COPASI API
4.16.103
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#include <CMCATask.h>
Public Member Functions | |
CMCATask (const CCopasiContainer *pParent=NULL) | |
CMCATask (const CMCATask &src, const CCopasiContainer *pParent=NULL) | |
virtual CCopasiMethod * | createMethod (const int &type) const |
virtual bool | initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream) |
void | load (CReadConfig &configBuffer) |
void | printResult (std::ostream *ostream) const |
virtual bool | process (const bool &useInitialValues) |
virtual bool | restore () |
virtual bool | updateMatrices () |
virtual | ~CMCATask () |
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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) |
virtual bool | setMethodType (const int &type) |
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 () |
Private Member Functions | |
void | cleanup () |
Friends | |
std::ostream & | operator<< (std::ostream &os, const CMCATask &A) |
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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static const std::string | TypeName [] |
static const unsigned int | ValidMethods [] |
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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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 46 of file CMCATask.h.
CMCATask::CMCATask | ( | const CCopasiContainer * | pParent = NULL | ) |
A pointer to the found elasticities A pointer to the found flux control coefficients. A pointer to the found concentration control coefficients. Default constructor
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 40 of file CMCATask.cpp.
References CCopasiContainer::add(), createMethod(), CCopasiMethod::mcaMethodReder, CCopasiTask::mpMethod, and CCopasiTask::mpProblem.
CMCATask::CMCATask | ( | const CMCATask & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CMCATask & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 49 of file CMCATask.cpp.
References CCopasiContainer::add(), createMethod(), CCopasiMethod::getSubType(), CCopasiTask::mpMethod, and CCopasiTask::mpProblem.
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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 64 of file CMCATask.cpp.
References CMCAMethod::createMethod().
Referenced by CMCATask().
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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 102 of file CMCATask.cpp.
References CModel::compileIfNecessary(), CCopasiProblem::getModel(), CReport::getStream(), CMCAProblem::getSubTask(), CSteadyStateTask::initialize(), CCopasiTask::initialize(), CCopasiMethod::isValidProblem(), CCopasiTask::mpCallBack, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mReport, CCopasiTask::NO_OUTPUT, and updateMatrices().
void CMCATask::load | ( | CReadConfig & | configBuffer | ) |
Loads parameters for this solver with data coming from a CReadConfig object. (CReadConfig object reads an input stream)
configbuffer | reference to a CReadConfig object. |
Definition at line 74 of file CMCATask.cpp.
References CReadConfig::getVariable(), CReadConfig::LOOP, CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CCopasiTask::mScheduled.
void CMCATask::printResult | ( | std::ostream * | ostream | ) | const |
This functionality is expected from the problem but has to be implemented here for the moment. This is called from the corresponding method of the problem
Definition at line 201 of file CMCATask.cpp.
References CSteadyStateMethod::found, CSteadyStateMethod::foundEquilibrium, CSteadyStateMethod::foundNegative, CCopasiProblem::getModel(), CMCAMethod::getScaledConcentrationCCAnn(), CMCAMethod::getScaledElasticitiesAnn(), CMCAMethod::getScaledFluxCCAnn(), CMCAMethod::getSteadyStateStatus(), CMCAProblem::getSubTask(), CMCAMethod::getUnscaledConcentrationCCAnn(), CMCAMethod::getUnscaledElasticitiesAnn(), CMCAMethod::getUnscaledFluxCCAnn(), CMCAProblem::isSteadyStateRequested(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, CSteadyStateMethod::notFound, and CMCAMethod::setModel().
Referenced by CMCAProblem::printResult().
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Process the task with or without initializing to the initial state.
const | bool & useInitialValues |
Reimplemented from CCopasiTask.
Definition at line 134 of file CMCATask.cpp.
References COutputInterface::AFTER, CModel::applyInitialValues(), COutputInterface::BEFORE, COutputInterface::DURING, CCopasiProblem::getModel(), CCopasiTask::mpCallBack, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::output(), CMCAMethod::process(), CSteadyStateTask::process(), CCopasiTask::setCallBack(), and CMCAMethod::setSteadyStateTask().
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Perform neccessary cleaup procedures
Reimplemented from CCopasiTask.
Definition at line 179 of file CMCATask.cpp.
References CCopasiTask::mpProblem, CSteadyStateTask::restore(), and CCopasiTask::restore().
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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 84 of file CMCATask.cpp.
References CCopasiProblem::getModel(), CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, CMCAMethod::resizeAllMatrices(), and CMCAMethod::setModel().
Referenced by initialize().
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