COPASI API
4.16.103
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#include <CODEExporterXPPAUT.h>
Public Member Functions | |
CODEExporterXPPAUT () | |
bool | exportClosingData (const CModel *copasiModel, std::ostream &os) |
virtual bool | exportSingleCompartment (const CCompartment *comp, std::string &expression, std::string &comments) |
void | exportSingleLine (const std::string &line, std::ostringstream &which) |
virtual bool | exportSingleMetabolite (const CMetab *metab, std::string &expression, std::string &comments) |
virtual bool | exportSingleModelEntity (const CModelEntity *tmp, std::string &expression, std::string &comments) |
virtual bool | exportSingleModVal (const CModelValue *modval, std::string &expression, std::string &comments) |
virtual bool | exportSingleObject (std::ostringstream &which, const std::string &name, const std::string &expression, const std::string &comments) |
virtual bool | exportSingleODE (const CModelEntity *mentity, std::string &equation, std::string &comments) |
virtual bool | exportSingleParameter (const CCopasiParameter *param, std::string &expression, std::string &comments) |
virtual bool | exportTitleData (const CCopasiDataModel *pDataModel, std::ostream &os) |
virtual std::string | exportTitleString (const size_t tmp) |
virtual std::string | getDisplayExpressionString (CExpression *tmp) |
virtual std::string | getDisplayFunctionString (CFunction *func) |
virtual std::string | KineticFunction2ODEmember (const CReaction *reac) |
std::string | setConcentrationName (const std::string &objName) |
std::string | setODEName (const std::string &objName) |
virtual void | setReservedNames () |
std::string | testName (const std::string &name) |
virtual std::string | translateObjectName (const std::string &realName) |
virtual std::string | translateTimeVariableName () |
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void | assembleSubTreeForMassAction (CEvaluationNode *newNode, CEvaluationNode *child1, CEvaluationNode *child2) |
CODEExporter () | |
virtual std::string | exportClosingString (const size_t tmp) |
bool | exportCompartments (const CModel *copasiModel) |
std::string | exportExpression (const CExpression *pExpression, const CCopasiDataModel *pDataModel) |
virtual bool | exportKineticFunction (CReaction *reac) |
virtual bool | exportKineticFunctionGroup (const CModel *copasiModel) |
virtual bool | exportMetabolites (const CModel *copasiModel) |
virtual bool | exportMetabolitesConcentrations (const CModel *copasiModel) |
bool | exportModelEntityExpression (CCopasiObject *obj, const CCopasiDataModel *pDataModel) |
bool | exportModelValues (const CModel *copasiModel) |
bool | exportModelValuesExpressions (const CModel *copasiModel) |
virtual std::string | exportNumber (double number) |
void | exportObjectNodesFromModel (const CCopasiDataModel *pDataModel) |
bool | exportODEs (const CModel *copasiModel) |
bool | exportReacParamsAndFuncs (const CModel *copasiModel) |
void | exportSimulatedObject (CCopasiObject *obj, const CCopasiDataModel *pDataModel) |
bool | exportSingleFunction (const CFunction *func) |
virtual bool | exportSingleFunction (const CFunction *func, std::set< std::string > &isExported) |
bool | exportSingleFunction (CEvaluationNode *pNode, const CReaction *reac, size_t &index) |
bool | exportSingleFunction (CEvaluationNode *pNode, const std::string &key, size_t &index) |
virtual bool | exportTitleData (const CModel *copasiModel, std::ostream &os) |
bool | exportToStream (const CCopasiDataModel *pDataModel, std::ostream &os) |
void | findFunctionsCalls (const CEvaluationNode *pNode) |
CCopasiObject * | findObjectFromRefresh (const CCopasiObject *tmp, const Refresh *ref) |
virtual std::string | getSingleLineComment () |
virtual bool | isEmptyString (std::string &str) |
std::string | isModelEntityExpressionODEExporterCompatible (CModelEntity *tmp, const CExpression *pExpression, const CCopasiDataModel *pDataModel) |
void | modifyTreeForMassAction (CFunction *tmpfunc) |
virtual bool | preprocess (const CModel *copasiModel) |
virtual | ~CODEExporter () |
Public Attributes | |
std::map< std::string, unsigned C_INT32 > | Frequancy |
std::set< std::string > | NameSet |
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std::ostringstream | assignment |
std::map< std::string, std::string > | equations |
std::ostringstream | fixed |
std::ostringstream | functions |
std::ostringstream | headers |
std::ostringstream | initial |
std::map< std::string, std::string > | NameMap |
std::ostringstream | ode |
std::string | timeKey |
Additional Inherited Members | |
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enum | Object { INITIAL = 0, FIXED, ASSIGNMENT, HEADERS, FUNCTIONS, ODEs } |
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std::set< std::string > | mExportedFunctions |
Definition at line 22 of file CODEExporterXPPAUT.h.
CODEExporterXPPAUT::CODEExporterXPPAUT | ( | ) |
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Reimplemented from CODEExporter.
Definition at line 624 of file CODEExporterXPPAUT.cpp.
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Reimplemented from CODEExporter.
Definition at line 398 of file CODEExporterXPPAUT.cpp.
