COPASI API
4.16.103
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#include <CTSSAProblem.h>
Public Member Functions | |
CTSSAProblem (const CCopasiContainer *pParent=NULL) | |
CTSSAProblem (const CTSSAProblem &src, const CCopasiContainer *pParent=NULL) | |
virtual bool | elevateChildren () |
const C_FLOAT64 & | getDuration () const |
const C_FLOAT64 & | getOutputStartTime () const |
const unsigned C_INT32 & | getStepNumber () const |
const C_FLOAT64 & | getStepSize () const |
void | setDuration (const C_FLOAT64 &duration) |
void | setOutputStartTime (const C_FLOAT64 &endTime) |
void | setStepNumber (const unsigned C_INT32 &stepNumber) |
void | setStepSize (const C_FLOAT64 &stepSize) |
void | setTimeSeriesRequested (bool flag) |
bool | timeSeriesRequested () const |
~CTSSAProblem () | |
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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 () |
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bool | addGroup (const std::string &name) |
bool | addParameter (const CCopasiParameter ¶meter) |
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 () |
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 () |
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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 () |
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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 () |
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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 () |
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CObjectInterface () | |
virtual | ~CObjectInterface () |
Private Member Functions | |
void | initializeParameter () |
void | initObjects () |
void | printResult (std::ostream *ostream) const |
bool | sync () |
Private Attributes | |
C_FLOAT64 * | mpDuration |
C_FLOAT64 * | mpOutputStartTime |
unsigned C_INT32 * | mpStepNumber |
C_FLOAT64 * | mpStepSize |
bool * | mpTimeSeriesRequested |
bool | mStepNumberSetLast |
Additional Inherited Members | |
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typedef parameterGroup::iterator | index_iterator |
typedef CCopasiContainer::objectMap::iterator | name_iterator |
typedef std::vector < CCopasiParameter * > | parameterGroup |
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enum | Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID } |
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typedef std::multimap < std::string, CCopasiObject * > | objectMap |
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typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
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typedef std::set< const CObjectInterface * > | ObjectSet |
typedef std::vector < CObjectInterface * > | UpdateSequence |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
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static const std::string | TypeName [] |
static const char * | XMLType [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
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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 } |
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CCopasiProblem (const CCopasiTask::Type &type, const CCopasiContainer *pParent=NULL) | |
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CCopasiParameterGroup () | |
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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 () |
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CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
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CProcessReport * | mpCallBack |
CModel * | mpModel |
CReport * | mpReport |
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std::string | mKey |
CCopasiObject * | mpValueReference |
size_t | mSize |
Value | mValue |
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objectMap | mObjects |
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static CRenameHandler * | smpRenameHandler = NULL |
CTSSAProblem class. This class describes the time scale separation analysis problem, i.e., it allows to specify for example initial conditions and number of steps.
Definition at line 32 of file CTSSAProblem.h.
CTSSAProblem::CTSSAProblem | ( | const CCopasiContainer * | pParent = NULL | ) |
Default constructor.
const | CCopasiContainer * pParent (default: NULL) |
CTSSAProblem class. This class describes the time scale separation analysis problem, i.e., it allows to specify for example initial conditions and number of steps. Default constructor.
Definition at line 45 of file CTSSAProblem.cpp.
References CONSTRUCTOR_TRACE, initializeParameter(), and initObjects().
CTSSAProblem::CTSSAProblem | ( | const CTSSAProblem & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor.
const | CTSSAProblem & src CCopasiContainer * pParent (default: NULL) |
Copy constructor.
const CTSSAProblem & | src |
Definition at line 63 of file CTSSAProblem.cpp.
References CONSTRUCTOR_TRACE, initializeParameter(), and initObjects().
CTSSAProblem::~CTSSAProblem | ( | ) |
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This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.
Reimplemented from CCopasiParameterGroup.
Definition at line 98 of file CTSSAProblem.cpp.
References C_FLOAT64, mpDuration, mpStepNumber, mpStepSize, CCopasiParameterGroup::removeParameter(), and setDuration().
const C_FLOAT64 & CTSSAProblem::getDuration | ( | ) | const |
Retrieve the end time.
Definition at line 180 of file CTSSAProblem.cpp.
References mpDuration.
Referenced by CQTSSAWidget::loadTask(), CTSSATask::process(), and CQTSSAWidget::saveTask().
const C_FLOAT64 & CTSSAProblem::getOutputStartTime | ( | ) | const |
Retrieve the end time.
Definition at line 188 of file CTSSAProblem.cpp.
References mpOutputStartTime.
Referenced by CTSSATask::process().
const unsigned C_INT32 & CTSSAProblem::getStepNumber | ( | ) | const |
Retrieve the number of time steps the method should integrate.
