COPASI API  4.16.103
Public Member Functions | List of all members
CMoietiesProblem Class Reference

#include <CMoietiesProblem.h>

Inheritance diagram for CMoietiesProblem:
Inheritance graph
Collaboration diagram for CMoietiesProblem:
Collaboration graph

Public Member Functions

 CMoietiesProblem (const CCopasiTask::Type &type=CCopasiTask::moieties, const CCopasiContainer *pParent=NULL)
 CMoietiesProblem (const CMoietiesProblem &src, const CCopasiContainer *pParent=NULL)
virtual void printResult (std::ostream *pOstream) const
virtual ~CMoietiesProblem ()
- Public Member Functions inherited from CCopasiProblem
 CCopasiProblem (const CCopasiProblem &src, const CCopasiContainer *pParent=NULL)
CModelgetModel () const
const CCopasiTask::TypegetType () const
virtual bool initialize ()
virtual void print (std::ostream *ostream) const
virtual bool restore (const bool &updateModel)
virtual bool setCallBack (CProcessReport *pCallBack)
virtual bool setModel (CModel *pModel)
virtual ~CCopasiProblem ()
- Public Member Functions inherited from CCopasiParameterGroup
bool addGroup (const std::string &name)
bool addParameter (const CCopasiParameter &parameter)
bool addParameter (const std::string &name, const CCopasiParameter::Type type)
template<class CType >
bool addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value)
void addParameter (CCopasiParameter *pParameter)
CCopasiParameterGroupassertGroup (const std::string &name)
template<class CType >
CCopasiParameterassertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue)
index_iterator beginIndex () const
name_iterator beginName () const
 CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL)
 CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup")
void clear ()
virtual bool elevateChildren ()
index_iterator endIndex () const
name_iterator endName () const
CCopasiParameterGroupgetGroup (const std::string &name)
const CCopasiParameterGroupgetGroup (const std::string &name) const
CCopasiParameterGroupgetGroup (const size_t &index)
const CCopasiParameterGroupgetGroup (const size_t &index) const
size_t getIndex (const std::string &name) const
std::string getKey (const std::string &name) const
std::string getKey (const size_t &index) const
virtual const std::string & getName (const size_t &index) const
virtual const CObjectInterfacegetObject (const CCopasiObjectName &cn) const
CCopasiParametergetParameter (const std::string &name)
const CCopasiParametergetParameter (const std::string &name) const
CCopasiParametergetParameter (const size_t &index)
const CCopasiParametergetParameter (const size_t &index) const
CCopasiParameter::Type getType (const std::string &name) const
CCopasiParameter::Type getType (const size_t &index) const
std::string getUniqueParameterName (const CCopasiParameter *pParameter) const
const CCopasiParameter::ValuegetValue (const std::string &name) const
const CCopasiParameter::ValuegetValue (const size_t &index) const
CCopasiParameter::ValuegetValue (const std::string &name)
CCopasiParameter::ValuegetValue (const size_t &index)
CCopasiParameterGroupoperator= (const CCopasiParameterGroup &rhs)
bool removeParameter (const std::string &name)
bool removeParameter (const size_t &index)
template<class CType >
bool setValue (const std::string &name, const CType &value)
template<class CType >
bool setValue (const size_t &index, const CType &value)
size_t size () const
bool swap (const size_t &iFrom, const size_t &iTo)
bool swap (index_iterator &from, index_iterator &to)
virtual ~CCopasiParameterGroup ()
- Public Member Functions inherited from CCopasiParameter
 CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL)
 CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CCopasiContainer *pParent=NULL, const std::string &objectType="Parameter")
virtual CCopasiObjectName getCN () const
virtual const std::string & getKey () const
virtual std::string getObjectDisplayName (bool regular=true, bool richtext=false) const
const CCopasiParameter::TypegetType () const
const ValuegetValue () const
ValuegetValue ()
virtual voidgetValuePointer () const
CCopasiObjectgetValueReference () const
bool isValidValue (const C_FLOAT64 &value) const
bool isValidValue (const C_INT32 &value) const
bool isValidValue (const unsigned C_INT32 &value) const
bool isValidValue (const bool &value) const
bool isValidValue (const std::string &value) const
bool isValidValue (const CCopasiObjectName &value) const
bool isValidValue (const std::vector< CCopasiParameter * > &value) const
CCopasiParameteroperator= (const CCopasiParameter &rhs)
template<class CType >
bool setValue (const CType &value)
bool setValue (const std::vector< CCopasiParameter * > &value)
virtual ~CCopasiParameter ()
- 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 objectMapgetObjects () const
virtual std::string getUnits () const
virtual const CCopasiObjectgetValueObject () 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 const DataObjectSetgetDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
CCopasiContainergetObjectAncestor (const std::string &type) const
CCopasiDataModelgetObjectDataModel ()
const CCopasiDataModelgetObjectDataModel () const
const std::string & getObjectName () const
CCopasiContainergetObjectParent () const
const std::string & getObjectType () const
virtual const
getPrerequisites () const
virtual RefreshgetRefresh () const
UpdateMethodgetUpdateMethod () 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
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 ()

