QFluxModeAnimation Class Reference

Inheritance diagram for QFluxModeAnimation:

Collaboration diagram for QFluxModeAnimation:

Public Member Functions
virtual void	getScales (std::vector< qreal > &scales, int step)
virtual void	initialize (const CCopasiDataModel &dataModel)
Public Member Functions inherited from CQCopasiAnimation
virtual void	applyToScene (CQLayoutScene &scene, int step)
	CQCopasiAnimation ()
std::vector < CQEffectDescription * > &	getEntries ()
virtual int	getNumSteps ()
ScaleMode	getScaleMode () const
virtual void	removeFromScene (CQLayoutScene &scene)
void	setScaleMode (ScaleMode mode)
virtual	~CQCopasiAnimation ()

Protected Attributes
std::map< size_t, std::string >	indexMap
Protected Attributes inherited from CQCopasiAnimation
std::vector < CQEffectDescription * >	mEntries
ScaleMode	mMode
int	mNumSteps
const CCopasiDataModel *	mpDataModel

Additional Inherited Members
Public Types inherited from CQCopasiAnimation
enum	ScaleMode { Global, Individual }

Detailed Description

Animation, that displays one fluxmode per frame

Definition at line 84 of file CQAnimationWindow.cpp.

Member Function Documentation

virtual void QFluxModeAnimation::getScales ( std::vector< qreal > &  scales, int  step  )

inlinevirtual

Reimplemented from CQCopasiAnimation.

Definition at line 115 of file CQAnimationWindow.cpp.

References CFluxMode::begin(), CFluxMode::end(), CEFMProblem::getFluxModes(), CCopasiTask::getProblem(), CEFMProblem::getReorderedReactions(), CCopasiDataModel::getTaskList(), CQCopasiAnimation::mEntries, CQCopasiAnimation::mNumSteps, and CQCopasiAnimation::mpDataModel.

  {
    if (mpDataModel == NULL) return;

    CEFMTask *task = dynamic_cast< CEFMTask * >((*mpDataModel->getTaskList())["Elementary Flux Modes"]);

    if (task == NULL) return;

    const CEFMProblem* problem = dynamic_cast<const CEFMProblem*>(task->getProblem());

    if (problem == NULL) return;

    const std::vector< CFluxMode >& fluxModes = problem->getFluxModes();
    mNumSteps = fluxModes.size();

    if (fluxModes.size() <= (size_t)step) return;

    const CFluxMode& mode = fluxModes[step];

    const std::vector< const CReaction * > &reordered = problem->getReorderedReactions();
    std::map<std::string, double> cnValueMap;

    CFluxMode::const_iterator modeIt = mode.begin();

    while (modeIt  != mode.end())
      {
        const size_t reactionIndex = (*modeIt).first;
        const double coefficient = (*modeIt).second;
        cnValueMap[reordered[reactionIndex]->getCN()] = qAbs(coefficient);
        ++modeIt;
      }

    for (size_t i = 0; i < mEntries.size(); ++i)
      scales.push_back(cnValueMap[mEntries[i]->getCN()]);
  }

virtual void QFluxModeAnimation::initialize ( const CCopasiDataModel &  dataModel )

inlinevirtual

Implements CQCopasiAnimation.

Definition at line 87 of file CQAnimationWindow.cpp.

References CCopasiVector< T >::begin(), CQEffectDescription::Colorize, CCopasiVector< T >::end(), CEFMProblem::getFluxModes(), CCopasiDataModel::getModel(), CCopasiTask::getProblem(), CModel::getReactions(), CCopasiDataModel::getTaskList(), indexMap, CQCopasiAnimation::mEntries, CQCopasiAnimation::mNumSteps, and CQCopasiAnimation::mpDataModel.

  {
    mpDataModel = &dataModel;
    const CModel& model = *dataModel.getModel();
    const CCopasiVector< CReaction > & reactions = model.getReactions();
    CCopasiVector< CReaction >::const_iterator it = reactions.begin();
    size_t count = 0;

    while (it != reactions.end())
      {
        mEntries.push_back(new CQEffectDescription((*it)->getCN(), CQEffectDescription::Colorize, Qt::black, Qt::red));
        indexMap[count] = (*it)->getCN();
        ++it;
        ++count;
      }

    // initialize number of steps
    CEFMTask *task = dynamic_cast< CEFMTask * >((*mpDataModel->getTaskList())["Elementary Flux Modes"]);

    if (task == NULL) return;

    const CEFMProblem* problem = dynamic_cast<const CEFMProblem*>(task->getProblem());

    if (problem == NULL) return;

    const std::vector< CFluxMode >& fluxModes = problem->getFluxModes();
    mNumSteps = fluxModes.size();
  }

Member Data Documentation

std::map<size_t, std::string> QFluxModeAnimation::indexMap

protected

Definition at line 152 of file CQAnimationWindow.cpp.

Referenced by initialize().

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The documentation for this class was generated from the following file:

• CQAnimationWindow.cpp