Retrieve the number of time steps the trajectory method should integrate.
Definition at line 140 of file CTSSAProblem.cpp.
References mpStepNumber.
Referenced by CQTSSAResultSubWidget::displayResult(), CTSSATask::initialize(), CQTSSAWidget::loadTask(), CQTSSAWidget::saveTask(), CQTSSAWidget::slotDuration(), and CQTSSAWidget::slotIntervalSize().
const C_FLOAT64 & CTSSAProblem::getStepSize | ( | ) | const |
Retrieve the size a integration step the method should do.
Retrieve the size a integration step the trajectory method should do.
Definition at line 160 of file CTSSAProblem.cpp.
References mpStepSize.
Referenced by CQTSSAWidget::loadTask(), CTSSATask::process(), CQTSSAWidget::saveTask(), CQTSSAWidget::slotDuration(), CQTSSAWidget::slotIntervals(), and CQTSSAWidget::slotIntervalSize().
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Intialize the method parameter
Definition at line 84 of file CTSSAProblem.cpp.
References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, CCopasiParameter::getValue(), mpDuration, mpOutputStartTime, mpStepNumber, mpStepSize, mpTimeSeriesRequested, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pUINT, and CCopasiParameter::UINT.
Referenced by CTSSAProblem().
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Definition at line 110 of file CTSSAProblem.cpp.
References C_INT32, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValueReference(), setDuration(), setStepNumber(), setStepSize(), and CCopasiObject::setUpdateMethod().
Referenced by CTSSAProblem().
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This is the output method for any rsult 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 | * ostream |
Reimplemented from CCopasiProblem.
Definition at line 265 of file CTSSAProblem.cpp.
References CCopasiTask::getMethod(), CCopasiObject::getObjectDataModel(), CCopasiProblem::print(), and CCopasiMethod::printResult().
Set the end time.
const C_FLOAT64 & | duration bool success |
Definition at line 168 of file CTSSAProblem.cpp.
References mpDuration, and sync().
Referenced by elevateChildren(), initObjects(), CQTSSAWidget::saveTask(), and CQTSSAWidget::slotDuration().
Set the end time.
const C_FLOAT64 & | endTime |
Definition at line 183 of file CTSSAProblem.cpp.
References mpOutputStartTime.
Set the number of time steps the method should integrate.
const unsigned C_INT32 & | stepNumber bool success |
Set the number of time steps the trajectory method should integrate.
const unsigned C_INT32 & | stepNumber |
Definition at line 127 of file CTSSAProblem.cpp.
References mpStepNumber, mStepNumberSetLast, and sync().
Referenced by initObjects(), CQTSSAWidget::saveTask(), and CQTSSAWidget::slotIntervals().
Set the size a integration step the method should do.
const C_FLOAT64 & | stepSize bool success |
Set the size a integration step the trajectory method should do.
const C_FLOAT64 & | stepSize |
Definition at line 147 of file CTSSAProblem.cpp.
References mpStepSize, mStepNumberSetLast, and sync().
Referenced by initObjects(), CQTSSAWidget::saveTask(), and CQTSSAWidget::slotIntervalSize().
void CTSSAProblem::setTimeSeriesRequested | ( | bool | flag | ) |
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This function synchronizes step size and number bool success
This function synchronizes step size and number
Definition at line 202 of file CTSSAProblem.cpp.
References C_FLOAT64, C_INT32, MCTSSAProblem, mpDuration, mpStepNumber, mpStepSize, mStepNumberSetLast, and CCopasiMessage::WARNING.
Referenced by setDuration(), setStepNumber(), and setStepSize().
bool CTSSAProblem::timeSeriesRequested | ( | ) | const |
Definition at line 196 of file CTSSAProblem.cpp.
References mpTimeSeriesRequested.
Referenced by CTSSATask::initialize().
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Definition at line 39 of file CTSSAProblem.h.
Referenced by elevateChildren(), getDuration(), initializeParameter(), setDuration(), and sync().
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Definition at line 59 of file CTSSAProblem.h.
Referenced by getOutputStartTime(), initializeParameter(), and setOutputStartTime().
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Definition at line 49 of file CTSSAProblem.h.
Referenced by elevateChildren(), getStepNumber(), initializeParameter(), setStepNumber(), and sync().
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Definition at line 44 of file CTSSAProblem.h.
Referenced by elevateChildren(), getStepSize(), initializeParameter(), setStepSize(), and sync().
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Definition at line 54 of file CTSSAProblem.h.
Referenced by initializeParameter(), setTimeSeriesRequested(), and timeSeriesRequested().
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Indicate whether the step number or step size was set last.
Definition at line 64 of file CTSSAProblem.h.
Referenced by setStepNumber(), setStepSize(), and sync().