Version 2 of “fbc”; see the
* "upperFluxBound" and "lowerFluxBound" attributes on FbcReactionPlugin.)
*
* @section fluxbound-attributes Attributes on FluxBound
*
* In addition to the common optional attributes "id" and "name", FluxBound
* takes three required attributes: "reaction", "operation" and "value".
* These three attributes define the meaning of the FluxBound, and are
* interpreted using the following expression:
* <center>
* <em>reaction</em> <em>operator</em> <em>value</em>
* </center>
*
* The "reaction" attribute takes a value of <code>SIdRef</code>. The value
* must be the identifier of a Reaction object defined within the enclosing
* model.
*
* The "operation" attribute takes a value from an enumeration
* (#FluxBoundOperation_t) of Boolean operations that represent mathemetical
* inequalities. Possible values for "operation" include
* <code>"greaterEqual"</code>, <code>"equal"</code>, and others.
*
* The "value" attribute takes a numerical value of type <code>double</code>,
* and represents the value of the flux bound. The permitted values include
* positive infinity (<code>"INF"</code>) and negative infinity
* (<code>"-INF"</code>).
*
* The following is an example of a set of flux bounds encoded in this form; it
* also demonstrates the use of ListOfFluxBounds.
*
* @verbatim
<fbc:listOfFluxBounds>
<fbc:fluxBound fbc:id="R1b" fbc:reaction="R1" fbc:operation="greaterEqual" fbc:value="1.2"/>
<fbc:fluxBound fbc:id="R2b" fbc:reaction="R2" fbc:operation="lessEqual" fbc:value="-1.2"/>
<fbc:fluxBound fbc:id="R3b" fbc:reaction="R3" fbc:operation="greaterEqual" fbc:value="-INF"/>
<fbc:fluxBound fbc:id="R4b" fbc:reaction="R4" fbc:operation="lessEqual" fbc:value="INF"/>
<fbc:fluxBound fbc:id="R5b" fbc:reaction="R5" fbc:operation="equal" fbc:value="1"/>
</fbc:listOfFluxBounds>
@endverbatim
*
* @note This class is only defined for Version 1 of the
* “fbc” package specification. It was replaced in
* Version 2 by a Parameter referenced by the "upperFluxBound" or
* "lowerFluxBound" attributes on an FbcReactionPlugin. FluxBound is
* therefore not used for Version 2 “fbc” models.
*
* @see ListOfFluxBounds
*/
#ifndef FluxBound_H__
#define FluxBound_H__
#include <sbml/common/extern.h>
#include <sbml/common/sbmlfwd.h>
#include <sbml/packages/fbc/common/fbcfwd.h>
LIBSBML_CPP_NAMESPACE_BEGIN
/**
* @enum FluxBoundOperation_t
* @brief Possible values for the FluxBound 'operation' attribute.
*
* The possible legal values are less than or equal to, greater than or
* equal to, or equal to. The two options <i>less than</i> and <i>greater
* than</i> are not legal values for the FluxBound 'operation' attribute,
* but are provided to allow backwards compatibility with an earlier
* version of the draft specification.
*/
typedef enum
{
FLUXBOUND_OPERATION_LESS_EQUAL /*!< Less than or equal to. */
, FLUXBOUND_OPERATION_GREATER_EQUAL /*!< Greater than or equal to.*/
, FLUXBOUND_OPERATION_LESS /*!< Less than. NOTE: ILLEGAL VALUE. */
, FLUXBOUND_OPERATION_GREATER /*!< Greater than. NOTE: ILLEGAL VALUE. */
, FLUXBOUND_OPERATION_EQUAL /*!< Equal to. */
, FLUXBOUND_OPERATION_UNKNOWN /*!< Unknown operation. */
} FluxBoundOperation_t;
LIBSBML_CPP_NAMESPACE_END
#ifdef __cplusplus
#include <string>
#include <sbml/SBase.h>
#include <sbml/ListOf.h>
#include <sbml/packages/fbc/extension/FbcExtension.h>
LIBSBML_CPP_NAMESPACE_BEGIN
class LIBSBML_EXTERN FluxBound : public SBase
{
protected:
/** @cond doxygenLibsbmlInternal */
// std::string mId;
// std::string mName;
std::string mReaction;
FluxBoundOperation_t mOperation;
std::string mOperationString;
double mValue;
/** @endcond */
public:
/**
* Creates a new FbcAssociation with the given SBML Level, Version, and
* “fbc”package version.
