COptMethodGA::COptMethodGA(const CCopasiContainer * pParent):
COptMethod(CCopasiTask::optimization, CCopasiMethod::GeneticAlgorithm, pParent),
mGenerations(0),
mPopulationSize(0),
mpRandom(NULL),
mVariableSize(0),
mIndividual(0),
mCrossOverFalse(0),
mCrossOver(0),
mEvaluationValue(DBL_MAX),
mValue(0),
mShuffle(0),
mLosses(0),
mPivot(0),
mMutationVarians(0.1),
mBestValue(DBL_MAX),
mBestIndex(C_INVALID_INDEX),
mGeneration(0)
{
addParameter("Number of Generations", CCopasiParameter::UINT, (unsigned C_INT32) 200);
addParameter("Population Size", CCopasiParameter::UINT, (unsigned C_INT32) 20);
addParameter("Random Number Generator", CCopasiParameter::UINT, (unsigned C_INT32) CRandom::mt19937);
addParameter("Seed", CCopasiParameter::UINT, (unsigned C_INT32) 0);
initObjects();
}
COptMethodSRES::COptMethodSRES(const COptMethodSRES & src,
const CDataContainer * pParent):
COptPopulationMethod(src, pParent),
mStopAfterStalledGenerations(0),
mEvaluationValue(std::numeric_limits< C_FLOAT64 >::max()),
mBestValue(std::numeric_limits< C_FLOAT64 >::max())
{initObjects();}
COptMethodPS::COptMethodPS(const CCopasiContainer * pParent):
COptMethod(CCopasiTask::optimization, CCopasiMethod::ParticleSwarm, pParent),
mIterationLimit(0),
mSwarmSize(0),
mVariance(0.0),
mpRandom(NULL),
mIteration(0),
mhIteration(C_INVALID_INDEX),
mVariableSize(0),
mIndividuals(),
mValues(),
mVelocities(),
mBestValues(),
mBestPositions(),
mShuffle(),
mInformants(),
mNumInformedMin(0),
mNumInformed(0),
mBestIndex(0),
mEvaluationValue(0),
mContinue(true)
{
addParameter("Iteration Limit", CCopasiParameter::UINT, (unsigned C_INT32) 2000);
addParameter("Swarm Size", CCopasiParameter::UINT, (unsigned C_INT32) 50);
addParameter("Std. Deviation", CCopasiParameter::UDOUBLE, (C_FLOAT64) 1.0e-6);
addParameter("Random Number Generator", CCopasiParameter::UINT, (unsigned C_INT32) CRandom::mt19937);
addParameter("Seed", CCopasiParameter::UINT, (unsigned C_INT32) 0);
initObjects();
}
// 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();
}
CPlotSpecification::CPlotSpecification(const std::string & name,
const CCopasiContainer * pParent,
const CPlotSpecification::Type & type):
CPlotItem(name, pParent, type),
items("Curves", this),
mActive(true)
{initObjects();}
CMetab::CMetab(const std::string & name,
const CCopasiContainer * pParent):
CModelEntity(name, pParent, "Metabolite",
CCopasiObject::NonUniqueName),
mConc(std::numeric_limits<C_FLOAT64>::quiet_NaN()),
mIConc(0.0),
mConcRate(0.0),
mIntensiveNoise(std::numeric_limits<C_FLOAT64>::quiet_NaN()),
mTT(0.0),
mpCompartment(NULL),
mpMoiety(NULL),
mIsInitialConcentrationChangeAllowed(true)
{
mKey = CCopasiRootContainer::getKeyFactory()->add("Metabolite", this);
initObjects();
setStatus(REACTIONS);
if (getObjectParent())
{
initCompartment(NULL);
setInitialConcentration(1.0);
setConcentration(1.0);
}
CONSTRUCTOR_TRACE;
}
int parseGame(const char *filename) {
initParser();
if (!parseGameFile(filename)) {
g_outputError("failed to parse game file %s\n", filename);
return 0;
}
/* make sure a room named "start" exists */
if (NULL == g_hash_table_lookup(roomParsedTable, "start")) {
g_outputError("room 'start' must be defined\n");
