adaptiveSA enum value | CCopasiMethod | |
add(CCopasiObject *pObject, const bool &adopt=true) | CCopasiContainer | virtual |
addDirectDependency(const CCopasiObject *pObject) | CCopasiObject | |
addGroup(const std::string &name) | CCopasiParameterGroup | |
addMatrixReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) | CCopasiContainer | inlineprotected |
addObjectReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) | CCopasiContainer | inlineprotected |
addParameter(const CCopasiParameter ¶meter) | CCopasiParameterGroup | |
addParameter(const std::string &name, const CCopasiParameter::Type type) | CCopasiParameterGroup | |
addParameter(const std::string &name, const CCopasiParameter::Type type, const CType &value) | CCopasiParameterGroup | inline |
addParameter(CCopasiParameter *pParameter) | CCopasiParameterGroup | |
addVectorReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) | CCopasiContainer | inlineprotected |
Array enum value | CCopasiObject | protected |
assertGroup(const std::string &name) | CCopasiParameterGroup | |
assertParameter(const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue) | CCopasiParameterGroup | inline |
beginIndex() const | CCopasiParameterGroup | |
beginName() const | CCopasiParameterGroup | |
BOOL enum value | CCopasiParameter | |
buildUpdateSequence(const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) | CCopasiObject | static |
calculateDerivatives(C_FLOAT64 *X1, C_FLOAT64 *Y1) | CTSSAMethod | protected |
calculateDerivativesX(C_FLOAT64 *X1, C_FLOAT64 *Y1) | CTSSAMethod | protected |
CCopasiContainer(const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container) | CCopasiContainer | |
CCopasiContainer(const CCopasiContainer &src, const CCopasiContainer *pParent=NULL) | CCopasiContainer | |
CCopasiMethod(const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL) | CCopasiMethod | protected |
CCopasiMethod(const CCopasiMethod &src, const CCopasiContainer *pParent=NULL) | CCopasiMethod | |
CCopasiObject() | CCopasiObject | protected |
CCopasiObject(const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | CCopasiObject | protected |
CCopasiObject(const CCopasiObject &src, const CCopasiContainer *pParent=NULL) | CCopasiObject | |
CCopasiParameter(const CCopasiParameter &src, const CCopasiContainer *pParent=NULL) | CCopasiParameter | |
CCopasiParameter(const std::string &name, const Type &type, const void *pValue=NULL, const CCopasiContainer *pParent=NULL, const std::string &objectType="Parameter") | CCopasiParameter | |
CCopasiParameterGroup() | CCopasiParameterGroup | protected |
CCopasiParameterGroup(const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL) | CCopasiParameterGroup | |
CCopasiParameterGroup(const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup") | CCopasiParameterGroup | |
CILDMMethod(const CCopasiContainer *pParent=NULL) | CILDMMethod | private |
CILDMMethod(const CILDMMethod &src, const CCopasiContainer *pParent=NULL) | CILDMMethod | |
clear() | CCopasiParameterGroup | |
clearDirectDependencies() | CCopasiObject | |
clearRefresh() | CCopasiObject | |
CN enum value | CCopasiParameter | |
CObjectInterface() | CObjectInterface | inline |
Container enum value | CCopasiObject | protected |
CoranaWalk enum value | CCopasiMethod | |
createAnnotationsM() | CILDMMethod | |
createMethod(CCopasiMethod::SubType subType=CCopasiMethod::unset) | CTSSAMethod | static |
