CMassAction Class Reference

#include <CMassAction.h>

Inheritance diagram for CMassAction:

Collaboration diagram for CMassAction:

Public Member Functions
virtual const C_FLOAT64 &	calcValue (const CCallParameters< C_FLOAT64 > &callParameters)
	CMassAction (const std::string &name="NoName", const CCopasiContainer *pParent=NULL)
	CMassAction (const CFunction &src, const CCopasiContainer *pParent=NULL)
	CMassAction (const TriLogic &reversible, const CCopasiContainer *pParent=NULL)
virtual bool	compile ()
virtual bool	dependsOn (const C_FLOAT64 *parameter, const CCallParameters< C_FLOAT64 > &callParameters) const
virtual bool	setInfix (const std::string &infix)
virtual std::string	writeMathML (const std::vector< std::vector< std::string > > &variables, bool expand=true, bool fullExpand=true) const
	~CMassAction ()
Public Member Functions inherited from CFunction
bool	addVariable (const std::string &name, CFunctionParameter::Role usage=CFunctionParameter::VARIABLE, const CFunctionParameter::DataType &type=CFunctionParameter::FLOAT64)
	CFunction (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const Type &type=Function)
	CFunction (const CFunction &src, const CCopasiContainer *pParent=NULL)
CFunction *	createCopy () const
void	createListOfParametersForMathML (std::vector< std::vector< std::string > > &env)
const std::string &	getKey () const
const std::string &	getSBMLId () const
virtual size_t	getVariableIndex (const std::string &name) const
CFunctionParameters &	getVariables ()
const CFunctionParameters &	getVariables () const
virtual const C_FLOAT64 &	getVariableValue (const size_t &index) const
const TriLogic &	isReversible () const
bool	isSuitable (const size_t noSubstrates, const size_t noProducts, const TriLogic reversible)
virtual void	load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH)
bool	operator== (const CFunction &rhs) const
virtual bool	setInfix (const std::string &infix, bool compile)
void	setReversible (const TriLogic &reversible)
void	setSBMLId (const std::string &id)
std::pair< CFunction *, CFunction * >	splitFunction (const CEvaluationNode *node, const std::string &name1, const std::string &name2) const
virtual void	writeMathML (std::ostream &out, size_t l=0) const
virtual	~CFunction ()
Public Member Functions inherited from CEvaluationTree
bool	calls (std::set< std::string > &list) const
	CEvaluationTree (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const Type &type=Function)
	CEvaluationTree (const CEvaluationTree &src, const CCopasiContainer *pParent=NULL)
bool	dependsOnTree (const std::string &name) const
CCopasiObject::DataObjectSet	getDeletedObjects () const
std::string::size_type	getErrorPosition () const
const std::string &	getInfix () const
const std::vector < CEvaluationNode * > &	getNodeList () const
CEvaluationNode *	getRoot ()
const CEvaluationNode *	getRoot () const
const CEvaluationTree::Type &	getType () const
bool	hasCircularDependency () const
bool	hasDiscontinuity () const
bool	isBoolean () const
bool	isUsable () const
bool	operator== (const CEvaluationTree &rhs) const
virtual bool	setRoot (CEvaluationNode *pRootNode)
bool	setTree (const ASTNode &pRootNode)
virtual ASTNode *	toAST (const CCopasiDataModel *pDataModel) const
bool	updateTree ()
virtual	~CEvaluationTree ()
Public Member Functions inherited from CCopasiContainer
virtual bool	add (CCopasiObject *pObject, const bool &adopt=true)
	CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)
	CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL)
virtual std::string	getChildObjectUnits (const CCopasiObject *pObject) const
virtual const CObjectInterface *	getObject (const CCopasiObjectName &cn) const
virtual const objectMap &	getObjects () const
virtual std::string	getUnits () const
virtual const CCopasiObject *	getValueObject () const
virtual bool	remove (CCopasiObject *pObject)
virtual	~CCopasiContainer ()
Public Member Functions inherited from CCopasiObject
void	addDirectDependency (const CCopasiObject *pObject)
	CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL)
void	clearDirectDependencies ()
void	clearRefresh ()
bool	dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const
void	getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const
virtual CCopasiObjectName	getCN () const
virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
CCopasiContainer *	getObjectAncestor (const std::string &type) const
CCopasiDataModel *	getObjectDataModel ()
const CCopasiDataModel *	getObjectDataModel () const
virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const
const std::string &	getObjectName () const
CCopasiContainer *	getObjectParent () const
const std::string &	getObjectType () const
virtual const CObjectInterface::ObjectSet &	getPrerequisites () const
virtual Refresh *	getRefresh () const
UpdateMethod *	getUpdateMethod () const
virtual void *	getValuePointer () const
bool	hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const
bool	hasUpdateMethod () const
bool	isArray () const
bool	isContainer () const
bool	isDataModel () const
bool	isMatrix () const
bool	isNameVector () const
bool	isNonUniqueName () const
virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const
bool	isReference () const
bool	isRoot () const
bool	isSeparator () const
bool	isStaticString () const
bool	isValueBool () const
bool	isValueDbl () const
bool	isValueInt () const
bool	isValueInt64 () const
bool	isValueString () const
bool	isVector () const
virtual bool	mustBeDeleted (const DataObjectSet &deletedObjects) const
virtual void	print (std::ostream *ostream) const
void	removeDirectDependency (const CCopasiObject *pObject)
void	setDirectDependencies (const DataObjectSet &directDependencies)
bool	setObjectName (const std::string &name)
virtual bool	setObjectParent (const CCopasiContainer *pParent)
void	setObjectValue (const C_FLOAT64 &value)
void	setObjectValue (const C_INT32 &value)
void	setObjectValue (const bool &value)
template<class CType >
void	setRefresh (CType *pType, void(CType::*method)(void))
template<class CType >
void	setUpdateMethod (CType *pType, void(CType::*method)(const C_FLOAT64 &))
template<class CType >
void	setUpdateMethod (CType *pType, void(CType::*method)(const C_INT32 &))
template<class CType >
void	setUpdateMethod (CType *pType, void(CType::*method)(const bool &))
virtual	~CCopasiObject ()
Public Member Functions inherited from CObjectInterface
	CObjectInterface ()
virtual	~CObjectInterface ()
Public Member Functions inherited from CAnnotation
bool	addUnsupportedAnnotation (const std::string &name, const std::string &xml)
	CAnnotation ()
	CAnnotation (const CAnnotation &src)
const std::string &	getMiriamAnnotation () const
const std::string &	getNotes () const
UnsupportedAnnotation &	getUnsupportedAnnotations ()
const UnsupportedAnnotation &	getUnsupportedAnnotations () const
bool	operator== (const CAnnotation &rhs) const
bool	removeUnsupportedAnnotation (const std::string &name)
bool	replaceUnsupportedAnnotation (const std::string &name, const std::string &xml)
void	setMiriamAnnotation (const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)
void	setNotes (const std::string &notes)
virtual	~CAnnotation ()