*
* @param level an unsigned int, the SBML Level to assign to this
* FluxObjective.
*
* @param version an unsigned int, the SBML Version to assign to this
* FluxObjective.
*
* @param pkgVersion an unsigned int, the SBML Fbc Version to assign to
* this FluxObjective.
*
* @copydetails doc_note_setting_lv_pkg
*/
FluxBound(unsigned int level = FbcExtension::getDefaultLevel(),
unsigned int version = FbcExtension::getDefaultVersion(),
unsigned int pkgVersion = FbcExtension::getDefaultPackageVersion());
/**
* Creates a new FluxBound with the given FbcPkgNamespaces object.
*
* @copydetails doc_what_are_sbml_package_namespaces
*
* @param fbcns the FbcPkgNamespaces object.
*
* @copydetails doc_note_setting_lv_pkg
*/
FluxBound(FbcPkgNamespaces* fbcns);
/**
* Copy constructor.
*
* @param source the instance to copy.
*/
FluxBound(const FluxBound& source);
/**
* Assignment operator.
*
* @param source the object whose values are used as the basis of the
* assignment.
*/
FluxBound& operator=(const FluxBound& source);
/**
* Destructor.
*/
virtual ~FluxBound ();
/**
* Returns the value of the "id" attribute of this FluxBound.
*
* @note Because of the inconsistent behavior of this function with
* respect to assignments and rules, it is now recommended to
* use the getIdAttribute() function instead.
*
* @copydetails doc_id_attribute
*
* @return the id of this FluxBound.
*
* @see getIdAttribute()
* @see setIdAttribute(const std::string& sid)
* @see isSetIdAttribute()
* @see unsetIdAttribute()
*/
virtual const std::string& getId () const;
/**
* Predicate returning @c true if this FluxBound's "id" attribute is set.
*
* @copydetails doc_isset_id
*/
virtual bool isSetId () const;
/**
* Sets the value of the "id" attribute of this FluxBound.
*
* @copydetails doc_set_id
*/
virtual int setId(const std::string& sid);
/**
* Unsets the value of the "id" attribute of this FluxBound object.
*
* @copydetails doc_unset_id
*/
virtual int unsetId ();
/**
* Returns the value of the "name" attribute of this FluxBound object.
*
* @copydetails doc_get_name
*/
virtual const std::string& getName () const;
/**
* Predicate returning @c true if this FluxBound's "name" attribute is set.
*
* @copydetails doc_isset_name
*/
virtual bool isSetName () const;
/**
* Sets the value of the "name" attribute of this FluxBound.
*
* @copydetails doc_set_name
*/
virtual int setName (const std::string& name);
/**
* Unsets the value of the "name" attribute of this FluxBound object.
*
* @copydetails doc_unset_name
*/
virtual int unsetName ();
/**
* Returns the value of the "reaction" attribute of this FluxBound object.
*
* @return the value of the "reaction" attribute of this FluxBound object.
*/
virtual const std::string& getReaction () const;
/**
* Predicate returning @c true if this FluxBound's "reaction" attribute is
* set.
*
* @return @c true if this FluxBound object's "reaction" attribute has been
* set, otherwise @c false is returned.
*/
virtual bool isSetReaction () const;
/**
* Sets the value of the "reaction" attribute of this FluxBound object.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*/
virtual int setReaction (const std::string& reaction);
/**
* Unsets the value of the "reaction" attribute of this FluxBound object.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int unsetReaction ();
/**
* Returns the value of the "operation" attribute of this FluxBound object.
*
* @return the value of the "operation" attribute of this FluxBound object.