crossSectionMethod enum value | CCopasiMethod | |
CTSSAMethod(const CCopasiMethod::SubType &subType, const CCopasiContainer *pParent=NULL) | CTSSAMethod | protected |
CTSSAMethod(const CTSSAMethod &src, const CCopasiContainer *pParent=NULL) | CTSSAMethod | |
CTSSAMethod::createMethod(CCopasiMethod::SubType subType) | CILDMMethod | friend |
DataModel enum value | CCopasiObject | protected |
DataObjectSet typedef | CCopasiObject | |
DataUpdateSequence typedef | CCopasiObject | |
dependsOn(DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const | CCopasiObject | |
deterministic enum value | CCopasiMethod | |
deuflhard(C_INT &slow, C_INT &info) | CILDMMethod | |
DifferentialEvolution enum value | CCopasiMethod | |
directMethod enum value | CCopasiMethod | |
DOUBLE enum value | CCopasiParameter | |
DsaLsodar enum value | CCopasiMethod | |
EFMAlgorithm enum value | CCopasiMethod | |
EFMBitPatternAlgorithm enum value | CCopasiMethod | |
EFMBitPatternTreeAlgorithm enum value | CCopasiMethod | |
elevateChildren() | CTSSAMethod | protectedvirtual |
EmptyList | CCopasiContainer | static |
emptyVectors() | CILDMMethod | |
endIndex() const | CCopasiParameterGroup | |
endName() const | CCopasiParameterGroup | |
EvalF(const C_INT *n, const C_FLOAT64 *t, const C_FLOAT64 *y, C_FLOAT64 *ydot) | CTSSAMethod | protectedstatic |
evalF(const C_FLOAT64 *t, const C_FLOAT64 *y, C_FLOAT64 *ydot) | CTSSAMethod | protected |
EvolutionaryProgram enum value | CCopasiMethod | |
EXPRESSION enum value | CCopasiParameter | |
FILE enum value | CCopasiParameter | |
Flag enum name | CCopasiObject | protected |
GeneticAlgorithm enum value | CCopasiMethod | |
GeneticAlgorithmSR enum value | CCopasiMethod | |
getAllDependencies(DataObjectSet &dependencies, const DataObjectSet &context) const | CCopasiObject | |
getChildObjectUnits(const CCopasiObject *pObject) const | CCopasiContainer | virtual |
getCN() const | CCopasiParameter | virtual |
getCurrentStep() const | CTSSAMethod | |
getDirectDependencies(const DataObjectSet &context=DataObjectSet()) const | CCopasiObject | virtual |
getGroup(const std::string &name) | CCopasiParameterGroup | |
getGroup(const std::string &name) const | CCopasiParameterGroup | |
getGroup(const size_t &index) | CCopasiParameterGroup | |
getGroup(const size_t &index) const | CCopasiParameterGroup | |
getIndex(const std::string &name) const | CCopasiParameterGroup | |
getKey(const std::string &name) const | CCopasiParameterGroup | |
getKey(const size_t &index) const | CCopasiParameterGroup | |
CCopasiParameter::getKey() const | CCopasiParameter | virtual |
getName(const size_t &index) const | CCopasiParameterGroup | virtual |
getObject(const CCopasiObjectName &cn) const | CCopasiParameterGroup | virtual |
getObjectAncestor(const std::string &type) const | CCopasiObject | |
getObjectDataModel() | CCopasiObject | |
getObjectDataModel() const | CCopasiObject | |
getObjectDisplayName(bool regular=true, bool richtext=false) const | CCopasiParameter | virtual |
getObjectName() const | CCopasiObject | |
getObjectParent() const | CCopasiObject | |
getObjects() const | CCopasiContainer | virtual |
getObjectType() const | CCopasiObject | |
getParameter(const std::string &name) | CCopasiParameterGroup | |
getParameter(const std::string &name) const | CCopasiParameterGroup | |
