COPASI API
4.16.103
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#include <CSSAMethod.h>
Public Member Functions | |
bool | calculate () |
CSSAMethod (const CSSAMethod &src, const CCopasiContainer *pParent=NULL) | |
CSSAMethod (const CCopasiContainer *pParent=NULL) | |
bool | initialize () |
TriLogic | isMixingStable (int indexEC) |
bool | isReactionReversed (int index) const |
bool | process (CProcessReport *handler) |
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void | calculateFluxModes () |
CEFMAlgorithm (const CEFMAlgorithm &src, const CCopasiContainer *pParent=NULL) | |
~CEFMAlgorithm () | |
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CEFMMethod (const CEFMMethod &src, const CCopasiContainer *pParent=NULL) | |
virtual bool | isValidProblem (const CCopasiProblem *pProblem) |
virtual | ~CEFMMethod () |
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CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL) | |
const CCopasiMethod::SubType & | getSubType () const |
const CCopasiTask::Type & | getType () const |
virtual void | load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH) |
virtual void | print (std::ostream *ostream) const |
virtual void | printResult (std::ostream *ostream) const |
virtual bool | setCallBack (CProcessReport *pCallBack) |
virtual | ~CCopasiMethod () |
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bool | addGroup (const std::string &name) |
bool | addParameter (const CCopasiParameter ¶meter) |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type) |
template<class CType > | |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value) |
void | addParameter (CCopasiParameter *pParameter) |
CCopasiParameterGroup * | assertGroup (const std::string &name) |
template<class CType > | |
CCopasiParameter * | assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue) |
index_iterator | beginIndex () const |
name_iterator | beginName () const |
CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL) | |
CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup") | |
void | clear () |
virtual bool | elevateChildren () |
index_iterator | endIndex () const |
name_iterator | endName () const |
CCopasiParameterGroup * | getGroup (const std::string &name) |
const CCopasiParameterGroup * | getGroup (const std::string &name) const |
CCopasiParameterGroup * | getGroup (const size_t &index) |
const CCopasiParameterGroup * | getGroup (const size_t &index) const |
size_t | getIndex (const std::string &name) const |
std::string | getKey (const std::string &name) const |
std::string | getKey (const size_t &index) const |
virtual const std::string & | getName (const size_t &index) const |
virtual const CObjectInterface * | getObject (const CCopasiObjectName &cn) const |
CCopasiParameter * | getParameter (const std::string &name) |
const CCopasiParameter * | getParameter (const std::string &name) const |
CCopasiParameter * | getParameter (const size_t &index) |
const CCopasiParameter * | getParameter (const size_t &index) const |
CCopasiParameter::Type | getType (const std::string &name) const |
CCopasiParameter::Type | getType (const size_t &index) const |
std::string | getUniqueParameterName (const CCopasiParameter *pParameter) const |
const CCopasiParameter::Value & | getValue (const std::string &name) const |
const CCopasiParameter::Value & | getValue (const size_t &index) const |
CCopasiParameter::Value & | getValue (const std::string &name) |
CCopasiParameter::Value & | getValue (const size_t &index) |
CCopasiParameterGroup & | operator= (const CCopasiParameterGroup &rhs) |
bool | removeParameter (const std::string &name) |
bool | removeParameter (const size_t &index) |
template<class CType > | |
bool | setValue (const std::string &name, const CType &value) |
template<class CType > | |
bool | setValue (const size_t &index, const CType &value) |
size_t | size () const |
bool | swap (const size_t &iFrom, const size_t &iTo) |
bool | swap (index_iterator &from, index_iterator &to) |
virtual | ~CCopasiParameterGroup () |
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CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL) | |
CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CCopasiContainer *pParent=NULL, const std::string &objectType="Parameter") | |
virtual CCopasiObjectName | getCN () const |
virtual const std::string & | getKey () const |
virtual std::string | getObjectDisplayName (bool regular=true, bool richtext=false) const |
const CCopasiParameter::Type & | getType () const |
const Value & | getValue () const |
Value & | getValue () |
virtual void * | getValuePointer () const |
CCopasiObject * | getValueReference () const |
bool | isValidValue (const C_FLOAT64 &value) const |
bool | isValidValue (const C_INT32 &value) const |
bool | isValidValue (const unsigned C_INT32 &value) const |
bool | isValidValue (const bool &value) const |
bool | isValidValue (const std::string &value) const |
bool | isValidValue (const CCopasiObjectName &value) const |
bool | isValidValue (const std::vector< CCopasiParameter * > &value) const |
CCopasiParameter & | operator= (const CCopasiParameter &rhs) |
template<class CType > | |
bool | setValue (const CType &value) |
bool | setValue (const std::vector< CCopasiParameter * > &value) |
virtual | ~CCopasiParameter () |
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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 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 const DataObjectSet & | getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const |
CCopasiContainer * | getObjectAncestor (const std::string &type) const |
CCopasiDataModel * | getObjectDataModel () |
const CCopasiDataModel * | getObjectDataModel () 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 |
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 |
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 () |
Protected Member Functions | |
bool | buildExtremeCurrents () |
bool | buildJacobian () |
bool | buildKineticMatrix () |
bool | buildStoichiometry () |
bool | decomposeJacobian () |
template<class CType > | |
CMatrix< CType > | diag (CVector< CType > vector) |
bool | testForMixingStability () |
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CEFMAlgorithm (const CCopasiContainer *pParent=NULL) | |
CEFMAlgorithm (const CCopasiMethod::SubType subType, const CCopasiContainer *pParent=NULL) | |
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CEFMMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL) | |
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CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL) | |
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CCopasiParameterGroup () | |
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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) | |
Friends | |
CEFMMethod * | CEFMMethod::createMethod (CCopasiMethod::SubType subType) |
Definition at line 28 of file CSSAMethod.h.