return 0;
}
initGlobalEvents();
initObjects();
initCreatures();
initRooms();
/* make sure we didn't have any issues parsing Lua scripts */
if (g_scriptError) {
return 0;
}
destroyParser();
return 1;
}
// 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();
}
IntroScene::IntroScene() {
setWindow();
setRenderer();
setRunning();
initObjects();
setObjects();
}
Level::Level() {
setWindow();
setRenderer();
setRunning();
initObjects();
setObjects();
}
COptMethodPraxis::COptMethodPraxis(const CCopasiContainer * pParent):
COptMethod(CCopasiTask::optimization, CCopasiMethod::Praxis, pParent),
mpPraxis(new FPraxisTemplate<COptMethodPraxis>(this, &COptMethodPraxis::evaluateFunction)),
mpCPraxis(new CPraxis())
{
addParameter("Tolerance", CCopasiParameter::DOUBLE, (C_FLOAT64) 1.e-005);
initObjects();
}
// Default constructor
CEFMProblem::CEFMProblem(const CCopasiContainer * pParent):
CCopasiProblem(CCopasiTask::optimization, pParent),
mFluxModes(),
mReorderedReactions()
{
initializeParameter();
initObjects();
}
void initAll() {
glClearColor(0.0,0.0,0.0,0.0);
initTexture();
initStructs();
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();
}
CFunctionDB::CFunctionDB(const std::string & name,
const CCopasiContainer * pParent):
CCopasiContainer(name, pParent, "FunctionDB"),
mFilename(),
mLoadedFunctions("Functions", this)
{
initObjects();
CONSTRUCTOR_TRACE;
}
COptMethodDE::COptMethodDE(const COptMethodDE & src,
const CCopasiContainer * pParent):
COptPopulationMethod(src, pParent),
mpPermutation(NULL),
mEvaluationValue(std::numeric_limits< C_FLOAT64 >::max()),
mMutationVarians(0.1),
mBestValue(std::numeric_limits< C_FLOAT64 >::max()),
mBestIndex(C_INVALID_INDEX)
{initObjects();}
CEFMAlgorithm::CEFMAlgorithm(const CCopasiMethod::SubType subType, const CCopasiContainer * pParent):
CEFMMethod(CCopasiTask::fluxMode, subType, pParent),
mpModel(NULL),
mStoi(),
mReversible(0),
mpCurrentTableau(NULL),
mpNextTableau(NULL),
mIndexSet()
{initObjects();}
// copy constructor
CEFMProblem::CEFMProblem(const CEFMProblem& src,
const CCopasiContainer * pParent):
CCopasiProblem(src, pParent),
mFluxModes(src.mFluxModes),
mReorderedReactions(src.mReorderedReactions)
{
initializeParameter();
initObjects();
}
CChemEqElement::CChemEqElement(const CChemEqElement & src,
const CCopasiContainer * pParent):
CCopasiContainer(src, pParent),
mMetaboliteKey(src.mMetaboliteKey),
mMultiplicity(src.mMultiplicity)
//mpMetabolite(src.mpMetabolite)
{
initObjects();
CONSTRUCTOR_TRACE;
}
CLNAMethod::CLNAMethod(const CLNAMethod & src,
const CCopasiContainer * pParent):
CCopasiMethod(src, pParent),
mpModel(NULL),
mSteadyStateResolution(src.mSteadyStateResolution),
mSSStatus(CSteadyStateMethod::notFound)
{
initializeParameter();
initObjects();
}
COptMethodPraxis::COptMethodPraxis(const CCopasiContainer * pParent,
const CTaskEnum::Method & methodType,
const CTaskEnum::Task & taskType):
COptMethod(pParent, methodType, taskType),
mpPraxis(new FPraxisTemplate<COptMethodPraxis>(this, &COptMethodPraxis::evaluateFunction)),
mpCPraxis(new CPraxis())
{
addParameter("Tolerance", CCopasiParameter::DOUBLE, (C_FLOAT64) 1.e-005);
initObjects();
}