getParameter(const size_t &index) | CCopasiParameterGroup | |
getParameter(const size_t &index) const | CCopasiParameterGroup | |
getPrerequisites() const | CCopasiObject | virtual |
getReacSlowSpacePrintAnn() const | CILDMMethod | inline |
getRefresh() const | CCopasiObject | virtual |
getSubType() const | CCopasiMethod | |
getTable(std::string name) | CTSSAMethod | inline |
getTableName() const | CTSSAMethod | inline |
getTMP1PrintAnn() const | CILDMMethod | inline |
getTMP2PrintAnn() const | CILDMMethod | inline |
getTMP3PrintAnn() const | CILDMMethod | inline |
getType() const | CCopasiMethod | |
CCopasiParameterGroup::getType(const std::string &name) const | CCopasiParameterGroup | |
CCopasiParameterGroup::getType(const size_t &index) const | CCopasiParameterGroup | |
getUniqueParameterName(const CCopasiParameter *pParameter) const | CCopasiParameterGroup | |
getUnits() const | CCopasiContainer | virtual |
getUpdateMethod() const | CCopasiObject | |
getValue(const std::string &name) const | CCopasiParameterGroup | |
getValue(const size_t &index) const | CCopasiParameterGroup | |
getValue(const std::string &name) | CCopasiParameterGroup | |
getValue(const size_t &index) | CCopasiParameterGroup | |
CCopasiParameter::getValue() const | CCopasiParameter | |
CCopasiParameter::getValue() | CCopasiParameter | |
getValueObject() const | CCopasiContainer | virtual |
getValuePointer() const | CCopasiParameter | virtual |
getValueReference() const | CCopasiParameter | |
getVec_TimeScale(int step) | CTSSAMethod | |
getVfastSpacePrintAnn() const | CILDMMethod | inline |
getVslowMetabPrintAnn() const | CILDMMethod | inline |
getVslowPrintAnn() const | CILDMMethod | inline |
getVslowSpacePrintAnn() const | CILDMMethod | inline |
GROUP enum value | CCopasiParameter | |
Gui enum value | CCopasiObject | protected |
hasCircularDependencies(DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const | CCopasiObject | |
hasUpdateMethod() const | CCopasiObject | |
HookeJeeves enum value | CCopasiMethod | |
Householder enum value | CCopasiMethod | |
hybrid enum value | CCopasiMethod | |
HybridGASA enum value | CCopasiMethod | |
hybridLSODA enum value | CCopasiMethod | |
hybridODE45 enum value | CCopasiMethod | |
index_iterator typedef | CCopasiParameterGroup | |
initializeAtol() | CTSSAMethod | protected |
initializeIntegrationsParameter() | CTSSAMethod | protected |
initializeParameter() | CILDMMethod | virtual |
initObjects() | CCopasiContainer | protected |
INT enum value | CCopasiParameter | |
integrationMethodStart(const CState *initialState) | CTSSAMethod | protected |
integrationStep(const double &deltaT) | CTSSAMethod | protected |
INVALID enum value | CCopasiParameter | |
isArray() const | CCopasiObject | |
isContainer() const | CCopasiObject | |
isDataModel() const | CCopasiObject | |
isMatrix() const | CCopasiObject | |
isNameVector() const | CCopasiObject | |
isNonUniqueName() const | CCopasiObject | |
isPrerequisiteForContext(const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const | CCopasiObject | virtual |
isReference() const | CCopasiObject | |
isRoot() const | CCopasiObject | |
isSeparator() const | CCopasiObject | |
isStaticString() const | CCopasiObject | |
isValidProblem(const CCopasiProblem *pProblem) | CTSSAMethod | virtual |
isValidValue(const C_FLOAT64 &value) const | CCopasiParameter | |
