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

#include <CSteadyStateProblem.h>

Inheritance diagram for CSteadyStateProblem:
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Collaboration diagram for CSteadyStateProblem:
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Public Member Functions

 CSteadyStateProblem (const CCopasiContainer *pParent=NULL)
 
 CSteadyStateProblem (const CSteadyStateProblem &src, const CCopasiContainer *pParent=NULL)
 
virtual bool initialize ()
 
bool isJacobianRequested () const
 
bool isStabilityAnalysisRequested () const
 
void load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::NEXT)
 
void setJacobianRequested (bool &jacobianRequested)
 
void setStabilityAnalysisRequested (bool &stabilityAnalysisRequested)
 
virtual ~CSteadyStateProblem ()
 
- Public Member Functions inherited from CCopasiProblem
 CCopasiProblem (const CCopasiProblem &src, const CCopasiContainer *pParent=NULL)
 
CModelgetModel () const
 
const CCopasiTask::TypegetType () const
 
virtual void print (std::ostream *ostream) const
 
virtual void printResult (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
CObjectInterface::ObjectSet
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
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 >
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
CProcessReportmpCallBack
 
CModelmpModel
 
CReportmpReport
 
- Protected Attributes inherited from CCopasiParameter
std::string mKey
 
CCopasiObjectmpValueReference
 
size_t mSize
 
Value mValue
 
- Protected Attributes inherited from CCopasiContainer
objectMap mObjects
 
- Static Protected Attributes inherited from CCopasiObject
static CRenameHandlersmpRenameHandler = NULL
 

Detailed Description

CSteadyStateProblem class. This class describes the steady state problem, i.e., it allows to specify for example initial conditions.

Created for Copasi by Stefan Hoops 2002

Definition at line 29 of file CSteadyStateProblem.h.

Constructor & Destructor Documentation

CSteadyStateProblem::CSteadyStateProblem ( const CCopasiContainer pParent = NULL)

The initial state, i.e., the starting conditions of the trajectroy. was a initial state set? Default constructor.

Parameters
constCCopasiContainer * pParent (default: NULL)

CSteadyStateProblem class. This class describes the steady state problem, i.e., it allows to specify for example initial conditions.

Created for Copasi by Stefan Hoops 2002 Default constructor.

Definition at line 43 of file CSteadyStateProblem.cpp.

References CCopasiParameterGroup::addParameter(), CCopasiParameter::BOOL, and CONSTRUCTOR_TRACE.

43  :
45  //mInitialState(),
46  //mHasInitialState(false)
47 {
48  addParameter("JacobianRequested", CCopasiParameter::BOOL, true);
49  addParameter("StabilityAnalysisRequested", CCopasiParameter::BOOL, true);
51 }
bool addParameter(const CCopasiParameter &parameter)
#define CONSTRUCTOR_TRACE
Definition: copasi.h:202
CSteadyStateProblem::CSteadyStateProblem ( const CSteadyStateProblem src,
const CCopasiContainer pParent = NULL 
)

Copy constructor.

Parameters
const CSteadyStateProblem &src CCopasiContainer * pParent (default: NULL)

Copy constructor.

Parameters
const CSteadyStateProblem &src

Definition at line 57 of file CSteadyStateProblem.cpp.

References CONSTRUCTOR_TRACE.

58  :
59  CCopasiProblem(src, pParent)
60  //mInitialState(src.mInitialState),
61  //mHasInitialState(src.mHasInitialState)
#define CONSTRUCTOR_TRACE
Definition: copasi.h:202
CSteadyStateProblem::~CSteadyStateProblem ( )
virtual

Destructor.

Definition at line 67 of file CSteadyStateProblem.cpp.

References DESTRUCTOR_TRACE.

#define DESTRUCTOR_TRACE
Definition: copasi.h:206

Member Function Documentation

bool CSteadyStateProblem::initialize ( )
virtual

Do all neccessary initialization so that calls to caluclate will be successful. This is called once from CCopasiTask::process()

Returns
bool succes

Reimplemented from CCopasiProblem.

Definition at line 70 of file CSteadyStateProblem.cpp.

