COPASI API
4.40.278
|
#include <CTauLeapMethod.h>
Public Member Functions | |
CTauLeapMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::tauLeap, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse) | |
CTauLeapMethod (const CTauLeapMethod &src, const CDataContainer *pParent) | |
virtual bool | elevateChildren () |
virtual bool | isValidProblem (const CCopasiProblem *pProblem) |
virtual void | start () |
virtual Status | step (const double &deltaT, const bool &final=false) |
~CTauLeapMethod () | |
![]() | |
CTrajectoryMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse) | |
CTrajectoryMethod (const CTrajectoryMethod &src, const CDataContainer *pParent) | |
const CVectorCore< C_INT > & | getRoots () const |
const bool & | integrateReducedModel () const |
void | setProblem (CTrajectoryProblem *problem) |
virtual void | stateChange (const CMath::StateChange &change) |
~CTrajectoryMethod () | |
![]() | |
CCopasiMethod (const CCopasiMethod &src, const CDataContainer *pParent) | |
virtual void | clearCallBack () |
const CProcessReportLevel & | getCallBack () const |
CMathContainer * | getMathContainer () const |
const CTaskEnum::Method & | getSubType () const |
const CTaskEnum::Task & | getType () const |
virtual void | load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH) |
CCopasiMethod & | operator= (const CCopasiMethod &rhs) |
virtual void | print (std::ostream *ostream) const |
virtual void | printResult (std::ostream *ostream) const |
virtual bool | setCallBack (CProcessReportLevel callBack) |
void | setMathContainer (CMathContainer *pContainer) |
virtual | ~CCopasiMethod () |
![]() | |
bool | addGroup (const std::string &name) |
void | addParameter (CCopasiParameter *pParameter) |
bool | addParameter (const CCopasiParameter ¶meter) |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All) |
template<class CType > | |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All) |
virtual bool | applyData (const CData &data, CUndoData::CChangeSet &changes) |
CCopasiParameterGroup * | assertGroup (const std::string &name, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All) |
template<class CType > | |
CType * | assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All) |
index_iterator | beginIndex () const |
const_name_iterator | beginName () const |
CCopasiParameterGroup (const CCopasiParameterGroup &src, const CDataContainer *pParent=NULL) | |
CCopasiParameterGroup (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="ParameterGroup") | |
void | clear () |
virtual void | createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const |
index_iterator | endIndex () const |
const_name_iterator | endName () const |
CCopasiParameterGroup & | getElementTemplates () |
const CCopasiParameterGroup & | getElementTemplates () const |
CCopasiParameterGroup * | getGroup (const size_t &index) |
const CCopasiParameterGroup * | getGroup (const size_t &index) const |
CCopasiParameterGroup * | getGroup (const std::string &name) |
const CCopasiParameterGroup * | getGroup (const std::string &name) const |
virtual size_t | getIndex (const CDataObject *pObject) const |
size_t | getIndex (const std::string &name) const |
std::string | getKey (const size_t &index) const |
std::string | getKey (const std::string &name) const |
virtual const std::string & | getName (const size_t &index) const |
virtual const CObjectInterface * | getObject (const CCommonName &cn) const |
CCopasiParameter * | getParameter (const size_t &index) |
const CCopasiParameter * | getParameter (const size_t &index) const |
CCopasiParameter * | getParameter (std::string name) |
const CCopasiParameter * | getParameter (std::string name) const |
CCopasiParameter::Type | getType (const size_t &index) const |
CCopasiParameter::Type | getType (const std::string &name) const |
std::string | getUniqueParameterName (const CCopasiParameter *pParameter) const |
template<class CType > | |
CType & | getValue (const size_t &index) |
template<class CType > | |
const CType & | getValue (const size_t &index) const |