CSSAMethod::CSSAMethod | ( | const CSSAMethod & | src, |
const CCopasiContainer * | pParent = NULL |
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CSSAMethod class. Methods to conduct Stoichiometric Stability Analysis.- Copy constructor.
const CSSAMethod & | src |
Definition at line 35 of file CSSAMethod.cpp.
CSSAMethod::CSSAMethod | ( | const CCopasiContainer * | pParent = NULL | ) |
Definition at line 40 of file CSSAMethod.cpp.
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Definition at line 418 of file CSSAMethod.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, C_INT32, CEFMAlgorithm::calculateFluxModes(), mExtremeCurrents, mNumReactions, CVector< CType >::resize(), and CVectorCore< CType >::size().
Referenced by calculate().
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Definition at line 379 of file CSSAMethod.cpp.
References CMatrix< CType >::array(), CCopasiVector< T >::begin(), C_FLOAT64, C_INT64, CCopasiVector< T >::end(), CModel::getMetabolitesX(), CModel::getNumIndependentReactionMetabs(), mIsBackwardReaction, mNumReactions, CEFMAlgorithm::mpModel, mTransposedKineticMatrix, CMatrix< CType >::resize(), and CCopasiVector< T >::size().
Referenced by calculate().
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Definition at line 358 of file CSSAMethod.cpp.
References CMatrix< CType >::array(), C_FLOAT64, CEFMAlgorithm::mpModel, CEFMAlgorithm::mStoi, mStoichiometry, and CMatrix< CType >::resize().
Referenced by calculate().
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Execute the optimization algorithm calling simulation routine when needed. It is noted that this procedure can give feedback of its progress by the callback function set with SetCallback. @ return success;
Reimplemented from CEFMAlgorithm.
Definition at line 152 of file CSSAMethod.cpp.
References buildExtremeCurrents(), buildKineticMatrix(), buildStoichiometry(), CProcessReport::finishItem(), initialize(), CEFMAlgorithm::mhSteps, CCopasiMethod::mpCallBack, CEFMAlgorithm::mpModel, and testForMixingStability().
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Definition at line 313 of file CSSAMethod.cpp.
References CMatrix< CType >::array(), C_FLOAT64, C_INT, dgemm_(), diag(), mExtremeCurrents, mStoichiometry, mTransformedSubJacobians, mTransposedKineticMatrix, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), and CMatrix< CType >::resize().
Referenced by testForMixingStability().
Definition at line 103 of file CSSAMethod.h.
References CMatrix< CType >::array(), CMatrix< CType >::resize(), CVectorCore< CType >::size(), and CMatrix< CType >::size().
Referenced by decomposeJacobian().
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Initialize arrays and pointer.
Reimplemented from CEFMAlgorithm.
Definition at line 46 of file CSSAMethod.cpp.
References CProcessReport::addItem(), C_INT32, CCopasiVector< T >::cleanup(), CCopasiProblem::getModel(), CCopasiObject::getObjectParent(), CCopasiTask::getProblem(), CModel::getReactions(), CModel::getRedStoi(), CEFMAlgorithm::mhSteps, mIsBackwardReaction, CEFMAlgorithm::mMaxStep, mNumReactions, CCopasiMethod::mpCallBack, CEFMAlgorithm::mpModel, mReactions, CEFMAlgorithm::mReversible, CEFMAlgorithm::mStep, CEFMAlgorithm::mStoi, pTask, and CCopasiParameter::UINT.
Referenced by calculate().
TriLogic CSSAMethod::isMixingStable | ( | int | indexEC | ) |
bool CSSAMethod::isReactionReversed | ( | int | index | ) | const |
Definition at line 199 of file CSSAMethod.cpp.
References mIsBackwardReaction.
Referenced by CEFMTask::getFluxModeDescription(), and CEFMTask::getReactionEquation().
bool CSSAMethod::process | ( | CProcessReport * | handler | ) |
Definition at line 146 of file CSSAMethod.cpp.
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Definition at line 203 of file CSSAMethod.cpp.
References C_FLOAT64, C_INT32, decomposeJacobian(), dsyev_(), mExtremeCurrents, mIsMixingStable, CEFMAlgorithm::mStoi, mTransformedSubJacobians, CVectorCore< CType >::size(), TriFalse, TriTrue, and TriUnspecified.
Referenced by calculate().
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Definition at line 74 of file CSSAMethod.h.
Referenced by buildExtremeCurrents(), decomposeJacobian(), and testForMixingStability().
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Definition at line 62 of file CSSAMethod.h.
Referenced by buildKineticMatrix(), initialize(), and isReactionReversed().
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Definition at line 79 of file CSSAMethod.h.
Referenced by isMixingStable(), and testForMixingStability().
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Definition at line 65 of file CSSAMethod.h.
Referenced by buildExtremeCurrents(), buildKineticMatrix(), and initialize().
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Definition at line 53 of file CSSAMethod.h.
Referenced by initialize().
Definition at line 56 of file CSSAMethod.h.
Referenced by buildStoichiometry(), and decomposeJacobian().
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Definition at line 59 of file CSSAMethod.h.
Definition at line 72 of file CSSAMethod.h.
Referenced by decomposeJacobian(), and testForMixingStability().
Definition at line 70 of file CSSAMethod.h.
Referenced by buildKineticMatrix(), and decomposeJacobian().