COPASI API
4.16.103
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#include <CTSSATask.h>
Public Member Functions | |
virtual CCopasiMethod * | createMethod (const int &type) const |
CTSSATask (const CCopasiContainer *pParent=NULL) | |
CTSSATask (const CTSSATask &src, const CCopasiContainer *pParent=NULL) | |
CState * | getState () |
const CTimeSeries & | getTimeSeries () const |
virtual bool | initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream) |
virtual bool | process (const bool &useInitialValues) |
void | processStart (const bool &useInitialValues) |
bool | processStep (const C_FLOAT64 &nextTime) |
virtual bool | restore () |
virtual bool | setMethodType (const int &type) |
virtual bool | updateMatrices () |
~CTSSATask () | |
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CCopasiTask (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const std::string &type="Task") | |
CCopasiTask (const Type &taskType, const CCopasiContainer *pParent=NULL, const std::string &type="Task") | |
CCopasiTask (const CCopasiTask &src, const CCopasiContainer *pParent=NULL) | |
void | cleanup () |
CProcessReport * | getCallBack () const |
const CDescription & | getDescription () const |
virtual const std::string & | getKey () const |
CCopasiMethod * | getMethod () |
const CCopasiMethod * | getMethod () const |
COutputHandler * | getOutputHandler () const |
const OutputFlag & | getOutputMode () const |
CCopasiProblem * | getProblem () |
const CCopasiProblem * | getProblem () const |
CReport & | getReport () |
const CResult & | getResult () const |
CCopasiParameterGroup * | getSliders () |
Type | getType () const |
const bool & | isScheduled () const |
const bool & | isUpdateModel () const |
virtual void | output (const COutputInterface::Activity &activity) |
virtual void | separate (const COutputInterface::Activity &activity) |
virtual bool | setCallBack (CProcessReport *pCallBack) |
void | setScheduled (const bool &scheduled) |
void | setType (const Type &type) |
void | setUpdateModel (const bool &updateModel) |
virtual | ~CCopasiTask () |
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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 CObjectInterface * | getObject (const CCopasiObjectName &cn) 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 CCopasiObjectName | getCN () const |
virtual const DataObjectSet & | getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const |
CCopasiContainer * | getObjectAncestor (const std::string &type) const |
CCopasiDataModel * | getObjectDataModel () |
const CCopasiDataModel * | getObjectDataModel () const |
virtual std::string | getObjectDisplayName (bool regular=true, bool richtext=false) 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 |
virtual void * | getValuePointer () 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 |
virtual void | print (std::ostream *ostream) 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 Attributes | |
static const unsigned int | ValidMethods [] |
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static const std::string | TypeName [] |
static const unsigned int | ValidMethods [] |
static const char * | XMLType [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
Private Member Functions | |
void | cleanup () |
Private Attributes | |
CState * | mpCurrentState |
const C_FLOAT64 * | mpCurrentTime |
CTSSAMethod * | mpTSSAMethod |
CTSSAProblem * | mpTSSAProblem |
CTimeSeries | mTimeSeries |
bool | mTimeSeriesRequested |
bool | mUpdateMoieties |
Additional Inherited Members | |
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enum | eOutputFlagBase { INITIALIZE = 0x01, STREAM = 0x02, FINISH = 0x04, REPORT = 0x10, PLOT = 0x20, TIME_SERIES = 0x40 } |
enum | OutputFlag { NO_OUTPUT = 0, OUTPUT_BEFORE = INITIALIZE, OUTPUT_AFTER = FINISH, OUTPUT = REPORT | PLOT | STREAM, OUTPUT_SE = REPORT | PLOT | INITIALIZE | STREAM | FINISH, OUTPUT_UI = REPORT | PLOT | TIME_SERIES | INITIALIZE | STREAM | FINISH, ONLY_TIME_SERIES = TIME_SERIES | INITIALIZE | STREAM | FINISH } |
enum | Type { steadyState = 0, timeCourse, scan, fluxMode, optimization, parameterFitting, mca, lyap, tssAnalysis, sens, moieties, crosssection, lna, unset } |
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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 bool | isValidMethod (const unsigned int &method, const unsigned int *validMethods) |
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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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std::string | Error |
std::string | Warning |
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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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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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CDescription | mDescription |
OutputFlag | mDoOutput |
std::string | mKey |
unsigned C_INT32 | mOutputCounter |
CProcessReport * | mpCallBack |
CState * | mpInitialState |
CCopasiMethod * | mpMethod |
COutputHandler * | mpOutputHandler |
CCopasiProblem * | mpProblem |
CCopasiParameterGroup * | mpSliders |
CReport | mReport |
CResult | mResult |
bool | mScheduled |
Type | mType |
bool | mUpdateModel |
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objectMap | mObjects |
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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 43 of file CTSSATask.h.
