COPASI API
4.16.103
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#include <CTrajectoryMethod.h>
Public Member Functions | |
CTrajectoryMethod (const CTrajectoryMethod &src, const CCopasiContainer *pParent=NULL) | |
const CVector< C_INT > & | getRoots () const |
virtual bool | isValidProblem (const CCopasiProblem *pProblem) |
void | setCurrentState (CState *currentState) |
void | setProblem (CTrajectoryProblem *problem) |
virtual void | start (const CState *initialState) |
virtual void | stateChanged () |
virtual Status | step (const double &deltaT) |
~CTrajectoryMethod () | |
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CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL) | |
const CCopasiMethod::SubType & | getSubType () const |
const CCopasiTask::Type & | getType () const |
virtual void | load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH) |
virtual void | print (std::ostream *ostream) const |
virtual void | printResult (std::ostream *ostream) const |
virtual bool | setCallBack (CProcessReport *pCallBack) |
virtual | ~CCopasiMethod () |
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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 () |
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 () |
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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 () |
Static Public Member Functions | |
static CTrajectoryMethod * | createMethod (CCopasiMethod::SubType subType=CCopasiMethod::deterministic) |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
Protected Member Functions | |
CTrajectoryMethod (const CCopasiMethod::SubType &subType, const CCopasiContainer *pParent=NULL) | |
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CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, 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) | |
Protected Attributes | |
CState * | mpCurrentState |
CTrajectoryProblem * | mpProblem |
CVector< C_INT > | mRoots |
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CProcessReport * | mpCallBack |
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std::string | mKey |
CCopasiObject * | mpValueReference |
size_t | mSize |
Value | mValue |
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objectMap | mObjects |
Private Member Functions | |
CTrajectoryMethod () | |
Additional Inherited Members | |
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static const std::string | SubTypeName [] |
static const char * | XMLSubType [] |
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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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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 43 of file CTrajectoryMethod.h.
Enumeration value for the return value
Enumerator | |
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FAILURE | |
NORMAL | |
ROOT |
Definition at line 49 of file CTrajectoryMethod.h.
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Default constructor.
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protected |
Default constructor.
const | CCopasiMethod::SubType & subType |
const | CCopasiContainer * pParent (default: NULL) |
Default constructor.
Definition at line 98 of file CTrajectoryMethod.cpp.
References CONSTRUCTOR_TRACE.
CTrajectoryMethod::CTrajectoryMethod | ( | const CTrajectoryMethod & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor.
const CTrajectoryMethod & | src |
const | CCopasiContainer * pParent (default: NULL) |
Copy constructor.
const CTrajectoryMethod & | src |
Definition at line 110 of file CTrajectoryMethod.cpp.
References CONSTRUCTOR_TRACE.
CTrajectoryMethod::~CTrajectoryMethod | ( | ) |
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Create a trajectory method for a special problem. Note: the returned object has to be released after use with delete a problem is also passed so that the method has a chance to choose an appropriate simulation method.
CTrajectoryMethod class. This class describes the interface to all integration methods. The various method like LSODA or Gillespie have to be derived from this class.
Created for COPASI by Stefan Hoops 2002
Definition at line 41 of file CTrajectoryMethod.cpp.
References CCopasiMethod::adaptiveSA, CHybridMethod::createHybridMethod(), CHybridMethodLSODA::createHybridMethodLSODA(), CCopasiMethod::deterministic, CCopasiMethod::directMethod, CCopasiMethod::DsaLsodar, fatalError, CCopasiMethod::hybrid, CCopasiMethod::hybridLSODA, CCopasiMethod::hybridODE45, CCopasiMethod::stochastic, CCopasiMethod::tauLeap, and CCopasiMethod::unset.
Referenced by CQTrajectoryWidget::createMethod(), CTrajectoryTask::createMethod(), CCrossSectionTask::createMethod(), and CTrajectoryTask::load().
Retrieve the roots.
Definition at line 181 of file CTrajectoryMethod.cpp.
References mRoots.
Referenced by CTrajectoryTask::processStep(), and CCrossSectionTask::processStep().
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Check if the method is suitable for this problem
Reimplemented from CCopasiMethod.
Reimplemented in CTrajectoryMethodDsaLsodar, CStochMethod, CTrajAdaptiveSA, CStochDirectMethod, CHybridMethodLSODA, CHybridMethodODE45, CHybridMethod, and CTauLeapMethod.
Definition at line 165 of file CTrajectoryMethod.cpp.
References CCopasiMessage::EXCEPTION, CCopasiMethod::isValidProblem(), and MCTrajectoryMethod.
