int main(int argc, char *argv[])
{
// Fix for Issue 1377, if locale is not set to the default one, some
// numbers will be displayed in the systems default locale:
setlocale(LC_ALL, "C");
// Fix of Issue with Text centering on OSX Mavericks
#ifdef Q_OS_MACX
if (QSysInfo::MacintoshVersion > QSysInfo::MV_10_8)
{
// fix Mac OS X 10.9 (mavericks) font issue
// https://bugreports.qt-project.org/browse/QTBUG-32789
QFont::insertSubstitution(".Lucida Grande UI", "Lucida Grande");
}
#endif
CQCopasiApplication a(argc, argv);
a.setAttribute(Qt::AA_DontShowIconsInMenus, false);
Q_INIT_RESOURCE(copasi);
// Parse the commandline options
try
{
// Create the root container.
CCopasiRootContainer::init(argc, argv, true);
}
catch (copasi::option_error & msg)
{
CQMessageBox::critical(NULL, "Initialization Error",
msg.what(),
QMessageBox::Ok , QMessageBox::Ok);
return 1;
}
#ifdef Darwin
std::string PluginDir;
COptions::getValue("CopasiDir", PluginDir);
PluginDir += "/Contents/plugins";
QApplication::setLibraryPaths(QStringList(FROM_UTF8(PluginDir)));
#endif // Darwin
// Create the global data model.
CCopasiRootContainer::addDatamodel();
// Create the main application window.
CopasiUI3Window *pWindow = CopasiUI3Window::create();
#ifdef COPASI_SBW_INTEGRATION
if (COptions::compareValue("SBWRegister", true))
goto finish;
#endif // COPASI_SBW_INTEGRATION
if (pWindow != NULL)
{
a.setMainWindow(pWindow);
a.exec();
}
finish:
try // To suppress any access violations during destruction works only under Windows
{
pdelete(pWindow);
CCopasiRootContainer::destroy();
}
catch (...)
{}
return 0;
}
pgsCast::~pgsCast()
{
pdelete(m_var);
}
void CQTrajectoryWidget::destroy()
{
pdelete(mpTrajectoryProblem);
}
bool CTrajectoryTask::initialize(const OutputFlag & of,
COutputHandler * pOutputHandler,
std::ostream * pOstream)
{
assert(mpProblem && mpMethod);
mpTrajectoryProblem = dynamic_cast<CTrajectoryProblem *>(mpProblem);
assert(mpTrajectoryProblem);
mpTrajectoryMethod = dynamic_cast<CTrajectoryMethod *>(mpMethod);
assert(mpTrajectoryMethod);
mpTrajectoryMethod->setProblem(mpTrajectoryProblem);
bool success = mpMethod->isValidProblem(mpProblem);
CCopasiParameter * pParameter = mpMethod->getParameter("Integrate Reduced Model");
if (pParameter != NULL)
mUpdateMoieties = *pParameter->getValue().pBOOL;
else
mUpdateMoieties = false;
pdelete(mpCurrentState);
mpCurrentState = new CState(mpTrajectoryProblem->getModel()->getState());
mpCurrentTime = &mpCurrentState->getTime();
//mpOutputStartTime = & mpTrajectoryProblem->getOutputStartTime();
// Handle the time series as a regular output.
