COPASI API
4.16.103
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#include <CEFMTask.h>
Public Member Functions | |
CEFMTask (const CCopasiContainer *pParent=NULL) | |
CEFMTask (const CEFMTask &src, const CCopasiContainer *pParent=NULL) | |
virtual CCopasiMethod * | createMethod (const int &type) const |
std::string | getFluxModeDescription (const CFluxMode &fluxMode) const |
const std::vector< CFluxMode > & | getFluxModes () const |
std::string | getInternalSpecies (const CFluxMode &fluxMode) const |
std::string | getNetReaction (const CFluxMode &fluxMode) const |
std::string | getReactionEquation (const std::map< size_t, C_FLOAT64 >::const_iterator &itReaction) const |
std::pair< C_FLOAT64, C_FLOAT64 > | getSpeciesChanges (const CFluxMode &fluxMode, const CMetab &metab) const |
virtual bool | initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream) |
virtual bool | process (const bool &useInitialValues) |
virtual bool | setCallBack (CProcessReport *pCallBack) |
virtual bool | setMethodType (const int &type) |
virtual | ~CEFMTask () |
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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 bool | restore () |
virtual void | separate (const COutputInterface::Activity &activity) |
void | setScheduled (const bool &scheduled) |
void | setType (const Type &type) |
void | setUpdateModel (const bool &updateModel) |
virtual bool | updateMatrices () |
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 Member Functions | |
static bool | isValidMethod (const unsigned C_INT32 &method, const unsigned C_INT32 *validMethods) |
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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) |
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 | |
std::map< const CMetab *, C_FLOAT64 > | getNetReactionData (const CFluxMode &fluxMode) const |
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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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 41 of file CEFMTask.h.
CEFMTask::CEFMTask | ( | const CCopasiContainer * | pParent = NULL | ) |
default constructor
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 55 of file CEFMTask.cpp.
References CCopasiContainer::add(), CEFMMethod::createMethod(), CCopasiTask::mpMethod, and CCopasiTask::mpProblem.
CEFMTask::CEFMTask | ( | const CEFMTask & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | COptTask & src |
Definition at line 64 of file CEFMTask.cpp.
References CCopasiContainer::add(), CEFMMethod::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 125 of file CEFMTask.cpp.
References CEFMMethod::createMethod().
Referenced by setMethodType().
std::string CEFMTask::getFluxModeDescription | ( | const CFluxMode & | fluxMode | ) | const |
Retrieve the description of the flux mode
const | CFluxMode & fluxMode |
Definition at line 132 of file CEFMTask.cpp.
References CFluxMode::begin(), C_INT32, CFluxMode::end(), getReactionIndex(), CCopasiMethod::getSubType(), CSSAMethod::isReactionReversed(), CCopasiTask::mpMethod, and CCopasiTask::mpProblem.
Referenced by CQNewMainWindow::checkForElementaryModesSlot(), CQFluxModeDM::data(), and CEFMProblem::printResult().
const std::vector< CFluxMode > & CEFMTask::getFluxModes | ( | ) | const |
Retrieve the Flux Modes
Definition at line 183 of file CEFMTask.cpp.
References CCopasiTask::mpProblem.
Referenced by CQEFMResultWidget::loadResult(), CEFMProblem::printResult(), CQEFMReactionDM::setTask(), CQEFMNetReactionDM::setTask(), CQFluxModeDM::setTask(), and CQEFMSpeciesDM::setTask().
std::string CEFMTask::getInternalSpecies | ( | const CFluxMode & | fluxMode | ) | const |
Retrieve the internal species for the given flux mode.
const | CFluxMode & fluxMode |
Definition at line 334 of file CEFMTask.cpp.
References CMetabNameInterface::getDisplayName(), CCopasiProblem::getModel(), getNetReactionData(), and CCopasiTask::getProblem().
Referenced by CQEFMNetReactionDM::data(), and CEFMProblem::printResult().
std::string CEFMTask::getNetReaction | ( | const CFluxMode & | fluxMode | ) | const |
Retrieve the net reaction for the given flux mode.
const | CFluxMode & fluxMode |
Definition at line 274 of file CEFMTask.cpp.
References CMetabNameInterface::getDisplayName(), CCopasiProblem::getModel(), getNetReactionData(), CCopasiTask::getProblem(), and CFluxMode::isReversible().
Referenced by CQEFMNetReactionDM::data(), and CEFMProblem::printResult().
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Retrieve the net reaction data for the given flux mode.
const | CFluxMode & fluxMode |
Definition at line 364 of file CEFMTask.cpp.
References CFluxMode::begin(), CCopasiVector< T >::begin(), CFluxMode::end(), CCopasiVector< T >::end(), CReaction::getChemEq(), CChemEq::getProducts(), getSpeciesChanges(), CChemEq::getSubstrates(), and CCopasiTask::mpProblem.
Referenced by getInternalSpecies(), and getNetReaction().
std::string CEFMTask::getReactionEquation | ( | const std::map< size_t, C_FLOAT64 >::const_iterator & | itReaction | ) | const |
Retrieve the reaction equation of the part of the flux mode pointed at by itReaction
const | std::map< size_t, C_FLOAT64 >::const_iterator & itReaction |
Definition at line 188 of file CEFMTask.cpp.
References CChemEqInterface::getChemEqString(), CCopasiProblem::getModel(), CEFMProblem::getReorderedReactions(), CCopasiMethod::getSubType(), CSSAMethod::isReactionReversed(), CReaction::isReversible(), CCopasiTask::mpMethod, and CCopasiTask::mpProblem.
Referenced by CQFluxModeDM::data(), and CEFMProblem::printResult().
std::pair< C_FLOAT64, C_FLOAT64 > CEFMTask::getSpeciesChanges | ( | const CFluxMode & | fluxMode, |
const CMetab & | metab | ||
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Retrieve the species changes for the given flux mode and species
Definition at line 216 of file CEFMTask.cpp.
References CFluxMode::begin(), CCopasiVector< T >::begin(), C_FLOAT64, CFluxMode::end(), CCopasiVector< T >::end(), CReaction::getChemEq(), CModelEntity::getKey(), CChemEq::getProducts(), CChemEq::getSubstrates(), and CCopasiTask::mpProblem.
Referenced by CQEFMSpeciesDM::data(), getNetReactionData(), and CEFMProblem::printResult().
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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 88 of file CEFMTask.cpp.
References CCopasiTask::initialize(), CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, and CCopasiTask::mpProblem.
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Check whether the given method is in the list of valid methods This list must end with CCopasiMethod::unset
const | unsigned C_INT32 & method |
const | unsigned C_INT32 * validMethods |
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Process the task with or without initializing to the initial state.
const | bool & useInitialValues |
Reimplemented from CCopasiTask.
Definition at line 104 of file CEFMTask.cpp.
References CCopasiTask::mpMethod.
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Set the call back of the task
CProcessReport | * pCallBack |
Reimplemented from CCopasiTask.
Definition at line 77 of file CEFMTask.cpp.
References CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiProblem::setCallBack(), CCopasiMethod::setCallBack(), and CCopasiTask::setCallBack().
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Set the method type applied to solve the task
const | CCopasiMethod::SubType & type |
Reimplemented from CCopasiTask.
Definition at line 109 of file CEFMTask.cpp.
References CCopasiContainer::add(), createMethod(), CCopasiMethod::getSubType(), CCopasiTask::mpMethod, and pdelete.
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The methods which can be selected for performing this task.
CEFMTask class.
This class implements a optimization task which is comprised of a of a problem and a method.
Definition at line 47 of file CEFMTask.h.