Static Public Attributes
static const char *	Infix []
Static Public Attributes inherited from CEvaluationTree
static const std::string	TypeName []
static const char *	XMLType []
Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Additional Inherited Members
Public Types inherited from CEvaluationTree
enum	Type {   Function = 0, MassAction, PreDefined, UserDefined,   Expression, MathExpression }
Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap
Public Types inherited from CCopasiObject
typedef std::set< const CCopasiObject * >	DataObjectSet
typedef std::vector< Refresh * >	DataUpdateSequence
Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet
typedef std::vector < CObjectInterface * >	UpdateSequence
Public Types inherited from CAnnotation
typedef std::map< std::string, std::string >	UnsupportedAnnotation
Static Public Member Functions inherited from CFunction
static bool	completeFunctionList (std::vector< CFunction * > &list, const size_t &added=0)
Static Public Member Functions inherited from CEvaluationTree
static CEvaluationTree *	copy (const CEvaluationTree &src)
static CEvaluationTree *	create (CEvaluationTree::Type type)
static CEvaluationNode *	fromAST (const ASTNode *pASTNode)
Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())
static void	setRenameHandler (CRenameHandler *rh)
Static Public Member Functions inherited from CAnnotation
static CAnnotation *	castObject (CCopasiObject *pObject)
static const CAnnotation *	castObject (const CCopasiObject *pObject)
Protected Types inherited from CCopasiObject
enum	Flag {   Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8,   Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80,   ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800,   Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000,   Root = 0x10000, Gui = 0x20000 }
Protected Member Functions inherited from CFunction
bool	initVariables ()
Protected Member Functions inherited from CEvaluationTree
void	buildCalculationSequence ()
void	calculate ()
bool	compileNodes ()
bool	parse ()
void	setType (const CEvaluationTree::Type &type)
Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
template<class CType >
CCopasiObject *	addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
void	initObjects ()
Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()
	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)
Protected Attributes inherited from CEvaluationTree
std::vector< CEvaluationNode * >	mCalculationSequence
std::string	mInfix
std::vector< CEvaluationNode * > *	mpNodeList
CEvaluationNode *	mpRoot
CEvaluationTree::Type	mType
bool	mUsable
C_FLOAT64	mValue
Protected Attributes inherited from CCopasiContainer
objectMap	mObjects
Protected Attributes inherited from CAnnotation
std::string	mKey
Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

CMassAction

Created for Copasi by Stefan Hoops (C) Stefan Hoops 2001

Definition at line 30 of file CMassAction.h.

