示例#1
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/**
 *   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();
}
示例#3
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// 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;
}
示例#5
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/**
 *   Default constructor.
 */
CTauLeapMethod::CTauLeapMethod(const CCopasiContainer * pParent):
    CTrajectoryMethod(CCopasiMethod::tauLeap, pParent),
    mReactionDependencies()
{
  mpRandomGenerator = CRandom::createGenerator(CRandom::mt19937);
  initializeParameter();
}
示例#6
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//  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();
}
示例#7
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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();
}
示例#8
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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();}
示例#9
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/**
 *  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();
}
示例#11
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/**
 *  Default constructor.
 */
CSteadyStateMethod::CSteadyStateMethod(CCopasiMethod::SubType subType,
                                       const CCopasiContainer * pParent):
    CCopasiMethod(CCopasiTask::steadyState, subType, pParent),
    mpProblem(NULL)
{
  initializeParameter();
  CONSTRUCTOR_TRACE;
}
示例#12
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//  Default constructor
CEFMProblem::CEFMProblem(const CCopasiContainer * pParent):
    CCopasiProblem(CCopasiTask::optimization, pParent),
    mFluxModes(),
    mReorderedReactions()
{
  initializeParameter();
  initObjects();
}
示例#13
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CLyapWolfMethod::CLyapWolfMethod(const CCopasiContainer * pParent):
  CLyapMethod(CCopasiMethod::lyapWolf, pParent),
  mpState(NULL)
{
  assert((void *) &mData == (void *) &mData.dim);

  mData.pMethod = this;
  initializeParameter();
}
示例#14
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CExperimentObjectMap::CDataColumn::CDataColumn(const std::string & name,
    const CDataContainer * pParent) :
  CCopasiParameterGroup(name, pParent),
  mpRole(NULL),
  mpObjectCN(NULL),
  mpScale(NULL)
{
  initializeParameter();
}
示例#15
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CConfigurationFile::CConfigurationFile(const CCopasiParameterGroup & group,
                                       const CCopasiContainer * pParent):
    CCopasiParameterGroup(group, pParent),
    mpRecentFiles(NULL),
    mpRecentSBMLFiles(NULL),
    mpRecentMIRIAMResources(NULL),
    mpApplicationFont(NULL),
    mpWebBrowser(NULL)
{initializeParameter();}
示例#16
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const CConfigurationFile & CConfigurationFile::operator=(const CCopasiParameterGroup & rhs)
{
  if (static_cast< CCopasiParameterGroup * >(this) == &rhs) return * this;

  CCopasiParameterGroup::operator=(rhs);
  initializeParameter();

  return *this;
}
示例#17
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// copy constructor
CEFMProblem::CEFMProblem(const CEFMProblem& src,
                         const CCopasiContainer * pParent):
    CCopasiProblem(src, pParent),
    mFluxModes(src.mFluxModes),
    mReorderedReactions(src.mReorderedReactions)
{
  initializeParameter();
  initObjects();
}
示例#18
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/**
 * Default constructor
 */
CLNAMethod::CLNAMethod(const CCopasiContainer* pParent):
  CCopasiMethod(CCopasiTask::lna, CCopasiMethod::linearNoiseApproximation, pParent),
  mpModel(NULL),
  mSteadyStateResolution(1.0e-9),
  mSSStatus(CSteadyStateMethod::notFound)
{
  initializeParameter();
  initObjects();
}
示例#19
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const CExperimentObjectMap & CExperimentObjectMap::operator=(const CCopasiParameterGroup & rhs)
{
  if (static_cast< CCopasiParameterGroup * >(this) == &rhs) return * this;

  CCopasiParameterGroup::operator=(rhs);
  initializeParameter();

  return *this;
}
示例#20
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CExperimentObjectMap::CDataColumn::CDataColumn(const CCopasiParameterGroup & group,
    const CCopasiContainer * pParent) :
  CCopasiParameterGroup(group, pParent),
  mpRole(NULL),
  mpObjectCN(NULL),
  mpScale(NULL)
{
  initializeParameter();
}
示例#21
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CLyapWolfMethod::CLyapWolfMethod(const CLyapWolfMethod & src,
                                 const CCopasiContainer * pParent):
  CLyapMethod(src, pParent),
  mContainerState()
{
  assert((void *) &mData == (void *) &mData.dim);

  mData.pMethod = this;
  initializeParameter();
}
示例#22
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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();}
示例#23
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/**
 *  Default constructor.
 */
CLyapProblem::CLyapProblem(const CCopasiContainer * pParent):
    CCopasiProblem(CCopasiTask::lyap, pParent),
    mpExponentNumber(NULL),
    //mpTimeSeriesRequested(NULL),
    mpDivergenceRequested(NULL),
    mpTransientTime(NULL)
{
  initializeParameter();
  CONSTRUCTOR_TRACE;
}
示例#24
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CLNAMethod::CLNAMethod(const CLNAMethod & src,
                       const CCopasiContainer * pParent):
  CCopasiMethod(src, pParent),
  mpModel(NULL),
  mSteadyStateResolution(src.mSteadyStateResolution),
  mSSStatus(CSteadyStateMethod::notFound)
{
  initializeParameter();
  initObjects();
}
示例#25
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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();
}
示例#26
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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();
}
示例#27
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/**
 *  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;
}
示例#28
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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();
}
示例#29
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/**
 *  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();
}
示例#30
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/**
 *  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;
}