mTimeSeriesRequested = mpTrajectoryProblem->timeSeriesRequested();
if ((pOutputHandler != NULL) &&
mTimeSeriesRequested &&
(of & CCopasiTask::TIME_SERIES))
{
mTimeSeries.allocate(mpTrajectoryProblem->getStepNumber());
pOutputHandler->addInterface(&mTimeSeries);
}
else
{
mTimeSeries.clear();
}
mpTrajectoryProblem->getModel()->getMathModel()->getProcessQueue().setContinueSimultaneousEvents(mpTrajectoryProblem->getContinueSimultaneousEvents());
if (mpTrajectoryProblem->getStartInSteadyState())
{
mpSteadyState =
dynamic_cast<CSteadyStateTask *>((*mpTrajectoryProblem->getObjectDataModel()->getTaskList())["Steady-State"]);
if (mpSteadyState == NULL) fatalError();
mpSteadyState->initialize(CCopasiTask::NO_OUTPUT, NULL, NULL);
}
else
{
mpSteadyState = NULL;
}
if (!CCopasiTask::initialize(of, pOutputHandler, pOstream)) success = false;
return success;
}
CreateNewGlobalQuantityCommand::~CreateNewGlobalQuantityCommand()
{
pdelete(mpGlobalQuantityData);
}
CPraxis::~CPraxis()
{
pdelete(mpRandom);
}
/*
* Destroys the object and frees any allocated resources
*/
CQPlotsWidget::~CQPlotsWidget()
{
pdelete(mpProxyModel);
pdelete(mpPlotDM);
// no need to delete child widgets, Qt does it all for us
}
UndoEventData::~UndoEventData()
{
// TODO Auto-generated destructor stub
pdelete(this->mEventAssignmentData);
}
DeleteEventCommand::~DeleteEventCommand()
{
// TODO Auto-generated destructor stub
pdelete(mpEventData);
}
CompartmentDataChangeCommand::~CompartmentDataChangeCommand()
{
pdelete(mpCompartmentUndoData);
}
// freeing the memory allocated above
foreach(UndoGlobalQuantityData * data, mpGlobalQuantityData)
{
pdelete(data);
}
/*
* Destroys the object and frees any allocated resources
*/
CQMathMatrixWidget::~CQMathMatrixWidget()
{
pdelete(mpJacobianAnn);
pdelete(mpJacobianAnnRed);
}
void CQSpeciesDetail::copy()
{
if (mpMetab == NULL) return;
CModel * pModel = NULL;
if (mpMetab) pModel = mpDataModel->getModel();
if (pModel == NULL) return; // for getting compartments and initializing cModelExpObj
// Create and customize compartment choices dialog
CQNameSelectionDialog * pDialog = new CQNameSelectionDialog(this);
pDialog->setWindowTitle("Choose a compartment");
pDialog->mpLblName->setText("compartment");
pDialog->mpSelectionBox->clear();
pDialog->mpSelectionBox->setDuplicatesEnabled(false);
pDialog->mpSelectionBox->setEditable(false); // at least for now, unless we want to add new compartment creation here.
// Use CModelExpansion for duplication
CModelExpansion cModelExpObj = CModelExpansion(pModel);
CModelExpansion::SetOfModelElements sourceObjects;
CModelExpansion::ElementsMap origToCopyMapping;
// for comboBox compartment list and setting compartment
CCopasiVectorNS< CCompartment > & Compartments = pModel->getCompartments();
CCopasiVectorN< CCompartment >::const_iterator it = Compartments.begin();
CCopasiVectorN< CCompartment >::const_iterator end = Compartments.end();
QStringList SelectionList;
// Collect and load list of compartment names in comboBox
for (; it != end; ++it)
{
SelectionList.append(FROM_UTF8(it->getObjectName()));
}
pDialog->setSelectionList(SelectionList);
//Set the current compartment as the default
mpCurrentCompartment = mpMetab->getCompartment();
// to use here, and for testing if compartment changed after executing the dialog
int origCompartmentIndex = pDialog->mpSelectionBox->findText(FROM_UTF8(mpCurrentCompartment->getObjectName()));