Constructor & Destructor Documentation

CMassAction::CMassAction	(	const std::string &	name = "NoName",
		const CCopasiContainer *	pParent = NULL
	)

Default constructor

Parameters

const	std::string & name (default: "NoName")
const	CCopasiContainer * pParent (default: NULL)

Definition at line 38 of file CMassAction.cpp.

                                                          :
    CFunction(name, pParent, CEvaluationTree::MassAction)
{}

CMassAction::CMassAction	(	const CFunction &	src,
		const CCopasiContainer *	pParent = NULL
	)

Copy constructor

Parameters

const CFunction &	src
const	CCopasiContainer * pParent (default: NULL)

Definition at line 43 of file CMassAction.cpp.

                                                          :
    CFunction(src, pParent)
{}

CMassAction::CMassAction	(	const TriLogic &	reversible,
		const CCopasiContainer *	pParent = NULL
	)

Specified constructor

Parameters

const

CCopasiContainer * pParent (default: NULL)

Definition at line 48 of file CMassAction.cpp.

References CONSTRUCTOR_TRACE, CCopasiMessage::ERROR, Infix, MCMassAction, setInfix(), TriFalse, and TriTrue.

                                                          :
    CFunction((reversible == TriTrue) ?
              "Mass action (reversible)" :
              "Mass action (irreversible)",
              pParent,
              CFunction::MassAction)
{
  CONSTRUCTOR_TRACE;

  if (reversible != TriFalse && reversible != TriTrue)
    CCopasiMessage(CCopasiMessage::ERROR, MCMassAction + 1);

  if (reversible == TriTrue)
    setInfix(Infix[0]);
  else
    setInfix(Infix[1]);
}

CMassAction::~CMassAction

(

)

Destructor

Definition at line 67 of file CMassAction.cpp.

References DESTRUCTOR_TRACE.

{DESTRUCTOR_TRACE;}

Member Function Documentation

const C_FLOAT64 & CMassAction::calcValue ( const CCallParameters< C_FLOAT64 > &  callParameters )

virtual

Calculates the value of the function

Parameters

const

CCallParameters<C_FLOAT64> & callParameters

Returns

const C_FLOAT64 & result

Reimplemented from CFunction.

Definition at line 69 of file CMassAction.cpp.

References CCallParameters< Type >::begin(), C_FLOAT64, CCallParameters< Type >::end(), CFunction::isReversible(), CEvaluationTree::mValue, and TriFalse.

{
  CCallParameters<C_FLOAT64>::const_iterator pCallParameters = callParameters.begin();

  CCallParameters<C_FLOAT64>::const_iterator Factor = (pCallParameters + 1)->vector->begin();
  CCallParameters<C_FLOAT64>::const_iterator End = (pCallParameters + 1)->vector->end();

  mValue = 0.0;

  if (Factor != End)
    {
      mValue = *(pCallParameters + 0)->value   // k1
               * *(Factor++)->value;      // first substrate.

      while (Factor != End)
        mValue *= *(Factor++)->value;
    }

  if (isReversible() == TriFalse)
    return mValue;

  C_FLOAT64 Products = 0.0;

  Factor = (pCallParameters + 3)->vector->begin();
  End = (pCallParameters + 3)->vector->end();

  if (Factor != End)
    {
      Products = *(pCallParameters + 2)->value // k2
                 * *(Factor++)->value;    // first product.

      while (Factor != End)
        Products *= *(Factor++)->value;
    }

  return mValue -= Products;
}

bool CMassAction::compile ( )

virtual

Compile the evaluation tree.

Reimplemented from CEvaluationTree.

Definition at line 164 of file CMassAction.cpp.

References CEvaluationTree::mUsable.

{
  mUsable = true;
  return true;
}

bool CMassAction::dependsOn ( const C_FLOAT64 *  parameter, const CCallParameters< C_FLOAT64 > &  callParameters  ) const

virtual

Returns whether the function depends on the given parameter &param const void * parameter &param const CCallParameters<C_FLOAT64> & callParameters &param bool dependsOn

Reimplemented from CFunction.