template<class CType > | |
CType & | getValue (const std::string &name) |
template<class CType > | |
const CType & | getValue (const std::string &name) const |
bool | haveTemplate () const |
virtual CUndoObjectInterface * | insert (const CData &data) |
CCopasiParameterGroup & | operator= (const CCopasiParameterGroup &rhs) |
virtual bool | remove (CDataObject *pObject) |
bool | removeParameter (CCopasiParameter *pParameter) |
bool | removeParameter (const size_t &index) |
bool | removeParameter (const std::string &name) |
virtual void | setUserInterfaceFlag (const UserInterfaceFlag &flag) |
template<class CType > | |
bool | setValue (const size_t &index, const CType &value) |
template<class CType > | |
bool | setValue (const std::string &name, const CType &value) |
size_t | size (const UserInterfaceFlag &require=UserInterfaceFlag::None, const UserInterfaceFlag &exclude=UserInterfaceFlag::None) const |
bool | swap (const size_t &iFrom, const size_t &iTo) |
bool | swap (index_iterator &from, index_iterator &to) |
virtual CData | toData () const |
virtual void | updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject) |
virtual | ~CCopasiParameterGroup () |
![]() | |
CCopasiParameter (const CCopasiParameter &src, const CDataContainer *pParent) | |
CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="Parameter") | |
virtual CCommonName | getCN () const override |
template<class CType > | |
const CType & | getDefault () const |
virtual const std::string & | getKey () const override |
virtual std::string | getObjectDisplayName () const override |
const CCopasiParameter::Type & | getType () const |
const UserInterfaceFlag & | getUserInterfaceFlag () const |
template<class CType > | |
std::vector< std::pair< CType, CType > > & | getValidValues () |
template<class CType > | |
const std::vector< std::pair< CType, CType > > & | getValidValues () const |
void * | getValidValuesPointer () const |
template<class CType > | |
CType & | getValue () |
template<class CType > | |
const CType & | getValue () const |
virtual void * | getValuePointer () const override |
CDataObject * | getValueReference () const |
bool | hasValidValues () const |
bool | isBasic () const |
bool | isDefault () const |
bool | isEditable () const |
bool | isUnsupported () const |
bool | isValidValue (const bool &value) const |
bool | isValidValue (const C_FLOAT64 &value) const |
bool | isValidValue (const C_INT32 &value) const |
bool | isValidValue (const CCommonName &value) const |
template<class CType > | |
bool | isValidValue (const CType &) const |
bool | isValidValue (const std::string &value) const |
bool | isValidValue (const std::vector< CCopasiParameter * > &value) const |
bool | isValidValue (const unsigned C_INT32 &value) const |
CCopasiParameter & | operator= (const CCopasiParameter &rhs) |
template<class CType > | |
bool | setDefault (const CType &defaultValue) |
bool | setDefault (const std::vector< CCopasiParameter * > &defaultValue) |
virtual bool | setObjectParent (const CDataContainer *pParent) override |
template<class CType , class Enum > | |
bool | setValidValues (const CEnumAnnotation< CType, Enum > &validValues) |
template<class CType > | |
bool | setValidValues (const std::vector< std::pair< CType, CType > > &validValues) |
template<class CType > | |
bool | setValue (const CType &value) |
bool | setValue (const std::vector< CCopasiParameter * > &value) |
virtual | ~CCopasiParameter () |
![]() | |
virtual bool | add (CDataObject *pObject, const bool &adopt=true) |
virtual bool | appendDeletedDependentData (CUndoData &undoData) const |
CDataContainer (const CDataContainer &src, const CDataContainer *pParent) | |
CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None) | |
virtual std::string | getChildObjectUnits (const CDataObject *pObject) const |
void | getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const |
virtual objectMap & | getObjects () |
virtual const objectMap & | getObjects () const |
virtual const std::string | getUnits () const override |