isValidValue(const C_INT32 &value) const | CCopasiParameter | |
isValidValue(const unsigned C_INT32 &value) const | CCopasiParameter | |
isValidValue(const bool &value) const | CCopasiParameter | |
isValidValue(const std::string &value) const | CCopasiParameter | |
isValidValue(const CCopasiObjectName &value) const | CCopasiParameter | |
isValidValue(const std::vector< CCopasiParameter * > &value) const | CCopasiParameter | |
isValueBool() const | CCopasiObject | |
isValueDbl() const | CCopasiObject | |
isValueInt() const | CCopasiObject | |
isValueInt64() const | CCopasiObject | |
isValueString() const | CCopasiObject | |
isVector() const | CCopasiObject | |
KEY enum value | CCopasiParameter | |
LevenbergMarquardt enum value | CCopasiMethod | |
linearNoiseApproximation enum value | CCopasiMethod | |
load(CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH) | CCopasiMethod | virtual |
LSODAR enum value | CCopasiMethod | |
lyapWolf enum value | CCopasiMethod | |
map_index(C_FLOAT64 *eval_r, C_INT *index, const C_INT &dim) | CTSSAMethod | protected |
map_index_desc(C_FLOAT64 *eval_r, C_INT *index, const C_INT &dim) | CTSSAMethod | protected |
mapTableToName | CTSSAMethod | |
mat_anal_fast_space(C_INT &slow) | CTSSAMethod | protected |
mat_anal_fast_space_thomas(C_INT &slow) | CTSSAMethod | protected |
mat_anal_metab(C_INT &slow) | CTSSAMethod | protected |
mat_anal_mod(C_INT &slow) | CTSSAMethod | protected |
mat_anal_mod_space(C_INT &slow) | CTSSAMethod | protected |
mAtol | CTSSAMethod | protected |
Matrix enum value | CCopasiObject | protected |
mcaMethodReder enum value | CCopasiMethod | |
mCfast | CTSSAMethod | protected |
mCurrentStep | CTSSAMethod | protected |
mCurrentTime | CTSSAMethod | protected |
mData | CTSSAMethod | protected |
mDtol | CTSSAMethod | protected |
mDWork | CTSSAMethod | protected |
mEPS | CTSSAMethod | protected |
mErrorMsg | CTSSAMethod | protected |
mIWork | CTSSAMethod | protected |
mJacobian | CTSSAMethod | protected |
mJacobian_initial | CTSSAMethod | protected |
mJType | CTSSAMethod | protected |
mKey | CCopasiParameter | protected |
mLSODA | CTSSAMethod | protected |
mLsodaStatus | CTSSAMethod | protected |
mObjects | CCopasiContainer | protected |
ModelEntity enum value | CCopasiObject | protected |
mpCallBack | CCopasiMethod | protected |
mpCurrentState | CTSSAMethod | protected |
mpModel | CTSSAMethod | protected |
mpProblem | CTSSAMethod | protected |
mpState | CTSSAMethod | protected |
mpValueReference | CCopasiParameter | mutableprotected |
mQ | CTSSAMethod | protected |
mQ_desc | CTSSAMethod | protected |
mQz | CTSSAMethod | protected |
mR | CTSSAMethod | protected |
mR_desc | CTSSAMethod | protected |
mReacSlowSpace | CILDMMethod | |
mReacSlowSpacePrint | CILDMMethod | |
mReducedModel | CTSSAMethod | protected |
mRtol | CTSSAMethod | protected |
mSize | CCopasiParameter | protected |
mSlow | CTSSAMethod | protected |
mState | CTSSAMethod | protected |
mTd | CTSSAMethod | protected |
mTd_save | CTSSAMethod | protected |
mTdInverse | CTSSAMethod | protected |
mTdInverse_save | CTSSAMethod | protected |
mTime | CTSSAMethod | protected |
mTMP1 | CILDMMethod | |
mTMP1Print | CILDMMethod | |
mTMP2 | CILDMMethod | |
mTMP2Print | CILDMMethod | |
mTMP3 | CILDMMethod | |
mTMP3Print | CILDMMethod | |
mustBeDeleted(const DataObjectSet &deletedObjects) const | CCopasiObject | virtual |
