/**
* Default constructor.
*/
CHybridMethod::CHybridMethod(const CCopasiContainer * pParent,
const CTaskEnum::Method & methodType,
const CTaskEnum::Task & taskType):
CTrajectoryMethod(pParent, methodType, taskType)
{
initializeParameter();
}
CTrajectoryMethodDsaLsodar::CTrajectoryMethodDsaLsodar(const CTrajectoryMethodDsaLsodar & src,
const CDataContainer * pParent):
CLsodaMethod(src, pParent)
{
mpRandomGenerator = CRandom::createGenerator(CRandom::mt19937);
initializeParameter();
}
// copy constructor
CFitProblem::CFitProblem(const CFitProblem& src,
const CCopasiContainer * pParent):
COptProblem(src, pParent),
mpParmSteadyStateCN(NULL),
mpParmTimeCourseCN(NULL),
mpExperimentSet(NULL),
mpSteadyState(NULL),
mpTrajectory(NULL),
mExperimentUpdateMethods(0, 0),
mExperimentConstraints(0, 0),
mExperimentDependentValues(src.mExperimentDependentValues),
mpTrajectoryProblem(NULL),
mpInitialState(NULL),
mResiduals(src.mResiduals),
mRMS(src.mRMS),
mSD(src.mSD),
mParameterSD(src.mParameterSD),
mFisher(src.mFisher),
mpFisherMatrixInterface(NULL),
mpFisherMatrix(NULL),
mCorrelation(src.mCorrelation),
mpCorrelationMatrixInterface(NULL),
mpCorrelationMatrix(NULL)
{
initObjects();
initializeParameter();
}
// virtual
bool CTrajectoryMethodDsaLsodar::elevateChildren()
{
bool success = CLsodaMethod::elevateChildren();
initializeParameter();
return success;
}
/**
* Default constructor.
*/
CTauLeapMethod::CTauLeapMethod(const CCopasiContainer * pParent):
CTrajectoryMethod(CCopasiMethod::tauLeap, pParent),
mReactionDependencies()
{
mpRandomGenerator = CRandom::createGenerator(CRandom::mt19937);
initializeParameter();
}
// Default constructor
CFitProblem::CFitProblem(const CCopasiTask::Type & type,
const CCopasiContainer * pParent):
COptProblem(type, pParent),
mpParmSteadyStateCN(NULL),
mpParmTimeCourseCN(NULL),
mpExperimentSet(NULL),
mpSteadyState(NULL),
mpTrajectory(NULL),
mExperimentUpdateMethods(0, 0),
mExperimentConstraints(0, 0),
mExperimentDependentValues(0),
mpTrajectoryProblem(NULL),
mpInitialState(NULL),
mResiduals(0),
mRMS(std::numeric_limits<C_FLOAT64>::quiet_NaN()),
mSD(std::numeric_limits<C_FLOAT64>::quiet_NaN()),
mParameterSD(0),
mFisher(0, 0),
mpFisherMatrixInterface(NULL),
mpFisherMatrix(NULL),
mCorrelation(0, 0),
mpCorrelationMatrixInterface(NULL),
mpCorrelationMatrix(NULL)
{
initObjects();
initializeParameter();
}
CStochDirectMethod::CStochDirectMethod(const CStochDirectMethod & src,
const CCopasiContainer * pParent):
CTrajectoryMethod(src, pParent),
mpRandomGenerator(NULL),
mNumReactions(0),
mMaxSteps(1000000),
mNextReactionTime(0.0),
mNextReactionIndex(C_INVALID_INDEX),
mA0(0.0),
mReactions(),
mPropensityObjects(),
mAmu(),
mUpdateSequences(),
mUpdateTimeDependentRoots(),
mHaveTimeDependentRoots(false),
mpRootValueCalculator(NULL),
mMaxStepsReached(false),
mTargetTime(src.mTargetTime),
mNumRoot(src.mNumRoot),
mRootsA(src.mRootsA),
mRootsB(src.mRootsB),
mRootsNonZero(src.mRootsNonZero),
mpRootValueOld(NULL),
mpRootValueNew(NULL)
{
initializeParameter();
}
CFitItem::CFitItem(const CCopasiParameterGroup & group,
const CCopasiContainer * pParent):
COptItem(group, pParent),
mpGrpAffectedExperiments(NULL),
mpGrpAffectedCrossValidations(NULL),
mLocalValue(0),
mpLocalMethod(new SpecificUpdateMethod<CFitItem, C_FLOAT64>(this, &CFitItem::setLocalValue))
{initializeParameter();}
/**
* Copy constructor.