CTSSATask::CTSSATask | ( | const CCopasiContainer * | pParent = NULL | ) |
Default constructor
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 61 of file CTSSATask.cpp.
References CCopasiContainer::add(), createMethod(), CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, mUpdateMoieties, CCopasiParameter::Value::pBOOL, and CCopasiMethod::tssILDM.
CTSSATask::CTSSATask | ( | const CTSSATask & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CTSSATask & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 82 of file CTSSATask.cpp.
References CCopasiContainer::add(), createMethod(), CCopasiParameterGroup::elevateChildren(), CCopasiMethod::getSubType(), CCopasiParameter::getValue(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, mUpdateMoieties, and CCopasiParameter::Value::pBOOL.
CTSSATask::~CTSSATask | ( | ) |
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Definition at line 114 of file CTSSATask.cpp.
References mpCurrentState, and pdelete.
Referenced by ~CTSSATask().
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Create a method of the specified type to solve the task. It is the duty of the caller to release the CCopasiMethod.
const | CCopasiMethod::SubType & type |
Reimplemented from CCopasiTask.
Definition at line 418 of file CTSSATask.cpp.
References CTSSAMethod::createMethod().
Referenced by CTSSATask(), and setMethodType().
CState * CTSSATask::getState | ( | ) |
Retrieves a pointer to current state of the integration.
Definition at line 425 of file CTSSATask.cpp.
References mpCurrentState.
const CTimeSeries & CTSSATask::getTimeSeries | ( | ) | const |
gets a reference to the time series
Definition at line 428 of file CTSSATask.cpp.
References mTimeSeries.
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Initialize the task. If an ostream is given this ostream is used instead of the target specified in the report. This allows nested tasks to share the same output device.
const | OutputFlag & of |
COutputHandler | * pOutputHandler |
std::ostream | * pOstream (default: NULL) |
Reimplemented from CCopasiTask.
Definition at line 138 of file CTSSATask.cpp.
References COutputHandler::addInterface(), CTimeSeries::allocate(), CTimeSeries::clear(), CCopasiProblem::getModel(), CCopasiParameterGroup::getParameter(), CModel::getState(), CTSSAProblem::getStepNumber(), CState::getTime(), CCopasiParameter::getValue(), CCopasiTask::initialize(), CCopasiMethod::isValidProblem(), mpCurrentState, mpCurrentTime, CCopasiTask::mpMethod, CCopasiTask::mpProblem, mpTSSAMethod, mpTSSAProblem, mTimeSeries, mTimeSeriesRequested, mUpdateMoieties, CCopasiParameter::Value::pBOOL, pdelete, CTSSAMethod::predifineAnnotation(), CTSSAMethod::setModel(), CTSSAMethod::setProblem(), and CTSSAProblem::timeSeriesRequested().
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Process the task with or without initializing to the initial state.
const | bool & useInitialValues |
Reimplemented from CCopasiTask.
Definition at line 194 of file CTSSATask.cpp.
