COPASI API  4.16.103
Public Member Functions | Private Member Functions | Private Attributes | List of all members
CLyapProblem Class Reference

#include <CLyapProblem.h>

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

 CLyapProblem (const CCopasiContainer *pParent=NULL)
 
 CLyapProblem (const CLyapProblem &src, const CCopasiContainer *pParent=NULL)
 
bool divergenceRequested () const
 
virtual bool elevateChildren ()
 
const unsigned C_INT32getExponentNumber () const
 
const C_FLOAT64getTransientTime () const
 
virtual void printResult (std::ostream *ostream) const
 
void setDivergenceRequested (bool flag)
 
void setExponentNumber (const unsigned C_INT32 &number)
 
void setTransientTime (const C_FLOAT64 &endTime)
 
 ~CLyapProblem ()
 
- 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 ()
 
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 ()
 

Private Member Functions

void initializeParameter ()
 

Private Attributes

bool * mpDivergenceRequested
 
unsigned C_INT32mpExponentNumber
 
C_FLOAT64mpTransientTime
 

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

CLyapProblem class.

Definition at line 25 of file CLyapProblem.h.

Constructor & Destructor Documentation

CLyapProblem::CLyapProblem ( const CCopasiContainer pParent = NULL)

Default constructor.

Parameters
constCCopasiContainer * pParent (default: NULL)

CLyapProblem class. Default constructor.

Definition at line 35 of file CLyapProblem.cpp.

References CONSTRUCTOR_TRACE, and initializeParameter().

35  :
37  mpExponentNumber(NULL),
38  //mpTimeSeriesRequested(NULL),
40  mpTransientTime(NULL)
41 {
44 }
unsigned C_INT32 * mpExponentNumber
Definition: CLyapProblem.h:32
void initializeParameter()
C_FLOAT64 * mpTransientTime
Definition: CLyapProblem.h:48
bool * mpDivergenceRequested
Definition: CLyapProblem.h:42
#define CONSTRUCTOR_TRACE
Definition: copasi.h:202
CLyapProblem::CLyapProblem ( const CLyapProblem src,
const CCopasiContainer pParent = NULL 
)

Copy constructor.

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

Copy constructor.

Parameters
const CLyapProblem &src

Definition at line 50 of file CLyapProblem.cpp.

References CONSTRUCTOR_TRACE, and initializeParameter().

51  :
52  CCopasiProblem(src, pParent),
53  mpExponentNumber(NULL),
54  //mpTimeSeriesRequested(NULL),
56  mpTransientTime(NULL)
57 {
60 }
unsigned C_INT32 * mpExponentNumber
Definition: CLyapProblem.h:32
void initializeParameter()
C_FLOAT64 * mpTransientTime
Definition: CLyapProblem.h:48
bool * mpDivergenceRequested
Definition: CLyapProblem.h:42
#define CONSTRUCTOR_TRACE
Definition: copasi.h:202
CLyapProblem::~CLyapProblem ( )

Destructor.

Definition at line 65 of file CLyapProblem.cpp.

References DESTRUCTOR_TRACE.

#define DESTRUCTOR_TRACE
Definition: copasi.h:206

Member Function Documentation

bool CLyapProblem::divergenceRequested ( ) const
bool CLyapProblem::elevateChildren ( )
virtual

This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.

Returns
bool success

Reimplemented from CCopasiParameterGroup.

Definition at line 68 of file CLyapProblem.cpp.

Referenced by initializeParameter().

69 {
70  return true;
71 }
const unsigned C_INT32 & CLyapProblem::getExponentNumber ( ) const
const C_FLOAT64 & CLyapProblem::getTransientTime ( ) const

Retrieve the end time.

Returns
"const C_FLOAT64 &" endTime

Definition at line 98 of file CLyapProblem.cpp.

References mpTransientTime.

Referenced by CLyapWolfMethod::calculate(), CLyapWolfMethod::isValidProblem(), CQLyapWidget::loadTask(), and CQLyapWidget::saveTask().