Referenced by CTauLeapMethod::isValidProblem(), CHybridMethod::isValidProblem(), CHybridMethodODE45::isValidProblem(), CHybridMethodLSODA::isValidProblem(), CStochDirectMethod::isValidProblem(), CTrajAdaptiveSA::isValidProblem(), CStochMethod::isValidProblem(), and CTrajectoryMethodDsaLsodar::isValidProblem().
Set a pointer to the current state. This method is used by CTrajectoryTask::process() The results of the simulation are passed via this CState variable
CState * | currentState |
Definition at line 124 of file CTrajectoryMethod.cpp.
References mpCurrentState.
Referenced by CTrajectoryTask::processStart(), and CCrossSectionTask::processStart().
void CTrajectoryMethod::setProblem | ( | CTrajectoryProblem * | problem | ) |
Set a pointer to the problem. This method is used by CTrajectory
CTrajectoryProblem * | problem |
Definition at line 134 of file CTrajectoryMethod.cpp.
References mpProblem.
Referenced by CTrajectoryTask::initialize(), and CCrossSectionTask::initialize().
This instructs the method to prepare for integration starting with the initialState given.
const CState * | initialState |
This instructs the method to calculate a a time step of deltaT starting with the initialState given. The new state (after deltaT) is expected in the current state. The return value is the actual timestep taken.
double & | deltaT |
const CState * | initialState |
Reimplemented in CTrajectoryMethodDsaLsodar, CLsodaMethod, CStochMethod, CTrajAdaptiveSA, CHybridMethodODE45, CStochDirectMethod, CHybridMethodLSODA, CHybridMethod, and CTauLeapMethod.
Definition at line 161 of file CTrajectoryMethod.cpp.
Referenced by CTrajectoryTask::processStart(), and CCrossSectionTask::processStart().
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Inform the trajectory method that the state has changed outside its control
Reimplemented in CTrajectoryMethodDsaLsodar, and CLsodaMethod.
Definition at line 138 of file CTrajectoryMethod.cpp.
Referenced by CTrajectoryTask::processStep(), and CCrossSectionTask::processStep().
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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 |
This instructs the method to calculate a 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 |
Reimplemented in CHybridMethodODE45, CTrajectoryMethodDsaLsodar, CLsodaMethod, CStochMethod, CTrajAdaptiveSA, CStochDirectMethod, CHybridMethodLSODA, CHybridMethod, and CTauLeapMethod.
Definition at line 149 of file CTrajectoryMethod.cpp.
References FAILURE.
Referenced by CTrajectoryTask::processStep(), and CCrossSectionTask::processStep().
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A pointer to the current state. This is set from outside with the setState() method and never changed anywhere else. It's used to report the results to the calling TrajectoryTask
Definition at line 63 of file CTrajectoryMethod.h.
Referenced by CHybridNextReactionLSODAMethod::doSingleStep(), CHybridNextReactionRKMethod::doSingleStep(), CTrajectoryMethodDsaLsodar::doSingleStep(), CHybridMethod::outputData(), CHybridMethodLSODA::outputData(), CHybridMethod::outputDebug(), CHybridMethodODE45::outputDebug(), CHybridMethodLSODA::outputDebug(), CHybridMethod::partitionSystem(), setCurrentState(), CTauLeapMethod::start(), CHybridMethod::start(), CStochDirectMethod::start(), CTrajAdaptiveSA::start(), CStochMethod::start(), CLsodaMethod::stateChanged(), CTrajectoryMethodDsaLsodar::stateChanged(), CTauLeapMethod::step(), CHybridMethod::step(), CHybridMethodLSODA::step(), CStochDirectMethod::step(), CTrajAdaptiveSA::step(), CStochMethod::step(), CLsodaMethod::step(), CTrajectoryMethodDsaLsodar::step(), and CHybridMethodODE45::step().
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A pointer to the trajectory problem.
Definition at line 68 of file CTrajectoryMethod.h.
Referenced by CHybridMethodLSODA::evalF(), CHybridMethodODE45::initMethod(), CHybridMethodLSODA::initMethod(), CHybridMethodLSODA::integrateDeterministicPart(), CHybridMethodLSODA::partitionSystem(), setProblem(), CTauLeapMethod::start(), CHybridMethod::start(), CHybridMethodLSODA::start(), CStochDirectMethod::start(), CHybridMethodODE45::start(), CTrajAdaptiveSA::start(), CStochMethod::start(), CLsodaMethod::start(), CTauLeapMethod::step(), CHybridMethod::step(), CHybridMethodLSODA::step(), CStochDirectMethod::step(), CTrajAdaptiveSA::step(), and CStochMethod::step().
Vector containing information on the current roots
Definition at line 73 of file CTrajectoryMethod.h.
Referenced by CLsodaMethod::createRootMask(), CLsodaMethod::evalR(), getRoots(), CLsodaMethod::peekAhead(), CLsodaMethod::start(), and CLsodaMethod::step().