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

#include <CMoietiesProblem.h>

Inheritance diagram for CMoietiesProblem:
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Collaboration diagram for CMoietiesProblem:
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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)
 
CModel * getModel () const
 
const CCopasiTask::Type & getType () 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)
 
CCopasiParameterGroup * assertGroup (const std::string &name)
 
template<class CType >
CCopasiParameter * assertParameter (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
 
CCopasiParameterGroup * getGroup (const std::string &name)
 
const CCopasiParameterGroup * getGroup (const std::string &name) const
 
CCopasiParameterGroup * getGroup (const size_t &index)
 
const CCopasiParameterGroup * getGroup (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 CObjectInterface * getObject (const CCopasiObjectName &cn) const
 
CCopasiParameter * getParameter (const std::string &name)
 
const CCopasiParameter * getParameter (const std::string &name) const
 
CCopasiParameter * getParameter (const size_t &index)
 
const CCopasiParameter * getParameter (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::Value & getValue (const std::string &name) const
 
const CCopasiParameter::Value & getValue (const size_t &index) const
 
CCopasiParameter::Value & getValue (const std::string &name)
 
CCopasiParameter::Value & getValue (const size_t &index)
 
CCopasiParameterGroup & operator= (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::Type & getType () const
 
const Value & getValue () const
 
Value & getValue ()
 
virtual void * getValuePointer () const
 
CCopasiObject * getValueReference () 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
 
CCopasiParameter & operator= (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 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 const DataObjectSet & getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
 
CCopasiContainer * getObjectAncestor (const std::string &type) const
 
CCopasiDataModel * getObjectDataModel ()
 
const CCopasiDataModel * getObjectDataModel () 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
 
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
CCopasiContainer::objectMap::iterator 		name_iterator
 
typedef std::vector
< CCopasiParameter * > 		parameterGroup
 
- Public Types inherited from CCopasiParameter
enum  Type {
  DOUBLE = 0, UDOUBLE, INT, UINT,
  BOOL, GROUP, STRING, CN,
  KEY, FILE, EXPRESSION, INVALID
}
 
- 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
 
- 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 * > 		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 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 >
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 CCopasiProblem
CProcessReport * mpCallBack
 
CModel * mpModel
 
CReport * mpReport
 
- Protected Attributes inherited from CCopasiParameter
std::string mKey
 
CCopasiObject * mpValueReference
 
size_t mSize
 
Value mValue
 
- Protected Attributes inherited from CCopasiContainer
objectMap mObjects
 
- Static Protected Attributes inherited from CCopasiObject
static CRenameHandler * smpRenameHandler = 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

Parameters
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.

Parameters
constCMoietiesProblem & src CCopasiContainer * pParent (default: NULL)

Definition at line 28 of file CMoietiesProblem.cpp.

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

Destructor

Definition at line 34 of file CMoietiesProblem.cpp.

35 {}

Member Function Documentation

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

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.

Parameters
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;
40 
41  // Print all Moieties
42  *pOstream << "Dependent Species" << "\t";
43  *pOstream << "Total Amount" << "\t";
44  *pOstream << "Expression" << std::endl;
45 
46  CCopasiVector< CMoiety >::const_iterator it = mpModel->getMoieties().begin();
47  CCopasiVector< CMoiety >::const_iterator end = mpModel->getMoieties().end();
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;
55 
56  // Print Reordered Stoichiometry Matrix
57  *pOstream << *dynamic_cast<const CArrayAnnotation *>(mpModel->getObject(CCopasiObjectName("Array=Stoichiometry(ann)"))) << std::endl;
58 
59  // Print Link Matrix
60  *pOstream << *dynamic_cast<const CArrayAnnotation *>(mpModel->getObject(CCopasiObjectName("Array=Link matrix(ann)"))) << std::endl;
61 
62  // Print Reduced Stoichiometry Matrix
63  *pOstream << *dynamic_cast<const CArrayAnnotation *>(mpModel->getObject(CCopasiObjectName("Array=Reduced stoichiometry(ann)"))) << std::endl;
64 
65  return;
66  }
CCopasiVector::begin
iterator begin()
Definition: CCopasiVector.h:185
CModel::getMoieties
const CCopasiVector< CMoiety > & getMoieties() const
Definition: CModel.cpp:1163
CCopasiVector::end
iterator end()
Definition: CCopasiVector.h:191
CCopasiProblem::mpModel
CModel * mpModel
Definition: CCopasiProblem.h:53
CCopasiContainer::getObject
virtual const CObjectInterface * getObject(const CCopasiObjectName &cn) const
Definition: CCopasiContainer.cpp:74
The documentation for this class was generated from the following files:
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