99 {return *mpTransientTime;}
C_FLOAT64 * mpTransientTime
Definition: CLyapProblem.h:48
void CLyapProblem::initializeParameter ( )
private

Load a trajectory problem

Parameters
CReadConfig &configBuffer
"CReadConfig::Modemode (Default: CReadConfig::NEXT) Allocates all group parameters and assures that they are properly initialized.

Definition at line 73 of file CLyapProblem.cpp.

References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, elevateChildren(), CCopasiParameter::getValue(), mpDivergenceRequested, mpExponentNumber, mpTransientTime, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pUINT, and CCopasiParameter::UINT.

Referenced by CLyapProblem().

74 {
76  assertParameter("ExponentNumber", CCopasiParameter::UINT, (unsigned C_INT32) 3)->getValue().pUINT;
78  assertParameter("DivergenceRequested", CCopasiParameter::BOOL, (bool) true)->getValue().pBOOL;
81 
83 }
unsigned C_INT32 * mpExponentNumber
Definition: CLyapProblem.h:32
C_FLOAT64 * mpTransientTime
Definition: CLyapProblem.h:48
bool * mpDivergenceRequested
Definition: CLyapProblem.h:42
#define C_INT32
Definition: copasi.h:90
const Value & getValue() const
unsigned C_INT32 * pUINT
virtual bool elevateChildren()
#define C_FLOAT64
Definition: copasi.h:92
CCopasiParameter * assertParameter(const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue)
void CLyapProblem::printResult ( std::ostream *  ostream) 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* ostream

Reimplemented from CCopasiProblem.

Definition at line 118 of file CLyapProblem.cpp.

References CCopasiObject::getObjectParent(), and CLyapTask::printResult().

119 {
120  CLyapTask* parent = dynamic_cast<CLyapTask*>(getObjectParent());
121 
122  if (!parent) return;
123 
124  parent->printResult(ostream);
125 }
void printResult(std::ostream *ostream) const
Definition: CLyapTask.cpp:292
CCopasiContainer * getObjectParent() const
void CLyapProblem::setDivergenceRequested ( bool  flag)

Definition at line 110 of file CLyapProblem.cpp.

References mpDivergenceRequested.

Referenced by CQLyapWidget::saveTask().

111 {
113 }
bool * mpDivergenceRequested
Definition: CLyapProblem.h:42
long int flag
Definition: f2c.h:52
void CLyapProblem::setExponentNumber ( const unsigned C_INT32 number)

Set the number of exponents to calculate

Parameters
const unsigned C_INT32 &

Definition at line 85 of file CLyapProblem.cpp.

References mpExponentNumber.

Referenced by CQLyapWidget::saveTask().

86 {
87  *mpExponentNumber = number;
88 }
unsigned C_INT32 * mpExponentNumber
Definition: CLyapProblem.h:32
void CLyapProblem::setTransientTime ( const C_FLOAT64 endTime)

Set the end time.

Parameters
const C_FLOAT64 &endTime

Definition at line 93 of file CLyapProblem.cpp.

References mpTransientTime.

Referenced by CQLyapWidget::saveTask().

94 {
95  *mpTransientTime = startTime;
96 }
C_FLOAT64 * mpTransientTime
Definition: CLyapProblem.h:48

Member Data Documentation

bool* CLyapProblem::mpDivergenceRequested
private

whether the divergence should also be calculated

Definition at line 42 of file CLyapProblem.h.

Referenced by divergenceRequested(), initializeParameter(), and setDivergenceRequested().

unsigned C_INT32* CLyapProblem::mpExponentNumber
private

Number of exponents to calculate. 0 means all.

Definition at line 32 of file CLyapProblem.h.

Referenced by getExponentNumber(), initializeParameter(), and setExponentNumber().

C_FLOAT64* CLyapProblem::mpTransientTime
private

Indicates at which point of time the calculation of exponents should be started.

Definition at line 48 of file CLyapProblem.h.

Referenced by getTransientTime(), initializeParameter(), and setTransientTime().


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