Definition at line 107 of file CMassAction.cpp.

References CCallParameters< Type >::begin(), CCallParameters< Type >::end(), CFunction::isReversible(), and TriTrue.

{
  if (parameter == callParameters[0].value) return true;

  CCallParameters<C_FLOAT64>::const_iterator it;
  CCallParameters<C_FLOAT64>::const_iterator end;

  it = callParameters[1].vector->begin();
  end = callParameters[1].vector->end();

  for (; it != end; it++) if (parameter == it->value) return true;

  if (isReversible() != TriTrue) return false;

  if (parameter == callParameters[2].value) return true;

  it = callParameters[3].vector->begin();
  end = callParameters[3].vector->end();

  for (; it != end; it++) if (parameter == it->value) return true;

  return false;
}

bool CMassAction::setInfix ( const std::string &  infix )

virtual

Set the infix description of the tree and compile it.

Parameters

const

std::string & infix

Returns

bool success

Reimplemented from CFunction.

Definition at line 132 of file CMassAction.cpp.

References CFunctionParameters::add(), CFunctionParameters::cleanup(), CFunctionParameter::FLOAT64, CFunction::getVariables(), CFunction::isReversible(), CFunctionParameter::PARAMETER, CFunctionParameter::PRODUCT, CFunction::setInfix(), CFunction::setReversible(), CFunctionParameter::SUBSTRATE, TriFalse, TriTrue, and CFunctionParameter::VFLOAT64.

Referenced by CMassAction().

{
  if (infix == "k1*PRODUCT<substrate_i>-k2*PRODUCT<product_j>")
    setReversible(TriTrue);
  else if (infix == "k1*PRODUCT<substrate_i>")
    setReversible(TriFalse);
  else
    return false;

  CFunction::setInfix(infix);
  getVariables().cleanup();

  getVariables().add("k1",
                     CFunctionParameter::FLOAT64,
                     CFunctionParameter::PARAMETER);
  getVariables().add("substrate",
                     CFunctionParameter::VFLOAT64,
                     CFunctionParameter::SUBSTRATE);

  if (isReversible() == TriTrue)
    {
      getVariables().add("k2",
                         CFunctionParameter::FLOAT64,
                         CFunctionParameter::PARAMETER);
      getVariables().add("product",
                         CFunctionParameter::VFLOAT64,
                         CFunctionParameter::PRODUCT);
    }

  return true;
}

std::string CMassAction::writeMathML ( const std::vector< std::vector< std::string > > &  variables, bool  expand = true, bool  fullExpand = true  ) const

virtual

Function to write the mathematical formula in format of MathML.

Parameters

std::ostream	& out
const	std::vector< std::vector< std::string > > & variables
bool	expand = true
bool	fullExpand

Returns

std::string

Reimplemented from CFunction.

Definition at line 173 of file CMassAction.cpp.

References CFunction::isReversible(), and TriTrue.

Referenced by CQExpressionWidget::writeMathML().

{
  std::ostringstream out;

  bool rev = (isReversible() == TriTrue);

  if (rev)
    out << "<mfenced>" << std::endl;

  out << "<mrow>" << std::endl;

  out << variables[0][0] << std::endl;

  size_t i, imax = variables[1].size();

  for (i = 0; i < imax; ++i)
    {
      out << "<mo>&CenterDot;</mo>" << std::endl;
      out << variables[1][i] << std::endl;
    }

  if (rev)
    {
      out << "<mo>-</mo>" << std::endl;
      out << variables[2][0] << std::endl;

      size_t i, imax = variables[3].size();

      for (i = 0; i < imax; ++i)
        {
          out << "<mo>&CenterDot;</mo>" << std::endl;
          out << variables[3][i] << std::endl;
        }
    }

  out << "</mrow>" << std::endl;

  if (rev)
    out << "</mfenced>" << std::endl;

  return out.str();
}

Member Data Documentation

const char * CMassAction::Infix

static

Initial value:

=
  {"k1*PRODUCT<substrate_i>-k2*PRODUCT<product_j>", "k1*PRODUCT<substrate_i>"}

CMassAction

Created for COPASI by Stefan Hoops (C) Stefan Hoops 2001

Definition at line 34 of file CMassAction.h.

Referenced by CMassAction(), CQValidatorFunction::validate(), and CQExpressionWidget::writeMathML().

---

The documentation for this class was generated from the following files:

• CMassAction.h
• CMassAction.cpp