pDialog->mpSelectionBox->setCurrentIndex(origCompartmentIndex);
it = Compartments.begin(); // Reuse Compartments iterator to set compartment choice
if (pDialog->exec() != QDialog::Rejected)
{
// Put species in different compartment (without name modification) by making
// duplicateMetab think the other compartment was duplicated from the original
if (origCompartmentIndex != pDialog->mpSelectionBox->currentIndex())
{
sourceObjects.addCompartment(mpMetab->getCompartment());
origToCopyMapping.add(mpMetab->getCompartment(), (it + pDialog->mpSelectionBox->currentIndex()).constCast());
}
sourceObjects.addMetab(mpMetab);
cModelExpObj.duplicateMetab(mpMetab, "_copy", sourceObjects, origToCopyMapping);
protectedNotify(ListViews::COMPARTMENT, ListViews::DELETE, "");//Refresh all
protectedNotify(ListViews::METABOLITE, ListViews::DELETE, ""); //Refresh all
protectedNotify(ListViews::REACTION, ListViews::DELETE, ""); //Refresh all
mpListView->switchToOtherWidget(C_INVALID_INDEX, origToCopyMapping.getDuplicateKey(mKey));
}
pdelete(pDialog);
}
void CQFittingResult::init()
{
unsigned C_INT32 i, imax;
// Set up the parameters table
mpParameters->setNumCols(mpParameters->numCols() + 1);
mpParameters->horizontalHeader()->setLabel(mpParameters->numCols() - 1, tr("Parameter"));
mpParameters->setNumCols(mpParameters->numCols() + 1);
mpParameters->horizontalHeader()->setLabel(mpParameters->numCols() - 1, tr("Value"));
mpParameters->setNumCols(mpParameters->numCols() + 1);
mpParameters->horizontalHeader()->setLabel(mpParameters->numCols() - 1, tr("Std. Deviation"));
mpParameters->setNumCols(mpParameters->numCols() + 1);
mpParameters->horizontalHeader()->setLabel(mpParameters->numCols() - 1, tr("Coeff. of Variation [%]"));
mpParameters->setNumCols(mpParameters->numCols() + 1);
mpParameters->horizontalHeader()->setLabel(mpParameters->numCols() - 1, tr("Gradient"));
mpParameters->setSizePolicy(QSizePolicy((QSizePolicy::SizeType)7, (QSizePolicy::SizeType)5, 0, 0, mpParameters->sizePolicy().hasHeightForWidth()));
mpParameters->setNumRows(0);
mpParameters->setNumCols(5);
mpParameters->setReadOnly(true);
for (i = 0, imax = mpParameters->numCols(); i != imax; i++)
mpParameters->adjustColumn(i);
// Set up the experiments table
mpExperiments->setNumCols(mpExperiments->numCols() + 1);
mpExperiments->horizontalHeader()->setLabel(mpExperiments->numCols() - 1, tr("Experiment"));
mpExperiments->setNumCols(mpExperiments->numCols() + 1);
mpExperiments->horizontalHeader()->setLabel(mpExperiments->numCols() - 1, tr("Objective Value"));
mpExperiments->setNumCols(mpExperiments->numCols() + 1);
mpExperiments->horizontalHeader()->setLabel(mpExperiments->numCols() - 1, tr("Root Mean Square"));
mpExperiments->setNumCols(mpExperiments->numCols() + 1);
mpExperiments->horizontalHeader()->setLabel(mpExperiments->numCols() - 1, tr("Error Mean"));
mpExperiments->setNumCols(mpExperiments->numCols() + 1);
mpExperiments->horizontalHeader()->setLabel(mpExperiments->numCols() - 1, tr("Error Mean Std. Deviation"));
mpExperiments->setSizePolicy(QSizePolicy((QSizePolicy::SizeType)7, (QSizePolicy::SizeType)5, 0, 0, mpExperiments->sizePolicy().hasHeightForWidth()));
mpExperiments->setNumRows(0);
mpExperiments->setNumCols(5);
mpExperiments->setReadOnly(true);
for (i = 0, imax = mpExperiments->numCols(); i != imax; i++)
mpExperiments->adjustColumn(i);
// Set up the experiments table
mpValues->setNumCols(mpValues->numCols() + 1);