virtual const CDataObject * | getValueObject () const override |
void | objectRenamed (CDataObject *pObject, const std::string &oldName) |
virtual | ~CDataContainer () |
![]() | |
void | addIssue (const CIssue &issue) |
void | addReference (const CDataContainer *pReference) |
virtual void | calculateValue () override |
CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL) | |
virtual void | destruct () override |
virtual const CDataObject * | getDataObject () const override |
CDataContainer * | getObjectAncestor (const std::string &type) const |
CDataModel * | getObjectDataModel () const |
const CObjectInterface * | getObjectFromCN (const CCommonName &cn) const |
const std::string & | getObjectName () const |
CDataContainer * | getObjectParent () const |
const std::string & | getObjectType () const |
virtual const CObjectInterface::ObjectSet & | getPrerequisites () const override |
virtual const CValidity & | getValidity () const override |
bool | hasFlag (const Flag &flag) const |
virtual bool | isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override |
bool | prerequisitsContains (const DataObjectSet &objects) const |
void | removeIssue (const CIssue &issue) |
void | removeReference (const CDataContainer *pReference) |
bool | setObjectName (const std::string &name) |
void | validityChanged (const CValidity &changedValidity) override |
void | validityRemoved (const CValidity &changedValidity) |
virtual | ~CDataObject () |
![]() | |
CObjectInterface () | |
CObjectInterface (const CObjectInterface &src) | |
virtual | ~CObjectInterface () |
![]() | |
CUndoObjectInterface () | |
CUndoObjectInterface (const CUndoObjectInterface &src) | |
bool | generateUuid () |
const xg::Guid & | getUuid () const |
bool | setUuid (const std::string &uuid) |
bool | setUuid (const xg::Guid &uuid) |
virtual | ~CUndoObjectInterface () |
Protected Member Functions | |
C_FLOAT64 | doSingleStep (C_FLOAT64 ds) |
void | updatePropensities () |
bool | updateSystem () |
![]() | |
void | output (const bool &useMoieties) |
virtual void | signalMathContainerChanged () |
![]() | |
CCopasiMethod (const CCopasiMethod &src) | |
CCopasiMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType) | |
![]() | |
CCopasiParameterGroup () | |
![]() | |
CCopasiParameter (const CCopasiParameter &src) | |
![]() | |
template<class CType > | |
CDataMatrixReference< CType > * | addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None) |
template<class CType > | |
CDataObjectReference< CType > * | addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None) |
template<class CType > | |
CDataVectorReference< CType > * | addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None) |
CDataContainer (const CDataContainer &src) | |
void | initObjects () |
![]() | |
CDataObject () | |
CDataObject (const std::string &name, const CDataContainer *pParent=static_cast< CDataContainer * >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None) | |
Private Member Functions | |
CTauLeapMethod () | |
void | initializeParameter () |
Additional Inherited Members | |
![]() | |
enum | Status { FAILURE = -1 , NORMAL = 0 , ROOT = 1 } |
![]() | |
typedef CDataObjectMap::const_type_iterator< CCopasiParameter > | const_name_iterator |
typedef std::vector< CCopasiParameter * > | elements |
typedef elements::iterator | index_iterator |
typedef CDataObjectMap::type_iterator< CCopasiParameter > | name_iterator |
![]() | |
enum class | eUserInterfaceFlag { editable , basic , unsupported , __SIZE } |
enum class | Type { DOUBLE = 0 , UDOUBLE , INT , UINT , BOOL , GROUP , STRING , CN , KEY , FILE , EXPRESSION , INVALID , __SIZE } |
typedef CFlags< eUserInterfaceFlag > | UserInterfaceFlag |
![]() | |
typedef CDataObjectMap | objectMap |
![]() | |
typedef std::set< const CDataObject * > | DataObjectSet |
enum | Flag { Container , Vector , Matrix , NameVector , Reference , ValueBool , ValueInt , ValueInt64 , ValueDbl , NonUniqueName , StaticString , ValueString , Separator , DisplayName , ModelEntity , Array , DataModel , Root , Gui , __SIZE } |