References CModelEntity::ASSIGNMENT, CODEExporter::assignment, exportSingleObject(), CModelEntity::FIXED, CODEExporter::fixed, CModelEntity::getKey(), CModelEntity::getStatus(), CODEExporter::initial, CODEExporter::NameMap, and CModelEntity::ODE.
void CODEExporterXPPAUT::exportSingleLine | ( | const std::string & | line, |
std::ostringstream & | which | ||
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Definition at line 261 of file CODEExporterXPPAUT.cpp.
References MCODEExporter, CCopasiMessage::size(), and CCopasiMessage::WARNING.
Referenced by exportSingleObject().
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Reimplemented from CODEExporter.
Definition at line 337 of file CODEExporterXPPAUT.cpp.
References CModelEntity::ASSIGNMENT, CODEExporter::assignment, exportSingleObject(), CModelEntity::FIXED, CODEExporter::fixed, CModelEntity::getKey(), CModelEntity::getStatus(), CODEExporter::initial, CMetab::isDependent(), CODEExporter::NameMap, CModelEntity::ODE, and CModelEntity::REACTIONS.
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Reimplemented from CODEExporter.
Definition at line 492 of file CODEExporterXPPAUT.cpp.
References CModelEntity::ASSIGNMENT, CODEExporter::assignment, exportSingleObject(), CModelEntity::FIXED, CODEExporter::fixed, CModelEntity::getKey(), CModelEntity::getStatus(), CODEExporter::initial, CODEExporter::NameMap, and CModelEntity::ODE.
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Reimplemented from CODEExporter.
Definition at line 445 of file CODEExporterXPPAUT.cpp.
References CModelEntity::ASSIGNMENT, CODEExporter::assignment, exportSingleObject(), CModelEntity::FIXED, CODEExporter::fixed, CModelEntity::getKey(), CModelEntity::getStatus(), CODEExporter::initial, CODEExporter::NameMap, and CModelEntity::ODE.
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Reimplemented from CODEExporter.
Definition at line 324 of file CODEExporterXPPAUT.cpp.
References exportSingleLine().
Referenced by exportSingleCompartment(), exportSingleMetabolite(), exportSingleModelEntity(), exportSingleModVal(), exportSingleODE(), and exportSingleParameter().
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Reimplemented from CODEExporter.
Definition at line 584 of file CODEExporterXPPAUT.cpp.
References exportSingleObject(), CModelEntity::getKey(), CODEExporter::isEmptyString(), CODEExporter::NameMap, and CODEExporter::ode.
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Reimplemented from CODEExporter.
Definition at line 550 of file CODEExporterXPPAUT.cpp.
References exportSingleObject(), CODEExporter::fixed, CCopasiParameter::getKey(), and CODEExporter::NameMap.
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Definition at line 57 of file CODEExporterXPPAUT.cpp.
References CTrajectoryProblem::getDuration(), CCopasiTask::getProblem(), and CTrajectoryProblem::getStepSize().
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Reimplemented from CODEExporter.
Definition at line 597 of file CODEExporterXPPAUT.cpp.
References CODEExporter::ASSIGNMENT, CODEExporter::FIXED, CODEExporter::FUNCTIONS, CODEExporter::HEADERS, CODEExporter::INITIAL, and CODEExporter::ODEs.
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Reimplemented from CODEExporter.
Definition at line 568 of file CODEExporterXPPAUT.cpp.
References CEvaluationNode::buildXPPString(), and CEvaluationTree::getRoot().
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Reimplemented from CODEExporter.
Definition at line 561 of file CODEExporterXPPAUT.cpp.
References CEvaluationNode::buildXPPString(), and CEvaluationTree::getRoot().
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Reimplemented from CODEExporter.
Definition at line 575 of file CODEExporterXPPAUT.cpp.
References CReaction::getKey(), and CODEExporter::NameMap.
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Reimplemented from CODEExporter.
Definition at line 251 of file CODEExporterXPPAUT.cpp.
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Reimplemented from CODEExporter.
Definition at line 246 of file CODEExporterXPPAUT.cpp.
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Reimplemented from CODEExporter.
Definition at line 224 of file CODEExporterXPPAUT.cpp.
References Frequancy, and NameSet.
std::string CODEExporterXPPAUT::testName | ( | const std::string & | name | ) |
This method tests whether the given XPPAUT name already assigned, put the new name (in cappital letters: all names can be upper or lower case) in the set of assigned names or modify the name
Definition at line 162 of file CODEExporterXPPAUT.cpp.
References CCopasiMessage::ERROR, fatalError, Frequancy, and NameSet.
Referenced by translateObjectName().
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This method adapt a Copasi name for XPPAUT syntax: all XPPAUT names can have up to 9 letters each. Names can not start with a number. Any other combination of letters and numbers is valid as is the underscore.
Reimplemented from CODEExporter.
Definition at line 80 of file CODEExporterXPPAUT.cpp.
References testName().
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Reimplemented from CODEExporter.
Definition at line 72 of file CODEExporterXPPAUT.cpp.
std::map< std::string, unsigned C_INT32 > CODEExporterXPPAUT::Frequancy |
Definition at line 78 of file CODEExporterXPPAUT.h.
Referenced by setReservedNames(), and testName().
std::set<std::string> CODEExporterXPPAUT::NameSet |
Definition at line 79 of file CODEExporterXPPAUT.h.
Referenced by setReservedNames(), and testName().