mpValues->horizontalHeader()->setLabel(mpValues->numCols() - 1, tr("Fitted Value"));
mpValues->setNumCols(mpValues->numCols() + 1);
mpValues->horizontalHeader()->setLabel(mpValues->numCols() - 1, tr("Objective Value"));
mpValues->setNumCols(mpValues->numCols() + 1);
mpValues->horizontalHeader()->setLabel(mpValues->numCols() - 1, tr("Root Mean Square"));
mpValues->setNumCols(mpValues->numCols() + 1);
mpValues->horizontalHeader()->setLabel(mpValues->numCols() - 1, tr("Error Mean"));
mpValues->setNumCols(mpValues->numCols() + 1);
mpValues->horizontalHeader()->setLabel(mpValues->numCols() - 1, tr("Error Mean Std. Deviation"));
mpValues->setSizePolicy(QSizePolicy((QSizePolicy::SizeType)7, (QSizePolicy::SizeType)5, 0, 0, mpValues->sizePolicy().hasHeightForWidth()));
mpValues->setNumRows(0);
mpValues->setNumCols(5);
mpValues->setReadOnly(true);
for (i = 0, imax = mpValues->numCols(); i != imax; i++)
mpValues->adjustColumn(i);
mpCorrelations->setLegendEnabled(false);
mpFisherInformation->setLegendEnabled(false);
#ifndef COPASI_CROSSVALIDATION
pdelete(mpCrossValidations);
pdelete(mpCrossValidationValues);
#endif // not COPASI_CROSSVALIDATION
}
CQEFMResultWidget::~CQEFMResultWidget()
{
pdelete(mpProxyModelNetReactions);
pdelete(mpProxyModelReactions);
pdelete(mpProxyModelSpecies);
}
CFitItem::~CFitItem()
{pdelete(mpLocalMethod);}
void CQRDFTreeView::clear()
{
mNode2Item.clear();
pdelete(mpGraph);
mpTreeWidget->clear();
}
// virtual
CMathObject::~CMathObject()
{
pdelete(mpExpression);
}
pgsAssign::~pgsAssign()
{
pdelete(m_var);
}
CPlotSelectionDialog::~CPlotSelectionDialog()
{
pdelete(this->mpOKButton);
pdelete(this->mpCancelButton);
pdelete(this->mpExpertCheckBox);
pdelete(this->mpXAxisLabel);
pdelete(this->mpYAxisLabel);
pdelete(this->mpXAxisSimpleSelectionWidget);
pdelete(this->mpYAxisSimpleSelectionWidget);
pdelete(this->mpXAxisObjectBrowserWidget);
pdelete(this->mpYAxisObjectBrowserWidget);
pdelete(this->mpXAxisSelectionBox);
pdelete(this->mpYAxisSelectionBox);
pdelete(this->mpSplitter);
pdelete(this->mpButtonBox);
pdelete(this->mpMainLayout);
pdelete(this->mpXAxisTmpVector);
pdelete(this->mpYAxisTmpVector);
}
void CTrajectoryTask::cleanup()
{
pdelete(mpCurrentState);
}
bool CQFittingWidget::loadTask()
{
CFitTask * pTask =
dynamic_cast< CFitTask * >(mpTask);
if (!pTask) return false;
loadCommon();
loadMethod();
CFitProblem * pProblem =
dynamic_cast<CFitProblem *>(mpTask->getProblem());
if (!pProblem) return false;
pdelete(mpExperimentSet)
CExperimentSet * pExperimentSet =
dynamic_cast<CExperimentSet *>(pProblem->getGroup("Experiment Set"));
mpExperimentSet = new CExperimentSet(*pExperimentSet, NO_PARENT);
mExperimentKeyMap.clear();
size_t i, imax = mpExperimentSet->getExperimentCount();
for (i = 0; i < imax; i++)
mExperimentKeyMap[pExperimentSet->getExperiment(i)->CCopasiParameter::getKey()] =
mpExperimentSet->getExperiment(i)->CCopasiParameter::getKey();
pdelete(mpCrossValidationSet)
CCrossValidationSet * pCrossValidationSet =
dynamic_cast<CCrossValidationSet *>(pProblem->getGroup("Validation Set"));
mpCrossValidationSet = new CCrossValidationSet(*pCrossValidationSet, NO_PARENT);
mCrossValidationKeyMap.clear();
imax = mpCrossValidationSet->getExperimentCount();
for (i = 0; i < imax; i++)
mCrossValidationKeyMap[pCrossValidationSet->getExperiment(i)->CCopasiParameter::getKey()] =
mpCrossValidationSet->getExperiment(i)->CCopasiParameter::getKey();