![]() | |
typedef std::vector< const CDataContainer * > | ContainerList |
typedef std::set< const CObjectInterface * > | ObjectSet |
![]() | |
static void | allocateValidValues (const Type &type, void *&pValidValues) |
static void | allocateValue (const Type &type, void *&pValue) |
static void | assignValue (const Type &type, void *&pValue, const void *pNewValue) |
static void | deleteValidValues (const Type &type, void *&pValidValues) |
static void | deleteValue (const Type &type, void *&pValue) |
static CCopasiParameter * | fromData (const CData &data, CUndoObjectInterface *pParent) |
![]() | |
static CDataContainer * | fromData (const CData &data, CUndoObjectInterface *pParent) |
![]() | |
static CDataObject * | fromData (const CData &data, CUndoObjectInterface *pParent) |
static void | sanitizeObjectName (std::string &name) |
![]() | |
static const CDataObject * | DataObject (const CObjectInterface *pInterface) |
static CObjectInterface * | GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName) |
![]() | |
template<class CType > | |
static CType * | fromData (const CData &, CUndoObjectInterface *) |
![]() | |
static const CEnumAnnotation< std::string, Type > | TypeName |
static const CEnumAnnotation< std::string, Type > | XMLType |
![]() | |
static const CObjectInterface::ContainerList | EmptyList |
![]() | |
static const bool | ReducedModel |
CTauLeapMethod::CTauLeapMethod | ( | const CDataContainer * | pParent, |
const CTaskEnum::Method & | methodType = CTaskEnum::Method::tauLeap , |
||
const CTaskEnum::Task & | taskType = CTaskEnum::Task::timeCourse |
||
) |
Specific constructor
const | CDataContainer * pParent |
const | CTaskEnum::Method & methodType (default: tauLeap) |
const | CTaskEnum::Task & taskType (default: timeCourse) |
Default constructor.
References initializeParameter().
CTauLeapMethod::CTauLeapMethod | ( | const CTauLeapMethod & | src, |
const CDataContainer * | pParent | ||
) |
Copy constructor
const | CTauLeapMethod & src |
const | CDataContainer * pParent (default: NULL) |
References initializeParameter().
CTauLeapMethod::~CTauLeapMethod | ( | ) |
Destructor.
|
private |
Default constructor.
Simulates the system over the next interval of time. The timestep is given as argument.
ds | A C_FLOAT64 specifying the timestep |
Initializes the solver and sets the model to be used.
model | A reference to an instance of a CModel Simulates the system over the next interval of time. The timestep is given as argument. |
ds | A C_FLOAT64 specifying the timestep |
References CVectorCore< CType >::array(), C_FLOAT64, CCopasiMessage::EXCEPTION, CMathReaction::getNumberBalance(), CRandom::getRandomCC(), CRandom::getRandomPoisson(), mAmu, mAvgDX, CTrajectoryMethod::mContainerState, MCTrajectoryMethod, mEpsilon, mFirstReactionSpeciesIndex, min, mK, mNumReactions, mNumReactionSpecies, mpRandomGenerator, mReactions, mSigDX, CVectorCore< CType >::size(), updatePropensities(), and updateSystem().
Referenced by step().
|
virtual |
This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.
Reimplemented from CCopasiParameterGroup.
References initializeParameter().
|
private |
Initialize the method parameter
References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), CCopasiParameterGroup::removeParameter(), CCopasiParameterGroup::setValue(), and CCopasiParameter::UINT.
Referenced by CTauLeapMethod(), and elevateChildren().
|
virtual |
Check if the method is suitable for this problem
Reimplemented from CTrajectoryMethod.
References CCopasiMessage::ERROR, CMathContainer::getCountODEs(), CTrajectoryProblem::getDuration(), CMathContainer::getEvents(), CMathContainer::getModel(), CMathContainer::getReactions(), CCopasiMethod::getSubType(), CTrajectoryMethod::isValidProblem(), MCTrajectoryMethod, CTaskEnum::MethodName, CCopasiMethod::mpContainer, CVectorCore< CType >::size(), and CModel::suitableForStochasticSimulation().
|
virtual |
This instructs the method to prepare for integration starting with the initialState given.