*/
const std::string& getOperation ();
/**
* Returns the value of the "operation" attribute of this FluxBound object.
*
* @return the value of the "operation" attribute of this FluxBound object.
*/
FluxBoundOperation_t getFluxBoundOperation () const;
/**
* Predicate returning @c true if this FluxBound's "operation" attribute is
* set.
*
* @return @c true if this FluxBound object's "operation" attribute has been set,
* otherwise @c false is returned.
*/
virtual bool isSetOperation () const;
/**
* Sets the value of the "operation" attribute of this FluxBound object.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*/
virtual int setOperation (const std::string& operation);
/**
* Sets the value of the "operation" attribute of this FluxBound object.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*/
virtual int setOperation (FluxBoundOperation_t operation);
/**
* Unsets the value of the "operation" attribute of this FluxBound object.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int unsetOperation ();
/**
* Returns the value of the "value" attribute of this FluxBound object.
*
* @return the value of the "value" attribute of this FluxBound object.
*/
virtual double getValue () const;
/**
* Predicate returning @c true if this FluxBound's "value" attribute is
* set.
*
* @return @c true if this FluxBound object's "value" attribute has been set,
* otherwise @c false is returned.
*/
virtual bool isSetValue () const;
/**
* Sets the value of the "value" attribute of this FluxBound object.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
*/
virtual int setValue (const double value);
/**
* Unsets the value of the "value" attribute of this FluxBound object.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int unsetValue ();
/**
* @copydoc doc_renamesidref_common
*/
virtual void renameSIdRefs(const std::string& oldid, const std::string& newid);
/**
* Returns the XML element name of this object.
*
* For FluxBound, the XML element name is always @c "fluxBound".
*
* @return the name of this element, i.e. @c "fluxBound".
*/
virtual const std::string& getElementName () const ;
/**
* Creates and returns a deep copy of this FluxBound object.
*
* @return a (deep) copy of this FluxBound object.
*/
virtual FluxBound* clone () const;
/**
* Returns the libSBML type code of this object instance.
*
* @copydetails doc_what_are_typecodes
*
* @return the SBML type code for this object:
* @sbmlconstant{SBML_FBC_FLUXBOUND, SBMLFbcTypeCode_t}.
*
* @copydetails doc_warning_typecodes_not_unique
*
* @see getElementName()
* @see getPackageName()
*/
virtual int getTypeCode () const;
/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to write out their contained
* SBML objects as XML elements. Be sure to call your parent's
* implementation of this method as well. For example:
*
* SBase::writeElements(stream);
* mReactants.write(stream);
* mProducts.write(stream);
* ...
*/
virtual void writeElements (XMLOutputStream& stream) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Accepts the given SBMLVisitor.
*
* @return the result of calling <code>v.visit()</code>, which indicates
* whether or not the Visitor would like to visit the SBML object's next
* sibling object (if available).
*/
virtual bool accept (SBMLVisitor& v) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument of this SBML object.
*
* @param d the SBMLDocument object to use.
*/
virtual void setSBMLDocument (SBMLDocument* d);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Enables/Disables the given package with this element and child
* elements (if any).
* (This is an internal implementation for enablePakcage function)
*
* @note Subclasses in which one or more child elements are defined
* must override this function.
*/
virtual void enablePackageInternal(const std::string& pkgURI,
const std::string& pkgPrefix, bool flag);
/** @endcond */
#ifndef SWIG
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this FluxBound.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName, bool& value)
const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this FluxBound.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName, int& value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this FluxBound.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName,
double& value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this FluxBound.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName,
unsigned int& value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this FluxBound.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName,
std::string& value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Gets the value of the "attributeName" attribute of this FluxBound.
*
* @param attributeName, the name of the attribute to retrieve.
*
* @param value, the address of the value to record.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int getAttribute(const std::string& attributeName,
const char* value) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Predicate returning @c true if this FluxBound's attribute "attributeName"
* is set.
*
* @param attributeName, the name of the attribute to query.