mpCheckRandomize->setChecked(pProblem->getRandomizeStartValues());
mpCreateParameterSets->setChecked(pProblem->getCreateParameterSets());
mpCheckStatistics->setChecked(pProblem->getCalculateStatistics());
mpParameters->load(mpDataModel, pProblem->getGroup("OptimizationItemList"), &mExperimentKeyMap, &mCrossValidationKeyMap);
if (CCopasiMessage::peekLastMessage().getType() == CCopasiMessage::ERROR)
{
CQMessageBox::critical(this, "Error loading Parameter estimation task",
CCopasiMessage::getAllMessageText().c_str(),
QMessageBox::Ok | QMessageBox::Default,
QMessageBox::NoButton);
}
mpParameters->setExperimentSet(const_cast<const CExperimentSet *&>(mpExperimentSet));
mpParameters->setCrossValidationSet(const_cast<const CCrossValidationSet *&>(mpCrossValidationSet));
mpConstraints->load(mpDataModel, pProblem->getGroup("OptimizationConstraintList"), &mExperimentKeyMap, &mCrossValidationKeyMap);
mpConstraints->setExperimentSet(const_cast<const CExperimentSet *&>(mpExperimentSet));
mpConstraints->setCrossValidationSet(const_cast<const CCrossValidationSet *&>(mpCrossValidationSet));
mChanged = false;
return true;
}
CILDMModifiedMethod::~CILDMModifiedMethod()
{
pdelete(mpState);
}
void CQFittingWidget::destroy()
{
pdelete(mpExperimentSet);
pdelete(mpCrossValidationSet);
}
int
waitup(int echildok, int *retstatus)
{
Envy *e;
int pid;
int slot;
Symtab *s;
Word *w;
Job *j;
char buf[ERRMAX];
Bufblock *bp;
int uarg = 0;
int done;
Node *n;
Process *p;
extern int runerrs;
/* first check against the proces slist */
if(retstatus)
for(p = phead; p; p = p->f)
if(p->pid == *retstatus){
*retstatus = p->status;
pdelete(p);
return(-1);
}
again: /* rogue processes */
pid = waitfor(buf);
if(pid == -1){
if(echildok > 0)
return(1);
else {
fprint(2, "mk: (waitup %d) ", echildok);
perror("mk wait");
Exit();
}
}
if(DEBUG(D_EXEC))
fprint(1, "waitup got pid=%d, status='%s'\n", pid, buf);
if(retstatus && pid == *retstatus){
*retstatus = buf[0]? 1:0;
return(-1);
}
slot = pidslot(pid);
if(slot < 0){
if(DEBUG(D_EXEC))
fprint(2, "mk: wait returned unexpected process %d\n", pid);
pnew(pid, buf[0]? 1:0);
goto again;
}
j = events[slot].job;
usage();
nrunning--;
events[slot].pid = -1;
if(buf[0]){
e = buildenv(j, slot);
bp = newbuf();
shprint(j->r->recipe, e, bp);
front(bp->start);
fprint(2, "mk: %s: exit status=%s", bp->start, buf);
freebuf(bp);
for(n = j->n, done = 0; n; n = n->next)
if(n->flags&DELETE){
if(done++ == 0)
fprint(2, ", deleting");
fprint(2, " '%s'", n->name);
delete(n->name);
}
fprint(2, "\n");
if(kflag){
runerrs++;
uarg = 1;
} else {
jobs = 0;
Exit();
}
}
for(w = j->t; w; w = w->next){
if((s = symlook(w->s, S_NODE, 0)) == 0)
continue; /* not interested in this node */
update(uarg, s->u.ptr);
}
if(nrunning < nproclimit)
sched();
return(0);
}
pgsGenRegex::~pgsGenRegex()
{
pdelete(m_regex);
pdelete(m_seed);
}
/*
* Destroys the object and frees any allocated resources
*/
CQParameterSetsWidget::~CQParameterSetsWidget()
{
pdelete(mpProxyModel);
pdelete(mpParameterSetsDM);
// no need to delete child widgets, Qt does it all for us
}
CCompressedColumnFormat::~CCompressedColumnFormat()
{
pdelete(mpValue);
pdelete(mpRowIndex);
pdelete(mpColumnStart);
}
/*
* Destroys the object and frees any allocated resources
*/
CQFunctionsWidget::~CQFunctionsWidget()
{
pdelete(mpProxyModel);
pdelete(mpFunctionDM);
// no need to delete child widgets, Qt does it all for us
}
TaskWidget::~TaskWidget()
{
pdelete(mpTaskThread);
}