* @param "const CSteadyStateMethod &" src
*/
CSteadyStateMethod::CSteadyStateMethod(const CSteadyStateMethod & src,
const CCopasiContainer * pParent):
CCopasiMethod(src, pParent),
mpProblem(src.mpProblem)
{
initializeParameter();
CONSTRUCTOR_TRACE;
}
/**
* Default constructor.
*/
CTrajectoryMethodDsaLsodar::CTrajectoryMethodDsaLsodar(const CDataContainer * pParent,
const CTaskEnum::Method & methodType,
const CTaskEnum::Task & taskType):
CLsodaMethod(pParent, methodType, taskType)
{
mpRandomGenerator = CRandom::createGenerator(CRandom::mt19937);
initializeParameter();
}
/**
* Default constructor.
*/
CSteadyStateMethod::CSteadyStateMethod(CCopasiMethod::SubType subType,
const CCopasiContainer * pParent):
CCopasiMethod(CCopasiTask::steadyState, subType, pParent),
mpProblem(NULL)
{
initializeParameter();
CONSTRUCTOR_TRACE;
}
// Default constructor
CEFMProblem::CEFMProblem(const CCopasiContainer * pParent):
CCopasiProblem(CCopasiTask::optimization, pParent),
mFluxModes(),
mReorderedReactions()
{
initializeParameter();
initObjects();
}
CLyapWolfMethod::CLyapWolfMethod(const CCopasiContainer * pParent):
CLyapMethod(CCopasiMethod::lyapWolf, pParent),
mpState(NULL)
{
assert((void *) &mData == (void *) &mData.dim);
mData.pMethod = this;
initializeParameter();
}
CExperimentObjectMap::CDataColumn::CDataColumn(const std::string & name,
const CDataContainer * pParent) :
CCopasiParameterGroup(name, pParent),
mpRole(NULL),
mpObjectCN(NULL),
mpScale(NULL)
{
initializeParameter();
}
CConfigurationFile::CConfigurationFile(const CCopasiParameterGroup & group,
const CCopasiContainer * pParent):
CCopasiParameterGroup(group, pParent),
mpRecentFiles(NULL),
mpRecentSBMLFiles(NULL),
mpRecentMIRIAMResources(NULL),
mpApplicationFont(NULL),
mpWebBrowser(NULL)
{initializeParameter();}
const CConfigurationFile & CConfigurationFile::operator=(const CCopasiParameterGroup & rhs)
{
if (static_cast< CCopasiParameterGroup * >(this) == &rhs) return * this;
CCopasiParameterGroup::operator=(rhs);
initializeParameter();
return *this;
}
// copy constructor
CEFMProblem::CEFMProblem(const CEFMProblem& src,
const CCopasiContainer * pParent):
CCopasiProblem(src, pParent),
mFluxModes(src.mFluxModes),
mReorderedReactions(src.mReorderedReactions)
{
initializeParameter();
initObjects();
}
/**
* Default constructor
*/
CLNAMethod::CLNAMethod(const CCopasiContainer* pParent):
CCopasiMethod(CCopasiTask::lna, CCopasiMethod::linearNoiseApproximation, pParent),
mpModel(NULL),
mSteadyStateResolution(1.0e-9),
mSSStatus(CSteadyStateMethod::notFound)
{
initializeParameter();
initObjects();
}
const CExperimentObjectMap & CExperimentObjectMap::operator=(const CCopasiParameterGroup & rhs)
{
if (static_cast< CCopasiParameterGroup * >(this) == &rhs) return * this;
CCopasiParameterGroup::operator=(rhs);
initializeParameter();
return *this;
}
CExperimentObjectMap::CDataColumn::CDataColumn(const CCopasiParameterGroup & group,
const CCopasiContainer * pParent) :
CCopasiParameterGroup(group, pParent),
mpRole(NULL),
mpObjectCN(NULL),
mpScale(NULL)
{
initializeParameter();
}
CLyapWolfMethod::CLyapWolfMethod(const CLyapWolfMethod & src,
const CCopasiContainer * pParent):
CLyapMethod(src, pParent),
mContainerState()
{
assert((void *) &mData == (void *) &mData.dim);
mData.pMethod = this;
initializeParameter();
}
CFitItem::CFitItem(const CFitItem & src,
const CCopasiContainer * pParent):
COptItem(src, pParent),
mpGrpAffectedExperiments(NULL),
#ifdef COPASI_CROSSVALIDATION
mpGrpAffectedCrossValidations(NULL),
#endif // COPASI_CROSSVALIDATION
mLocalValue(0),
mpLocalMethod(new SpecificUpdateMethod<CFitItem, C_FLOAT64>(this, &CFitItem::setLocalValue))
{initializeParameter();}
/**
* Default constructor.