Manager::Manager(PlotsData *data, QObject *root, QObject *parent) :
QObject(parent),
data(data),
root(root),
menu(0),
step(10)
{
initObjects();
createConnections();
}
CEFMAlgorithm::CEFMAlgorithm(const CEFMAlgorithm & src,
const CCopasiContainer * pParent):
CEFMMethod(src, pParent),
mpModel(NULL),
mStoi(),
mReversible(0),
mpCurrentTableau(NULL),
mpNextTableau(NULL),
mIndexSet()
{initObjects();}
CChemEqElement::CChemEqElement(const std::string & name,
const CCopasiContainer * pParent):
CCopasiContainer(name, pParent, "Chemical Equation Element"),
mMetaboliteKey(),
mMultiplicity(0)
//mpMetabolite(NULL)
{
initObjects();
CONSTRUCTOR_TRACE;
}
CEFMAlgorithm::CEFMAlgorithm(const CDataContainer * pParent,
const CTaskEnum::Method & methodType,
const CTaskEnum::Task & taskType):
CEFMMethod(pParent, methodType, taskType),
mpModel(NULL),
mStoi(),
mReversible(0),
mpCurrentTableau(NULL),
mpNextTableau(NULL),
mIndexSet()
{initObjects();}
COptMethodNelderMead::COptMethodNelderMead(const CCopasiContainer * pParent,
const CTaskEnum::Method & methodType,
const CTaskEnum::Task & taskType):
COptMethod(pParent, methodType, taskType)
{
addParameter("Iteration Limit", CCopasiParameter::UINT, (unsigned C_INT32) 200);
addParameter("Tolerance", CCopasiParameter::UDOUBLE, (C_FLOAT64) 1.e-005);
addParameter("Scale", CCopasiParameter::UDOUBLE, (C_FLOAT64) 10.0);
initObjects();
}
// *******
// * QYCBCRLabView
// *******
YCbCrLabView::YCbCrLabView(QWidget *parent) :
QWidget(parent),
m_pGraphicsView(NULL),
m_pGraphicsViewOverlay(NULL),
m_pGraphicsScene(NULL),
m_pGraphicsSceneOverlay(NULL)
{
createObjects();
createActions();
initObjects();
createAnimations();
}
MainWindow::MainWindow()
: QMainWindow(),
m_api(trace::API_GL),
m_initalCallNum(-1),
m_selectedEvent(0),
m_stateEvent(0),
m_nonDefaultsLookupEvent(0)
{
m_ui.setupUi(this);
initObjects();
initConnections();
}
void Quiddiards::initializeGL(){
glClearColor(0.0, 0.0, 0.0, 0.0);
glClearDepth(1.0);
glEnable(GL_AUTO_NORMAL);
glShadeModel(GL_SMOOTH);
glEnable(GL_DEPTH_TEST);
glDepthFunc(GL_LEQUAL);
glHint(GL_PERSPECTIVE_CORRECTION_HINT, GL_NICEST);
glEnable(GL_CULL_FACE);
glCullFace(GL_BACK);
//glDisable(GL_BLEND);
//glBlendFunc(GL_ONE, GL_ZERO);
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
//glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_REPEAT);
//glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_REPEAT);
/* camera */
camera = FOLLOW;
theta = 45;
phi = 45;
radius = MAXRANGE / 2;
initObjects(); // init objects first, since others may base on them
loadResources();
initLights();
ambLight = true;
sunLight = true;
spotLight = true;
pause = false;
/* flag nurbs object */
nurbs = gluNewNurbsRenderer();
gluNurbsProperty(nurbs, GLU_SAMPLING_TOLERANCE, 25.0);
gluNurbsProperty(nurbs, GLU_DISPLAY_MODE, GLU_FILL);
/* quadric object */
quad = gluNewQuadric();
gluQuadricDrawStyle(quad, GLU_FILL);
gluQuadricNormals(quad, GLU_SMOOTH);
gluQuadricTexture(quad, true);
timer = new QTimer;
connect(timer, SIGNAL(timeout()), SLOT(animate()));
timer->start(interval);
msec = clock();
/* particle system */
ps = new ParticleSystem(200, -10.0f);
}
/**
* 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();
}