Reimplemented from CTrajectoryMethod.
References CVectorCore< CType >::array(), C_FLOAT64, C_INT32, CMathContainer::getCountDependentSpecies(), CMathContainer::getCountFixedEventTargets(), CMathContainer::getCountIndependentSpecies(), CMathContainer::getCountODEs(), CMathContainer::getMathObject(), CMathContainer::getPropensities(), CMathContainer::getRandomGenerator(), CMathContainer::getReactions(), CVectorCore< CType >::initialize(), CRandom::initialize(), mAmu, mAvgDX, CTrajectoryMethod::mContainerState, mEpsilon, mFirstReactionSpeciesIndex, mK, mMaxSteps, mNumReactions, mNumReactionSpecies, CCopasiMethod::mpContainer, mpRandomGenerator, mPropensityObjects, mRandomSeed, mReactions, mSigDX, mUseRandomSeed, CVector< CType >::resize(), CVectorCore< CType >::size(), CTrajectoryMethod::start(), and CMathContainer::updateSimulatedValues().
|
virtual |
This instructs the method to calculate a time step of deltaT starting with the current state, i.e., the result of the previous step. The new state (after deltaT) is expected in the current state. The return value is the actual timestep taken.
const | double & deltaT |
const | bool & final (default: false) |
Reimplemented from CTrajectoryMethod.
References C_FLOAT64, doSingleStep(), CCopasiMessage::EXCEPTION, CTrajectoryProblem::getAutomaticStepSize(), MCTrajectoryMethod, mMaxSteps, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, CTrajectoryMethod::mpProblem, CTrajectoryMethod::NORMAL, and CMathContainer::updateSimulatedValues().
|
protected |
Calculate the propensities for all reactions
References CVectorCore< CType >::array(), C_FLOAT64, CMathObject::calculateValue(), mA0, mAmu, mNumReactions, and mPropensityObjects.
Referenced by doSingleStep().
|
protected |
Updates the system according to the probabilistic number of firings mK[i] of each reaction i
References CVectorCore< CType >::array(), C_FLOAT64, CMathReaction::fireMultiple(), CTrajectoryMethod::mContainerState, mFirstReactionSpeciesIndex, mK, mNumReactions, mNumReactionSpecies, and mReactions.
Referenced by doSingleStep().
|
protected |
Total propensity (sum over mAmu[i])
Referenced by updatePropensities().
|
protected |
A reference to the math container's propensity values
Referenced by doSingleStep(), start(), and updatePropensities().
For tau-selection method
Referenced by doSingleStep(), and start().
|
protected |
The tolerance ratio x(t+t')< eps*x(t)
Referenced by doSingleStep(), and start().
|
protected |
index of first species in a CState
Referenced by doSingleStep(), start(), and updateSystem().
The k-values of the reactions, that is the probabilistic number of firings within one leap.
Referenced by doSingleStep(), start(), and updateSystem().
|
protected |
|
protected |
Number of reactions.
Referenced by doSingleStep(), start(), updatePropensities(), and updateSystem().
|
protected |
Number of variable metabolites.
Referenced by doSingleStep(), start(), and updateSystem().
|
protected |
The random number generator.
Referenced by doSingleStep(), and start().
|
protected |
A reference to the math container's propensity objects
Referenced by start(), and updatePropensities().
|
protected |
The random seed to use.
Referenced by start().
|
protected |
A reference to the math container's reactions
Referenced by doSingleStep(), start(), and updateSystem().
For tau-selection method
Referenced by doSingleStep(), and start().
|
protected |
Specifies if the mRandomSeed should be used. otherwise a randomly chosen seed is used.
Referenced by start().