*/
CLyapProblem::CLyapProblem(const CCopasiContainer * pParent):
CCopasiProblem(CCopasiTask::lyap, pParent),
mpExponentNumber(NULL),
//mpTimeSeriesRequested(NULL),
mpDivergenceRequested(NULL),
mpTransientTime(NULL)
{
initializeParameter();
CONSTRUCTOR_TRACE;
}
CLNAMethod::CLNAMethod(const CLNAMethod & src,
const CCopasiContainer * pParent):
CCopasiMethod(src, pParent),
mpModel(NULL),
mSteadyStateResolution(src.mSteadyStateResolution),
mSSStatus(CSteadyStateMethod::notFound)
{
initializeParameter();
initObjects();
}
CLyapWolfMethod::CLyapWolfMethod(const CCopasiContainer * pParent,
const CTaskEnum::Method & methodType,
const CTaskEnum::Task & taskType):
CLyapMethod(pParent, methodType, taskType),
mContainerState()
{
assert((void *) &mData == (void *) &mData.dim);
mData.pMethod = this;
initializeParameter();
}
CILDMModifiedMethod::CILDMModifiedMethod(const CILDMModifiedMethod & src,
const CCopasiContainer * pParent):
CTSSAMethod(src, pParent) //,
//mpState(NULL),
//mY(NULL)
{
// assert((void *) &mData == (void *) &mData.dim);
mData.pMethod = this;
initializeParameter();
}
/**
* Copy constructor.
* @param "const CSteadyStateMethod &" src
*/
CSteadyStateMethod::CSteadyStateMethod(const CSteadyStateMethod & src,
const CCopasiContainer * pParent):
CCopasiMethod(src, pParent),
mpProblem(src.mpProblem),
mContainerState(),
mContainerStateReduced(),
mpContainerStateTime(NULL),
mCompartmentVolumes()
{
initializeParameter();
CONSTRUCTOR_TRACE;
}
CLsodaMethod::CLsodaMethod(const CLsodaMethod & src,
const CCopasiContainer * pParent):
CTrajectoryMethod(src, pParent),
mMethodState(),
mY(NULL),
mRootMask(src.mRootMask)
{
assert((void *) &mData == (void *) &mData.dim);
mData.pMethod = this;
initializeParameter();
}
/**
* Copy constructor.
* @param "const CSensProblem &" src
*/
CSensProblem::CSensProblem(const CSensProblem & src,
const CDataContainer * pParent):
CCopasiProblem(src, pParent),
mpSubTaskType(NULL),
mpTargetFunctions(NULL),
mpVariablesGroup(NULL),
mpResultAnnotation(NULL),
mpScaledResultAnnotation(NULL),
mpCollapsedResultAnnotation(NULL)
{
initializeParameter();
initObjects();
}
/**
* Default constructor.
*/
CSteadyStateMethod::CSteadyStateMethod(const CCopasiContainer * pParent,
const CTaskEnum::Method & methodType,
const CTaskEnum::Task & taskType):
CCopasiMethod(pParent, methodType, taskType),
mpProblem(NULL),
mContainerState(),
mContainerStateReduced(),
mpContainerStateTime(NULL),
mCompartmentVolumes()
{
initializeParameter();
CONSTRUCTOR_TRACE;
}