mValue | CCopasiParameter | protected |
mVec_mReacSlowSpace | CILDMMethod | |
mVec_mTMP1 | CILDMMethod | |
mVec_mTMP2 | CILDMMethod | |
mVec_mTMP3 | CILDMMethod | |
mVec_mVfastSpace | CILDMMethod | |
mVec_mVslow | CILDMMethod | |
mVec_mVslowMetab | CILDMMethod | |
mVec_mVslowSpace | CILDMMethod | |
mVec_SlowModes | CTSSAMethod | protected |
mVec_TimeScale | CTSSAMethod | protected |
mVfast_space | CTSSAMethod | protected |
mVfastSpacePrint | CILDMMethod | |
mVslow | CTSSAMethod | protected |
mVslow_metab | CTSSAMethod | protected |
mVslow_space | CTSSAMethod | protected |
mVslowMetabPrint | CILDMMethod | |
mVslowPrint | CILDMMethod | |
mVslowSpacePrint | CILDMMethod | |
mY | CTSSAMethod | protected |
mY_cons | CTSSAMethod | protected |
mY_initial | CTSSAMethod | protected |
mYdot | CTSSAMethod | protected |
name_iterator typedef | CCopasiParameterGroup | |
NameVector enum value | CCopasiObject | protected |
NelderMead enum value | CCopasiMethod | |
newton(C_FLOAT64 *ys, C_INT &slow, C_INT &info) | CILDMMethod | |
Newton enum value | CCopasiMethod | |
NonUniqueName enum value | CCopasiObject | protected |
objectMap typedef | CCopasiContainer | |
ObjectSet typedef | CObjectInterface | |
operator=(const CCopasiParameterGroup &rhs) | CCopasiParameterGroup | |
CCopasiParameter::operator=(const CCopasiParameter &rhs) | CCopasiParameter | |
orthog(C_INT &number1, C_INT &number2) | CTSSAMethod | protected |
parameterGroup typedef | CCopasiParameterGroup | |
ParticleSwarm enum value | CCopasiMethod | |
Praxis enum value | CCopasiMethod | |
pReacSlowSpacePrintAnn | CILDMMethod | |
predifineAnnotation() | CTSSAMethod | virtual |
print(std::ostream *ostream) const | CCopasiMethod | virtual |
printResult(std::ostream *ostream) const | CILDMMethod | virtual |
pTmp1 | CILDMMethod | |
pTMP1 | CILDMMethod | |
pTMP1PrintAnn | CILDMMethod | |
pTmp2 | CILDMMethod | |
pTMP2 | CILDMMethod | |
pTMP2PrintAnn | CILDMMethod | |
pTMP3 | CILDMMethod | |
pTmp3 | CILDMMethod | |
pTMP3PrintAnn | CILDMMethod | |
pTmp4 | CILDMMethod | |
pTmp5 | CILDMMethod | |
pVfastSpacePrintAnn | CILDMMethod | |
pVslowMetabPrintAnn | CILDMMethod | |
pVslowPrintAnn | CILDMMethod | |
pVslowSpacePrintAnn | CILDMMethod | |
RandomSearch enum value | CCopasiMethod | |
RandomSearchMaster enum value | CCopasiMethod | |
Reference enum value | CCopasiObject | protected |
remove(CCopasiObject *pObject) | CCopasiContainer | virtual |
removeDirectDependency(const CCopasiObject *pObject) | CCopasiObject | |
removeParameter(const std::string &name) | CCopasiParameterGroup | |
removeParameter(const size_t &index) | CCopasiParameterGroup | |
returnCurrentTime(int step) | CTSSAMethod | |
Root enum value | CCopasiObject | protected |
scanMethod enum value | CCopasiMethod | |
ScatterSearch enum value | CCopasiMethod | |
schur(C_INT &info) | CTSSAMethod | protected |
schur_desc(C_INT &info) | CTSSAMethod | protected |
sensMethod enum value | CCopasiMethod | |
Separator enum value | CCopasiObject | protected |
setAnnotationM(size_t step) | CILDMMethod | virtual |
setCallBack(CProcessReport *pCallBack) | CCopasiMethod | virtual |
setCurrentState(CState *currentState) | CTSSAMethod | |
setDirectDependencies(const DataObjectSet &directDependencies) | CCopasiObject | |
setModel(CModel *model) | CTSSAMethod | |
setObjectName(const std::string &name) | CCopasiObject | |