*
* @return @c true if this FluxBound's attribute "attributeName" has been
* set, otherwise @c false is returned.
*/
virtual bool isSetAttribute(const std::string& attributeName) const;
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this FluxBound.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName, bool value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this FluxBound.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName, int value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this FluxBound.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName, double value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this FluxBound.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName,
unsigned int value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this FluxBound.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName,
const std::string& value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Sets the value of the "attributeName" attribute of this FluxBound.
*
* @param attributeName, the name of the attribute to set.
*
* @param value, the value of the attribute to set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int setAttribute(const std::string& attributeName, const char*
value);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Unsets the value of the "attributeName" attribute of this FluxBound.
*
* @param attributeName, the name of the attribute to query.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
virtual int unsetAttribute(const std::string& attributeName);
/** @endcond */
#endif /* !SWIG */
protected:
/** @cond doxygenLibsbmlInternal */
/**
* Create and return an SBML object of this class, if present.
*
* @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 */
/** @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);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to read values from the given
* XMLAttributes set into their specific fields. Be sure to call your
* parent's implementation of this method as well.
*/
virtual void readAttributes (const XMLAttributes& attributes,
const ExpectedAttributes& expectedAttributes);
/** @endcond */
/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to write their XML attributes
* to the XMLOutputStream. Be sure to call your parent's implementation
* of this method as well. For example:
*
* SBase::writeAttributes(stream);
* stream.writeAttribute( "id" , mId );
* stream.writeAttribute( "name", mName );
* ...
*/
virtual void writeAttributes (XMLOutputStream& stream) const;
/** @endcond */
};
/**
* @class ListOfFluxBounds
* @sbmlbrief{fbc} A list of FluxBound objects.
*
* The ListOfFluxBounds is a container for the FluxBound elements of a Model.
* It is only defined for Version 1 of the “fbc”
* specification, and was replaced in Version 2 by Parameter elements
* referenced by the "upperFluxBound" or "lowerFluxBound" attributes on an
* FbcReactionPlugin. FluxBound and ListOfFluxBounds are not used for
* Version 2 “fbc” models.
*
* @copydetails doc_what_is_listof
*
* @see FluxBound
*
* @note This class and FluxBound are only defined for Version 1 of the
* “fbc” package specification. These classes are not used in
* Version 2 of “fbc”.
*/
class LIBSBML_EXTERN ListOfFluxBounds : public ListOf
{
public:
/**
* Creates and returns a deep copy of this ListOfFluxBounds.
*
* @return a (deep) copy of this ListOfFluxBounds.
*/
virtual ListOfFluxBounds* clone () const;
/**
* Creates a new ListOfFluxBounds with the given level, version, and package version.
*
* @param level the SBML Level.
* @param version the Version within the SBML Level.
* @param pkgVersion the version of the package.
*
* @copydetails doc_note_setting_lv_pkg
*/
ListOfFluxBounds(unsigned int level = FbcExtension::getDefaultLevel(),
unsigned int version = FbcExtension::getDefaultVersion(),
unsigned int pkgVersion = FbcExtension::getDefaultPackageVersion());
/**
* Creates a new ListOfFluxBounds with the given FbcPkgNamespaces object.
*
* @copydetails doc_what_are_sbml_package_namespaces
*
* @param fbcns the FbcPkgNamespaces object.
*
* @copydetails doc_note_setting_lv_pkg
*/
ListOfFluxBounds(FbcPkgNamespaces* fbcns);
/**
* Get a FluxBound from the ListOfFluxBounds.
*
* @param n the index number of the FluxBound to get.
*
* @return the nth FluxBound in this ListOfFluxBounds.
*
* @see size()
*/
virtual FluxBound* get(unsigned int n);
/**
* Get a FluxBound from the ListOfFluxBounds.
*
* @param n the index number of the FluxBound to get.
*
* @return the nth FluxBound in this ListOfFluxBounds.
*
* @see size()
*/
virtual const FluxBound * get(unsigned int n) const;
/**
* Get a FluxBound from the ListOfFluxBounds
* based on its identifier.
