CKinFunction Class Reference

#include <CKinFunction.h>

Inheritance diagram for CKinFunction:

Collaboration diagram for CKinFunction:

Public Member Functions
	CKinFunction (const std::string &name="NoName", const CCopasiContainer *pParent=NULL)
	CKinFunction (const CFunction &src, CReadConfig *configBuffer=NULL, const CCopasiContainer *pParent=NULL)
	CKinFunction (const CKinFunction &src, const CCopasiContainer *pParent=NULL)
void	cleanup ()
std::vector< CNodeK * > &	getNodes ()
	~CKinFunction ()
Public Member Functions inherited from CFunction
bool	addVariable (const std::string &name, CFunctionParameter::Role usage=CFunctionParameter::VARIABLE, const CFunctionParameter::DataType &type=CFunctionParameter::FLOAT64)
virtual const C_FLOAT64 &	calcValue (const CCallParameters< C_FLOAT64 > &callParameters)
	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)
virtual bool	dependsOn (const C_FLOAT64 *parameter, const CCallParameters< C_FLOAT64 > &callParameters) const
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)
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 std::string	writeMathML (const std::vector< std::vector< std::string > > &variables, bool expand=true, bool fullExpand=true) 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)
virtual bool	compile ()
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 ()

Private Member Functions
void	cleanupNodes ()
void	createParameters ()

Private Attributes
unsigned C_INT32	mNidx
std::vector< CNodeK * >	mNodes
std::vector< CCopasiObject * >	ObjList

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)
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
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

Definition at line 37 of file CKinFunction.h.

Constructor & Destructor Documentation

CKinFunction::CKinFunction	(	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 CKinFunction.cpp.

References CONSTRUCTOR_TRACE.

                                                            :
    CFunction(name, pParent, CFunction::UserDefined)
{
  CONSTRUCTOR_TRACE;
}

CKinFunction::CKinFunction	(	const CFunction &	src,
		CReadConfig *	configBuffer = NULL,
		const CCopasiContainer *	pParent = NULL
	)

Copy constructor

Parameters

const CFunction &	src
CReadConfig *	configBuffer (Default = NULL)
const	CCopasiContainer * pParent (default: NULL)

Definition at line 45 of file CKinFunction.cpp.

References C_INT32, cleanupNodes(), CONSTRUCTOR_TRACE, createParameters(), CReadConfig::getVariable(), and mNodes.

                                                            :
    CFunction(src, pParent)
{
  CONSTRUCTOR_TRACE;

  if (configBuffer)
    {
      C_INT32 i, Size;
      configBuffer->getVariable("Nodes", "C_INT32", &Size);
      mNodes.resize(Size);

      for (i = 0; i < Size; i++)
        {
          mNodes[i] = new CNodeK;
          mNodes[i]->load(*configBuffer);
        }

      createParameters();

      cleanupNodes();
    }

  //  compile();
}

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

Copy constructor

Parameters

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

Definition at line 72 of file CKinFunction.cpp.

References CONSTRUCTOR_TRACE.

                                                            :
    CFunction(src, pParent)
{
  CONSTRUCTOR_TRACE;
  //compile();
}

CKinFunction::~CKinFunction

(

)

Destructor

Definition at line 80 of file CKinFunction.cpp.

References cleanup(), DESTRUCTOR_TRACE, and ObjList.

{
  /*  int i;
    for (i=0; i<ObjList.size(); i++)
     ObjList[i] = NULL;
  */
  ObjList.clear();
  cleanup();
  DESTRUCTOR_TRACE;
}

Member Function Documentation

void CKinFunction::cleanup

(

)

Cleanup

Definition at line 91 of file CKinFunction.cpp.

References cleanupNodes().

Referenced by ~CKinFunction().

{
  cleanupNodes();
}

void CKinFunction::cleanupNodes ( )

private

Cleanup nodes

Definition at line 248 of file CKinFunction.cpp.

References mNodes.

Referenced by CKinFunction(), and cleanup().

{
  size_t i, imax = mNodes.size();

  for (i = 0; i < imax; i++)
    if (mNodes[i]) delete mNodes[i];

  mNodes.clear();
  return;
}

void CKinFunction::createParameters ( )

private

This function indentify the object from name This connects the nodes to build the binary function tree This function is part of the algorithm that builds the binary tree. The expression to the right of the current node (mNidx) is parsed until an operand with a left priority <= the argument (right priority) is encounterd. The pointer to the top node of the parsed expression is returned.

Parameters

C_INT16

priority

Returns

CNodeK * This function is part of the algorithm that builds the binary tree. It returns a pointer to next primary node. Here next is with repect to the internal counter mNidx. If the node is a dead end, i.e., any contant a pointer the node is returned. If then node is '(' the expression between the node and the matching ')' is parsed and a pointer to the resulting top node is returned. If the node is a function or a unary minus the argument is parsed and a pointer to the function node is returned.

CNodeK * This function creates the parameter description for older file versions

Definition at line 97 of file CKinFunction.cpp.