setObjectParent(const CCopasiContainer *pParent) | CCopasiObject | virtual |
setObjectValue(const C_FLOAT64 &value) | CCopasiObject | |
setObjectValue(const C_INT32 &value) | CCopasiObject | |
setObjectValue(const bool &value) | CCopasiObject | |
setProblem(CTSSAProblem *problem) | CTSSAMethod | |
setRefresh(CType *pType, void(CType::*method)(void)) | CCopasiObject | inline |
setRenameHandler(CRenameHandler *rh) | CCopasiObject | inlinestatic |
setUpdateMethod(CType *pType, void(CType::*method)(const C_FLOAT64 &)) | CCopasiObject | inline |
setUpdateMethod(CType *pType, void(CType::*method)(const C_INT32 &)) | CCopasiObject | inline |
setUpdateMethod(CType *pType, void(CType::*method)(const bool &)) | CCopasiObject | inline |
setValue(const std::string &name, const CType &value) | CCopasiParameterGroup | inline |
setValue(const size_t &index, const CType &value) | CCopasiParameterGroup | inline |
CCopasiParameter::setValue(const CType &value) | CCopasiParameter | inline |
CCopasiParameter::setValue(const std::vector< CCopasiParameter * > &value) | CCopasiParameter | |
setVectors(int slowMode) | CILDMMethod | |
SimulatedAnnealing enum value | CCopasiMethod | |
size() const | CCopasiParameterGroup | |
smpRenameHandler | CCopasiObject | protectedstatic |
SRES enum value | CCopasiMethod | |
start(const CState *initialState) | CILDMMethod | virtual |
StaticString enum value | CCopasiObject | protected |
Statistics enum value | CCopasiMethod | |
SteepestDescent enum value | CCopasiMethod | |
step(const double &deltaT) | CILDMMethod | virtual |
stochastic enum value | CCopasiMethod | |
STRING enum value | CCopasiParameter | |
SubType enum name | CCopasiMethod | |
SubTypeName | CCopasiMethod | static |
swap(const size_t &iFrom, const size_t &iTo) | CCopasiParameterGroup | |
swap(index_iterator &from, index_iterator &to) | CCopasiParameterGroup | |
sylvester(C_INT slow, C_INT &info) | CTSSAMethod | protected |
tableNames | CTSSAMethod | |
tauLeap enum value | CCopasiMethod | |
transformation_norm(C_INT &slow, C_INT &info) | CILDMMethod | |
TruncatedNewton enum value | CCopasiMethod | |
tssCSP enum value | CCopasiMethod | |
tssILDM enum value | CCopasiMethod | |
tssILDMModified enum value | CCopasiMethod | |
Type enum name | CCopasiParameter | |
TypeName | CCopasiParameter | static |
UDOUBLE enum value | CCopasiParameter | |
UINT enum value | CCopasiParameter | |
unset enum value | CCopasiMethod | |
update_nid(C_INT *index, C_INT *nid, const C_INT &dim) | CTSSAMethod | protected |
update_pid(C_INT *index, C_INT *pid, const C_INT &dim) | CTSSAMethod | protected |
UpdateSequence typedef | CObjectInterface | |
ValueBool enum value | CCopasiObject | protected |
ValueDbl enum value | CCopasiObject | protected |
ValueInt enum value | CCopasiObject | protected |
ValueInt64 enum value | CCopasiObject | protected |
ValueString enum value | CCopasiObject | protected |
Vector enum value | CCopasiObject | protected |
XMLSubType | CCopasiMethod | static |
XMLType | CCopasiParameter | static |
~CCopasiContainer() | CCopasiContainer | virtual |
~CCopasiMethod() | CCopasiMethod | virtual |
~CCopasiObject() | CCopasiObject | virtual |
~CCopasiParameter() | CCopasiParameter | virtual |
~CCopasiParameterGroup() | CCopasiParameterGroup | virtual |
~CILDMMethod() | CILDMMethod | |
~CObjectInterface() | CObjectInterface | inlinevirtual |
~CTSSAMethod() | CTSSAMethod | |