References CProcessReport::addItem(), COutputInterface::AFTER, COutputInterface::BEFORE, C_FLOAT64, COutputInterface::DURING, CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, CProcessReport::finishItem(), CTSSAProblem::getDuration(), CCopasiException::getMessage(), CCopasiProblem::getModel(), CTSSAProblem::getOutputStartTime(), CTSSAProblem::getStepSize(), MCTSSAMethod, MCTSSAProblem, CCopasiTask::mpCallBack, mpCurrentState, mpCurrentTime, mpTSSAProblem, mUpdateMoieties, CCopasiTask::output(), processStart(), processStep(), CProcessReport::progressItem(), CProcessReport::setName(), CModel::setState(), tbl(), tble(), tfl(), tfle(), and CModel::updateSimulatedValues().
void CTSSATask::processStart | ( | const bool & | useInitialValues | ) |
Starts the process of integration by calling CTSSAMethod::start
const | bool & useInitialValues |
Definition at line 319 of file CTSSATask.cpp.
References CModel::applyInitialValues(), CCopasiProblem::getModel(), CModel::getState(), mpCurrentState, mpTSSAMethod, mpTSSAProblem, CTSSAMethod::setCurrentState(), and CTSSAMethod::start().
Referenced by process().
bool CTSSATask::processStep | ( | const C_FLOAT64 & | nextTime | ) |
Integrates one step
const | C_FLOAT64 & nextTime |
Definition at line 332 of file CTSSATask.cpp.
References C_FLOAT64, CCopasiMessage::EXCEPTION, CCopasiProblem::getModel(), MCTSSAMethod, mpCurrentState, mpCurrentTime, mpTSSAMethod, mpTSSAProblem, mUpdateMoieties, CModel::setState(), CTSSAMethod::step(), and CModel::updateSimulatedValues().
Referenced by process().
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Perform necessary cleanup procedures
Reimplemented from CCopasiTask.
Definition at line 384 of file CTSSATask.cpp.
References CCopasiProblem::getModel(), CModel::getState(), mpCurrentState, CCopasiTask::mpProblem, CCopasiTask::mUpdateModel, mUpdateMoieties, CCopasiTask::restore(), CModel::setInitialState(), CModel::setState(), CModel::updateInitialValues(), and CModel::updateSimulatedValues().
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Set the method type applied to solve the task
const | CCopasiMethod::SubType & type |
Reimplemented from CCopasiTask.
Definition at line 401 of file CTSSATask.cpp.
References CCopasiContainer::add(), createMethod(), CCopasiMethod::getSubType(), CCopasiTask::isValidMethod(), CCopasiTask::mpMethod, pdelete, and ValidMethods.
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Resizes result matrices and updates array annotations for a specific task. This is used when we need to know about the data structures of a task result without actually performing the task, e.g. when selecting objects for output. For now we assume that this functionality is also performed when initialize() is called.
Reimplemented from CCopasiTask.
Definition at line 119 of file CTSSATask.cpp.
References CCopasiProblem::getModel(), CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, CTSSAMethod::predifineAnnotation(), and CTSSAMethod::setModel().
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A pointer to the current state of the integration.
Definition at line 82 of file CTSSATask.h.
Referenced by cleanup(), getState(), initialize(), process(), processStart(), processStep(), and restore().
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A pointer to the current time of the integration.
Definition at line 87 of file CTSSATask.h.
Referenced by initialize(), process(), and processStep().
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A pointer to the method
Definition at line 72 of file CTSSATask.h.
Referenced by initialize(), processStart(), and processStep().
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A pointer to the Problem
Definition at line 67 of file CTSSATask.h.
Referenced by initialize(), process(), processStart(), and processStep().
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the time series (if requested)
Definition at line 62 of file CTSSATask.h.
Referenced by getTimeSeries(), and initialize().
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whether the time series should be stored in mTimeSeries
Definition at line 57 of file CTSSATask.h.
Referenced by initialize().
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Indicates whether we need to update moieties.
Definition at line 77 of file CTSSATask.h.
Referenced by CTSSATask(), initialize(), process(), processStep(), and restore().
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The methods which can be selected for performing this task.
Definition at line 50 of file CTSSATask.h.
Referenced by CQTSSAWidget::init(), and setMethodType().