References CCopasiProblem::mpModel.

Referenced by CSteadyStateTask::initialize().

71 {
72  if (!mpModel) return false;
73 
74  return true;
75 }
CModel * mpModel
bool CSteadyStateProblem::isJacobianRequested ( ) const

Retrieve whether the jacobian is requested.

Returns
bool jacobianRequested

Definition at line 88 of file CSteadyStateProblem.cpp.

References CCopasiParameter::getValue(), and CCopasiParameter::Value::pBOOL.

Referenced by StateSubwidget::loadAll(), SteadyStateWidget::loadTask(), and CSteadyStateTask::process().

89 {return * getValue("JacobianRequested").pBOOL;}
const Value & getValue() const
bool CSteadyStateProblem::isStabilityAnalysisRequested ( ) const

Retrieve whether the stabilty analysis is requested.

Returns
bool stabilityAnalysisRequested

Definition at line 102 of file CSteadyStateProblem.cpp.

References CCopasiParameter::getValue(), and CCopasiParameter::Value::pBOOL.

Referenced by StateSubwidget::loadAll(), SteadyStateWidget::loadTask(), and CSteadyStateTask::process().

103 {return * getValue("StabilityAnalysisRequested").pBOOL;}
const Value & getValue() const
void CSteadyStateProblem::load ( CReadConfig configBuffer,
CReadConfig::Mode  mode = CReadConfig::NEXT 
)

Load a trajectory problem

Parameters
CReadConfig &configBuffer
"CReadConfig::Modemode (Default: CReadConfig::NEXT)

Load a steadystate problem

Parameters
CReadConfig &configBuffer

Definition at line 109 of file CSteadyStateProblem.cpp.

References CCopasiDataModel::getModel(), CCopasiObject::getObjectDataModel(), CCopasiParameter::getValue(), CReadConfig::getVariable(), CReadConfig::getVersion(), CReadConfig::LOOP, CCopasiProblem::mpModel, and CCopasiParameterGroup::setValue().

111 {
112  if (configBuffer.getVersion() < "4.0")
113  {
114  CCopasiDataModel* pDataModel = getObjectDataModel();
115  assert(pDataModel != NULL);
116  mpModel = pDataModel->getModel();
117  //mInitialState = mpModel->getInitialState();
118  //mHasInitialState = false;
119  configBuffer.getVariable("RepStabilityAnalysis", "bool" ,
120  getValue("StabilityAnalysisRequested").pBOOL,
122  setValue("JacobianRequested",
123  * getValue("StabilityAnalysisRequested").pBOOL);
124  }
125 }
CCopasiDataModel * getObjectDataModel()
std::string getVersion()
Definition: CReadConfig.cpp:76
const Value & getValue() const
bool setValue(const std::string &name, const CType &value)
C_INT32 getVariable(const std::string &name, const std::string &type, void *pout, CReadConfig::Mode mode=CReadConfig::NEXT)
Definition: CReadConfig.cpp:81
CModel * mpModel
void CSteadyStateProblem::setJacobianRequested ( bool &  jacobianRequested)

Set whether the jacobian is requested.

Parameters
bool& jacobianRequested

Set whether the jacobian is requested.

Parameters
bool* jacobianRequested

Definition at line 81 of file CSteadyStateProblem.cpp.

References CCopasiParameterGroup::setValue().

Referenced by SteadyStateWidget::saveTask().

82 {setValue("JacobianRequested", jacobianRequested);}
bool setValue(const std::string &name, const CType &value)
void CSteadyStateProblem::setStabilityAnalysisRequested ( bool &  stabilityAnalysisRequested)

Set whether stabilty analysis is requested.

Parameters
bool& stabilityAnalysisRequested

Set whether stabilty analysis is requested.

Parameters
bool* stabilityAnalysisRequested

Definition at line 95 of file CSteadyStateProblem.cpp.

References CCopasiParameterGroup::setValue().

Referenced by CLNATask::process(), and SteadyStateWidget::saveTask().

96 {setValue("StabilityAnalysisRequested", stabilityAnalysisRequested);}
bool setValue(const std::string &name, const CType &value)

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