*
* @param sid a string representing the identifier
* of the FluxBound to get.
*
* @return FluxBound in this ListOfFluxBounds
* with the given @p sid or @c NULL if no such
* FluxBound exists.
*
* @see get(unsigned int n)
* @see size()
*/
virtual FluxBound* get (const std::string& sid);
/**
* Get a FluxBound from the ListOfFluxBounds
* based on its identifier.
*
* @param sid a string representing the identifier
* of the FluxBound to get.
*
* @return FluxBound in this ListOfFluxBounds
* with the given @p sid or @c NULL if no such
* FluxBound exists.
*
* @see get(unsigned int n)
* @see size()
*/
virtual const FluxBound* get (const std::string& sid) const;
/**
* Removes the nth item from this ListOfFluxBounds 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 FluxBound* remove (unsigned int n);
/**
* Removes item in this ListOfFluxBounds 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 FluxBound* remove (const std::string& sid);
/**
* Returns the libSBML type code for the SBML objects
* contained in this ListOf object.
*
* @copydetails doc_what_are_typecodes
*
* @return the SBML type code for objects contained in this list:
* @sbmlconstant{SBML_FBC_FLUXBOUND, SBMLTypeCode_t} (default).
*
* @see getElementName()
* @see getPackageName()
*/
virtual int getItemTypeCode () const;
/**
* Returns the XML element name of this object.
*
* For ListOfFluxBounds, the XML element name is always @c "listOfFluxBounds".
*
* @return the name of this element, i.e. @c "listOfFluxBounds".
*/
virtual const std::string& getElementName () const;
protected:
/** @cond doxygenLibsbmlInternal */
/**
* Create and return an SBML object of this class, if present.
*
* @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);
virtual void writeXMLNS (XMLOutputStream& stream) const;
/** @endcond */
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
#ifndef SWIG
LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
/**
* Creates a new FluxBound_t structure using the given SBML @p level
* and @p version, and the @p pkgVersion package version.
*
* @param level an unsigned int, the SBML Level to assign to this
* FluxBound_t.
* @param version an unsigned int, the SBML Version to assign to this
* FluxBound_t.
* @param pkgVersion an unsigned int, the SBML 'fbc' package Version to assign to this
* FluxBound_t.
*
* @return a pointer to the newly created FluxBound_t structure.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
FluxBound_t *
FluxBound_create(unsigned int level, unsigned int version, unsigned int pkgVersion);
/**
* Takes an FluxBound_t structure and returns its identifier.
*
* @param fb the FluxBound_t structure whose identifier is sought.
*
* @return the identifier of the given FluxBound_t, as a pointer to a string.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
const char *
FluxBound_getId(FluxBound_t * fb);
/**
* Predicate returning @c 1 (true) or @c 0 (false) depending on whether the given
* FluxBound_t structure's identifier is set.
*
* @param fb the FluxBound_t structure to query.
*
* @return @c 1 (true) if the "id" attribute of the given
* FluxBound_t structure is set, @c 0 (false) otherwise.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_isSetId(FluxBound_t * fb);
/**
* Assigns the identifier of an FluxBound_t structure.
*
* This makes a copy of the string passed in the parameter @p sid.
*
* @param fb the FluxBound_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 @p sid of NULL is equivalent to
* unsetting the "id" attribute.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_setId(FluxBound_t * fb, const char * sid);
/**
* Unsets the "id" attribute of the given FluxBound_t structure.
*
* @param fb the FluxBound_t structure to unset.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_unsetId(FluxBound_t * fb);
/**
* Takes a FluxBound_t structure and returns its name.
*
* @param fb the FluxBound_t whose name is sought.
*
* @return the name of the given FluxBound_t, as a pointer to a string.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
const char *
FluxBound_getName(FluxBound_t * fb);
/**
* Predicate returning @c 1 (true) or @c 0 (false) depending on whether the given
* FluxBound_t structure's name is set.
*
* @param fb the FluxBound_t structure to query.