References CFunctionParameters::add(), CCopasiVectorN< CType >::add(), CEvaluationNode::buildInfix(), C_INVALID_INDEX, CFunctionParameters::cleanup(), CCopasiVector< T >::cleanup(), CEvaluationNode::CONSTANT, fatalError, CFunctionParameter::FLOAT64, CCopasiVectorN< CType >::getIndex(), CCopasiObject::getObjectName(), CEvaluationTree::getType(), CFunction::getVariables(), mNodes, CFunctionParameter::MODIFIER, CEvaluationTree::mpNodeList, CEvaluationTree::mpRoot, N_IDENTIFIER, N_KCONSTANT, N_MODIFIER, N_NOP, N_PRODUCT, N_SUBSTRATE, N_VOLUME, CFunctionParameter::PARAMETER, pdelete, CFunctionParameter::PRODUCT, CFunction::setInfix(), CFunctionParameter::setType(), CFunctionParameter::setUsage(), CCopasiVector< T >::size(), CFunctionParameter::SUBSTRATE, and CFunctionParameter::VOLUME.

Referenced by CKinFunction().

{
  CCopasiVectorN < CFunctionParameter > Substrates;
  CCopasiVectorN < CFunctionParameter > Products;
  CCopasiVectorN < CFunctionParameter > Modifiers;
  CCopasiVectorN < CFunctionParameter > Parameters;
  CCopasiVectorN < CFunctionParameter > Volumes;

  size_t i, imax = mNodes.size();

  CFunctionParameter *pParameter;

  for (i = 0; i < imax; i++)
    {
      if (mNodes[i]->getType() == N_IDENTIFIER)
        {
          // We need to check that we have no reserved name.
          const char *Reserved[] =
            {"pi", "exponentiale", "true", "false", "infinity", "nan",
             "PI", "EXPONENTIALE", "TRUE", "FALSE", "INFINITY", "NAN"
            };

          std::string Name = mNodes[i]->getName();
          size_t j, jmax = 12;

          for (j = 0; j < jmax; j++)
            if (Name == Reserved[j]) break;

          if (j != jmax)
            {
              // It is save to prepend the identifyer with '_' since this is not allowed in
              // Gepasi but within COPASI.
              std::string OldName = Name;
              Name = "_" + Name;

              // We have to replace the corresponding CEvaluationNodes to reflect the change.
              std::vector< CEvaluationNode * >::iterator it = mpNodeList->begin();
              std::vector< CEvaluationNode * >::iterator end = mpNodeList->end();

              for (; it != end; ++it)
                if (((*it)->getType() & 0xFF000000) == CEvaluationNode::CONSTANT &&
                    (*it)->getData() == OldName)
                  (*it)->setData(Name);

              // The Infix has changed we need to update it.
              setInfix(mpRoot->buildInfix());
            }

          pParameter = new CFunctionParameter(Name);
          pParameter->setType(CFunctionParameter::FLOAT64);

          switch (mNodes[i]->getSubtype())
            {
              case N_SUBSTRATE:
                pParameter->setUsage(CFunctionParameter::SUBSTRATE);

                if (Substrates.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
                  Substrates.add(pParameter, false);
                else
                  pdelete(pParameter);

                break;

              case N_PRODUCT:
                pParameter->setUsage(CFunctionParameter::PRODUCT);

                if (Products.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
                  Products.add(pParameter, false);
                else
                  pdelete(pParameter);

                break;

              case N_MODIFIER:
                pParameter->setUsage(CFunctionParameter::MODIFIER);

                if (Modifiers.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
                  Modifiers.add(pParameter, false);
                else
                  pdelete(pParameter);

                break;

              case N_KCONSTANT:
              case N_NOP:
                pParameter->setUsage(CFunctionParameter::PARAMETER);

                if (Parameters.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
                  Parameters.add(pParameter, false);
                else
                  pdelete(pParameter);

                break;

              case N_VOLUME:
                pParameter->setUsage(CFunctionParameter::VOLUME);

                if (Volumes.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
                  Volumes.add(pParameter, false);
                else
                  pdelete(pParameter);

                break;

              default:
                pdelete(pParameter);
                fatalError();
            }
        }
    }

  getVariables().cleanup();

  imax = Substrates.size();

  for (i = 0; i < imax; i++)
    getVariables().add(Substrates[i], true);

  Substrates.cleanup();

  imax = Products.size();

  for (i = 0; i < imax; i++)
    getVariables().add(Products[i], true);

  Products.cleanup();

  imax = Modifiers.size();

  for (i = 0; i < imax; i++)
    getVariables().add(Modifiers[i], true);

  Modifiers.cleanup();

  imax = Parameters.size();

  for (i = 0; i < imax; i++)
    getVariables().add(Parameters[i], true);

  Parameters.cleanup();

  imax = Volumes.size();

  for (i = 0; i < imax; i++)
    getVariables().add(Volumes[i], true);

  Volumes.cleanup();
}

std::vector< CNodeK * > & CKinFunction::getNodes

(

)

Retreives the nodes of the function

Definition at line 246 of file CKinFunction.cpp.

References mNodes.

{return mNodes;}

Member Data Documentation

unsigned C_INT32 CKinFunction::mNidx

private

Internal variable

Definition at line 52 of file CKinFunction.h.

std::vector< CNodeK * > CKinFunction::mNodes

private

The vector of nodes of the binary tree of the function 0..* <{CNodeK}>

Definition at line 46 of file CKinFunction.h.

Referenced by CKinFunction(), cleanupNodes(), createParameters(), and getNodes().

std::vector<CCopasiObject*> CKinFunction::ObjList

private

Definition at line 48 of file CKinFunction.h.

Referenced by ~CKinFunction().

---

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

• CKinFunction.h
• CKinFunction.cpp