COPASI API
4.16.103
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#include <CODEExporterBM.h>
Public Member Functions | |
CODEExporterBM () | |
virtual bool | exportSingleCompartment (const CCompartment *comp, std::string &expression, std::string &comments) |
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 bool | exportClosingData (const CModel *copasiModel, std::ostream &os) |
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, size_t > | 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 20 of file CODEExporterBM.h.
CODEExporterBM::CODEExporterBM | ( | ) |
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Reimplemented from CODEExporter.
Definition at line 279 of file CODEExporterBM.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 218 of file CODEExporterBM.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 355 of file CODEExporterBM.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 317 of file CODEExporterBM.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 207 of file CODEExporterBM.cpp.
Referenced by exportSingleCompartment(), exportSingleMetabolite(), exportSingleModelEntity(), exportSingleModVal(), exportSingleODE(), and exportSingleParameter().
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Reimplemented from CODEExporter.
Definition at line 413 of file CODEExporterBM.cpp.
References exportSingleObject(), CModelEntity::getKey(), CODEExporter::NameMap, and CODEExporter::ode.
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Reimplemented from CODEExporter.
Definition at line 406 of file CODEExporterBM.cpp.
References exportSingleObject(), CODEExporter::fixed, CCopasiParameter::getKey(), and CODEExporter::NameMap.
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Definition at line 56 of file CODEExporterBM.cpp.
References CTrajectoryProblem::getDuration(), CCopasiTask::getProblem(), and CTrajectoryProblem::getStepSize().
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Reimplemented from CODEExporter.
Definition at line 445 of file CODEExporterBM.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 431 of file CODEExporterBM.cpp.
References CEvaluationNode::buildBerkeleyMadonnaString(), and CEvaluationTree::getRoot().
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Reimplemented from CODEExporter.
Definition at line 424 of file CODEExporterBM.cpp.
References CEvaluationNode::buildBerkeleyMadonnaString(), and CEvaluationTree::getRoot().
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Reimplemented from CODEExporter.
Definition at line 438 of file CODEExporterBM.cpp.
References CReaction::getKey(), and CODEExporter::NameMap.
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Reimplemented from CODEExporter.
Definition at line 197 of file CODEExporterBM.cpp.
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Reimplemented from CODEExporter.
Definition at line 202 of file CODEExporterBM.cpp.
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Reimplemented from CODEExporter.
Definition at line 194 of file CODEExporterBM.cpp.
std::string CODEExporterBM::testName | ( | const std::string & | name | ) |
This method tests whether the given Berkeley Madonna 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 158 of file CODEExporterBM.cpp.
References Frequancy, and NameSet.
Referenced by translateObjectName().
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This method adapt a Copasi name for Berkeley Madonna syntax: 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 82 of file CODEExporterBM.cpp.
References testName().
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Reimplemented from CODEExporter.
Definition at line 74 of file CODEExporterBM.cpp.
std::map< std::string, size_t > CODEExporterBM::Frequancy |
Definition at line 72 of file CODEExporterBM.h.
Referenced by testName().
std::set<std::string> CODEExporterBM::NameSet |
Definition at line 73 of file CODEExporterBM.h.
Referenced by testName().