Additional Inherited Members

- Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator index_iterator
typedef std::vector
< CCopasiParameter * > 
- Public Types inherited from CCopasiParameter
enum  Type {
- Public Types inherited from CCopasiContainer
typedef std::multimap
< std::string, CCopasiObject * > 
- Public Types inherited from CCopasiObject
typedef std::set< const
CCopasiObject * > 
typedef std::vector< Refresh * > DataUpdateSequence
- Public Types inherited from CObjectInterface
typedef std::set< const
CObjectInterface * > 
typedef std::vector
< CObjectInterface * > 
- 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 Attributes inherited from CCopasiParameter
static const std::string TypeName []
static const char * XMLType []
- Static Public Attributes inherited from CCopasiContainer
static const std::vector
< CCopasiContainer * > 
- 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 CCopasiProblem
 CCopasiProblem (const CCopasiTask::Type &type, const CCopasiContainer *pParent=NULL)
- Protected Member Functions inherited from CCopasiParameterGroup
 CCopasiParameterGroup ()
- Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObjectaddMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
template<class CType >
CCopasiObjectaddObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
template<class CType >
CCopasiObjectaddVectorReference (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 CCopasiProblem
- Protected Attributes inherited from CCopasiParameter
std::string mKey
size_t mSize
Value mValue
- Protected Attributes inherited from CCopasiContainer
objectMap mObjects
- Static Protected Attributes inherited from CCopasiObject
static CRenameHandlersmpRenameHandler = NULL

Detailed Description

Definition at line 19 of file CMoietiesProblem.h.

Constructor & Destructor Documentation

CMoietiesProblem::CMoietiesProblem ( const CCopasiTask::Type type = CCopasiTask::moieties,
const CCopasiContainer pParent = NULL 

Default constructor

constCCopasiTask::Type & type (default: moieties)
constCCopasiContainer * pParent (default: NULL)

Definition at line 22 of file CMoietiesProblem.cpp.

23  :
24  CCopasiProblem(type, pParent)
25 {}
CMoietiesProblem::CMoietiesProblem ( const CMoietiesProblem src,
const CCopasiContainer pParent = NULL 

Copy constructor.

constCMoietiesProblem & src CCopasiContainer * pParent (default: NULL)

Definition at line 28 of file CMoietiesProblem.cpp.

29  :
30  CCopasiProblem(src, pParent)
31 {}
CMoietiesProblem::~CMoietiesProblem ( )


Definition at line 34 of file CMoietiesProblem.cpp.

35 {}

Member Function Documentation

void CMoietiesProblem::printResult ( std::ostream *  pOstream) const

This is the output method for any result of a problem. The default implementation provided with CCopasiProblem. Does only print "Not implmented." To overide this default behaviour one needs to reimplement the virtual printResult function.

std::ostream* pOstream

Reimplemented from CCopasiProblem.

Definition at line 37 of file CMoietiesProblem.cpp.

References CCopasiVector< T >::begin(), CCopasiVector< T >::end(), CModel::getMoieties(), CCopasiContainer::getObject(), and CCopasiProblem::mpModel.

38  {
39  if (mpModel == NULL) return;
41  // Print all Moieties
42  *pOstream << "Dependent Species" << "\t";
43  *pOstream << "Total Amount" << "\t";
44  *pOstream << "Expression" << std::endl;
48  for (; it != end; ++it)
49  {
50  *pOstream << (*it)->getObjectName() << "\t";
51  *pOstream << (*it)->getNumber() << "\t";
52  *pOstream << (*it)->getDescription(mpModel) << std::endl;
53  }
54  *pOstream << std::endl;
56  // Print Reordered Stoichiometry Matrix
57  *pOstream << *dynamic_cast<const CArrayAnnotation *>(mpModel->getObject(CCopasiObjectName("Array=Stoichiometry(ann)"))) << std::endl;
59  // Print Link Matrix
60  *pOstream << *dynamic_cast<const CArrayAnnotation *>(mpModel->getObject(CCopasiObjectName("Array=Link matrix(ann)"))) << std::endl;
62  // Print Reduced Stoichiometry Matrix
63  *pOstream << *dynamic_cast<const CArrayAnnotation *>(mpModel->getObject(CCopasiObjectName("Array=Reduced stoichiometry(ann)"))) << std::endl;
65  return;
66  }
iterator begin()
const CCopasiVector< CMoiety > & getMoieties() const
Definition: CModel.cpp:1163
iterator end()
CModel * mpModel
virtual const CObjectInterface * getObject(const CCopasiObjectName &cn) const

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