*
* @return @c 1 (true) if the "name" attribute of the given
* FluxBound_t structure is set, @c 0 (false) otherwise.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_isSetName(FluxBound_t * fb);
/**
* Sets the name of the given FluxBound_t to a copy of @p name.
*
* @param fb the FluxBound_t structure to set.
* @param name the name to assign to the given FluxBound_t's "name" attribute.
*
* @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 FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_setName(FluxBound_t * fb, const char * name);
/**
* Unsets the "name" attribute of the given FluxBound_t structure.
*
* @param fb the FluxBound_t structure to unset.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_unsetName(FluxBound_t * fb);
/**
* Takes a FluxBound_t structure and returns its reaction.
*
* @param fb the FluxBound_t whose reaction is sought.
*
* @return the reaction of the given FluxBound_t, as a pointer to a string.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
const char *
FluxBound_getReaction(FluxBound_t * fb);
/**
* Predicate returning @c 1 (true) or @c 0 (false) depending on whether the given
* FluxBound_t structure's reaction is set.
*
* @param fb the FluxBound_t structure to query.
*
* @return @c 1 (true) if the "reaction" attribute of the given
* FluxBound_t structure is set, @c 0 (false) otherwise.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_isSetReaction(FluxBound_t * fb);
/**
* Sets the reaction of the given FluxBound_t to a copy of @p reaction.
*
* @param fb the FluxBound_t structure to set.
* @param reaction the reaction to assign to the given FluxBound_t's "reaction" attribute.
*
* @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 "reaction" attribute.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_setReaction(FluxBound_t * fb, const char * reaction);
/**
* Unsets the "reaction" attribute of the given FluxBound_t structure.
*
* @param fb the FluxBound_t structure to unset.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_unsetReaction(FluxBound_t * fb);
/**
* Takes a FluxBound_t structure and returns its operation.
*
* @param fb the FluxBound_t whose operation is sought.
*
* @return the operation of the given FluxBound_t, as a pointer to a string.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
const char *
FluxBound_getOperation(FluxBound_t * fb);
/**
* Predicate returning @c 1 (true) or @c 0 (false) depending on whether the given
* FluxBound_t structure's operation is set.
*
* @param fb the FluxBound_t structure to query.
*
* @return @c 1 (true) if the "operation" attribute of the given
* FluxBound_t structure is set, @c 0 (false) otherwise.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_isSetOperation(FluxBound_t * fb);
/**
* Sets the operation of the given FluxBound_t to a copy of @p operation.
*
* @param fb the FluxBound_t structure to set.
* @param operation the operation to assign to the given FluxBound_t's "operation" attribute.
*
* @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 "operation" attribute.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_setOperation(FluxBound_t * fb, const char * operation);
/**
* Unsets the "operation" attribute of the given FluxBound_t structure.
*
* @param fb the FluxBound_t structure to unset.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_unsetOperation(FluxBound_t * fb);
/**
* Takes a FluxBound_t structure and returns its value.
*
* @param fb the FluxBound_t whose value is sought.
*
* @return the value attribute of the given FluxBound_t, as a @c double.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
double
FluxBound_getValue(FluxBound_t * fb);
/**
* Predicate returning @c 1 (true) or @c 0 (false) depending on whether the given
* FluxBound_t structure's value is set.
*
* @param fb the FluxBound_t structure to query.
*
* @return @c 1 (true) if the "value" attribute of the given
* FluxBound_t structure is set, @c 0 (false) otherwise.
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_isSetValue(FluxBound_t * fb);
/**
* Sets the "value" attribute of the given FluxBound_t
* structure.
*
* @param fb the FluxBound_t structure.
*
* @param value the value of value to assign to the "value" attribute.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_setValue(FluxBound_t * fb, double value);
/**
* Unsets the "value" attribute of the given FluxBound_t structure.
*
* @param fb the FluxBound_t structure to unset.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBound_unsetValue(FluxBound_t * fb);
/**
* Returns the string version of the provided #FluxBoundOperation_t enumeration.
*
* @param type the #FluxBoundOperation_t enumeration to convert.
*
* @return A string corresponding to the given effect: "lessEqual",
* "greaterEqual", "equal", or @c NULL if the value is
* @sbmlconstant{FLUXBOUND_OPERATION_UNKNOWN, FluxBoundOperation_t}
* or another invalid enumeration value.
*
* @note In an earlier version of this specification, "less" and "greater" were
* options that were dropped in the final version of the specification.
* Accordingly, "less" is always converted to "lessEqual", and "greater" is
* always converted to "greaterEqual".
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
const char*
FluxBoundOperation_toString(FluxBoundOperation_t type);
/**
* Returns the #FluxBoundOperation_t enumeration corresponding to
* the given string, or
* @sbmlconstant{FLUXBOUND_OPERATION_UNKNOWN, FluxBoundOperation_t}
* if there is
* no such match. The matching is case-sensitive: "lessEqual" will
* return @sbmlconstant{FLUXBOUND_OPERATION_LESS_EQUAL, FluxBoundOperation_t}, but "lessequal" will return
* @sbmlconstant{FLUXBOUND_OPERATION_UNKNOWN, FluxBoundOperation_t}.
*
* @param s the string to convert to a #FluxBoundOperation_t.
*
* @return The corresponding #FluxBoundOperation_t, or
* @sbmlconstant{FLUXBOUND_OPERATION_UNKNOWN, FluxBoundOperation_t} if no match found.
*
* @note In an earlier version of this specification, "less" and "greater" were
* options that were dropped in the final version of the specification.
* Accordingly, "less" is always converted to "lessEqual", and "greater" is
* always converted to "greaterEqual".
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
FluxBoundOperation_t
FluxBoundOperation_fromString(const char* s);
/**
* Predicate returning @c 1 (true) or @c 0 (false) depending on whether the given
* #FluxBoundOperation_t is valid.
*
* @param type the #FluxBoundOperation_t enumeration to query.
*
* @return @c 1 (true) if the FluxBoundOperation_t is
* @sbmlconstant{FLUXBOUND_OPERATION_LESS_EQUAL, FluxBoundOperation_t},
* @sbmlconstant{FLUXBOUND_OPERATION_GREATER_EQUAL, FluxBoundOperation_t},
* @sbmlconstant{FLUXBOUND_OPERATION_LESS, FluxBoundOperation_t},
* @sbmlconstant{FLUXBOUND_OPERATION_GREATER, FluxBoundOperation_t}, or
* @sbmlconstant{FLUXBOUND_OPERATION_EQUAL, FluxBoundOperation_t};
* @c 0 (false) otherwise (including
* @sbmlconstant{FLUXBOUND_OPERATION_UNKNOWN, FluxBoundOperation_t}).
*
* @note In an earlier version of this specification, "less" and "greater" were
* options that were dropped in the final version of the specification.
* Accordingly, "less" is always converted to "lessEqual", and "greater" is
* always converted to "greaterEqual".
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBoundOperation_isValidFluxBoundOperation(FluxBoundOperation_t type);
/**
* Predicate returning @c 1 (true) or @c 0 (false) depending
* on whether the given string is a valid #FluxBoundOperation_t.
* The matching is case-sensitive: "lessEqual" will return @c 1 (true), but
* "lessequal" will return @c 0 (false).
*
* @param s the string to query.
*
* @return @c 1 (true) if the string is
* "lessEqual", "greaterEqual", "less", "greater", or "equal"; @c 0 (false) otherwise.
*
* @note In an earlier version of this specification, "less" and "greater" were
* options that were dropped in the final version of the specification.
* Accordingly, "less" is always converted to "lessEqual", and "greater" is
* always converted to "greaterEqual".
*
* @memberof FluxBound_t
*/
LIBSBML_EXTERN
int
FluxBoundOperation_isValidFluxBoundOperationString(const char* s);
END_C_DECLS
LIBSBML_CPP_NAMESPACE_END
#endif /* !SWIG */
#endif /* FluxBound_H__ */
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