bool CQSpecieDM::insertRows(int position, int rows, const QModelIndex&)
{
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
if (pDataModel->getModel()->getCompartments().size() == 0)
{
pDataModel->getModel()->createCompartment("compartment");
emit notifyGUI(ListViews::COMPARTMENT, ListViews::ADD, pDataModel->getModel()->getCompartments()[0]->getKey());
}
beginInsertRows(QModelIndex(), position, position + rows - 1);
for (int row = 0; row < rows; ++row)
{
mpSpecies =
pDataModel->getModel()->createMetabolite(TO_UTF8(createNewName("species", COL_NAME_SPECIES)), "", 1.0, CModelEntity::REACTIONS);
if (mNotify)
{
emit notifyGUI(ListViews::METABOLITE, ListViews::ADD, mpSpecies->getKey());
}
}
endInsertRows();
return true;
}
void CQCompartment::deleteCompartment()
{
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
if (pModel == NULL) return;
if (mpCompartment == NULL) return;
QMessageBox::StandardButton choice =
CQMessageBox::confirmDelete(this, "compartment",
FROM_UTF8(mpCompartment->getObjectName()),
mpCompartment->getDeletedObjects());
switch (choice)
{
case QMessageBox::Ok:
{
pDataModel->getModel()->removeCompartment(mKey);
protectedNotify(ListViews::COMPARTMENT, ListViews::DELETE, mKey);
protectedNotify(ListViews::COMPARTMENT, ListViews::DELETE, ""); //Refresh all as there may be dependencies.
break;
}
default:
break;
}
mpListView->switchToOtherWidget(111, "");
}
void CQCompartment::slotBtnDelete()
{
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
if (pModel == NULL) return;
if (mpCompartment == NULL) return;
QMessageBox::StandardButton choice =
CQMessageBox::confirmDelete(this, "compartment",
FROM_UTF8(mpCompartment->getObjectName()),
mpCompartment->getDeletedObjects());
switch (choice)
{
case QMessageBox::Ok:
{
unsigned C_INT32 Index =
pDataModel->getModel()->getCompartments().getIndex(mpCompartment->getObjectName());
pDataModel->getModel()->removeCompartment(mKey);
std::string deletedKey = mKey;
//std::string moveToKey = "";
unsigned C_INT32 Size =
pDataModel->getModel()->getCompartments().size();
QObject *pParent = parent();
CTabWidget * pTabWidget = NULL;
while (pParent != NULL &&
(pTabWidget = dynamic_cast< CTabWidget *>(pParent)) == NULL)
{
pParent = pParent->parent();
}
if (pTabWidget != NULL)
{
if (Size > 0)
pTabWidget->enter(pDataModel->getModel()->getCompartments()[std::min(Index, Size - 1)]->getKey());
else
pTabWidget->enter("");
}
protectedNotify(ListViews::COMPARTMENT, ListViews::DELETE, deletedKey);
protectedNotify(ListViews::COMPARTMENT, ListViews::DELETE, ""); //Refresh all as there may be dependencies.
break;
}
default:
break;
}
}
void test000053::test4_bug1000()
{
// load the CPS file
// export to SBML
// check the resulting SBML model
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(test000053::MODEL_STRING_4));
const CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
CPPUNIT_ASSERT(pModel->getModelValues().size() == 0);
CPPUNIT_ASSERT(pModel->getReactions().size() == 0);
CPPUNIT_ASSERT(pModel->getMetabolites().size() == 1);
const CMetab* pMetab = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "A");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::ASSIGNMENT);
const CExpression* pExpr = pMetab->getExpressionPtr();
CPPUNIT_ASSERT(pExpr != NULL);
const CEvaluationNode* pRoot = pExpr->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(pRoot->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pRoot->subType()) == CEvaluationNode::S_DOUBLE);
const CEvaluationNodeNumber* pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pRoot);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 1.5) / 1.5) < 1e-6);
}
void SliderDialog::editSlider()
{
SliderSettingsDialog* pSettingsDialog = new SliderSettingsDialog(this);
// set the list of sliders that is already known
CCopasiObject* object = (CCopasiObject*)getTaskForFolderId(mCurrentFolderId);
if (!object) return;
CCopasiDataModel * pDataModel = object->getObjectDataModel();
assert(pDataModel != NULL);
pSettingsDialog->setModel(pDataModel->getModel());
std::vector<CSlider*>* pVector = getCSlidersForCurrentFolderId();
pSettingsDialog->setDefinedSliders(*pVector);
//pSettingsDialog->disableObjectChoosing(true);
pSettingsDialog->setSlider(mpCurrSlider->getCSlider());
if (pSettingsDialog->exec() == QDialog::Accepted)
{
addSlider(pSettingsDialog->getSlider());
mpCurrSlider->updateSliderData();
/*
if ((!mpCurrSlider->isEnabled()) && mpCurrSlider->getCSlider()->compile())
{
mpCurrSlider->setEnabled(true);
}
*/
}
delete pSettingsDialog;
delete pVector;
}
void test000080::test_mass_action_recognition_bug()
{
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
try
{
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(test000080::MODEL_STRING1));
}
catch (...)
{
// there should not be an exception
CPPUNIT_ASSERT(false);
}
const CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getReactions().size() == 1);
const CReaction* pReaction = pModel->getReactions()[0];
CPPUNIT_ASSERT(pReaction != NULL);
const CFunction* pFun = pReaction->getFunction();
CPPUNIT_ASSERT(pFun != NULL);
CPPUNIT_ASSERT(pFun->getType() == CEvaluationTree::UserDefined);
}
RemoveGlobalQuantityRowsCommand::RemoveGlobalQuantityRowsCommand(
QModelIndexList rows, CQGlobalQuantityDM * pGlobalQuantityDM, const QModelIndex&)
: CCopasiUndoCommand("Global Quantity", GLOBALQUANTITY_REMOVE)
, mpGlobalQuantityDM(pGlobalQuantityDM)
, mRows(rows)
, mpGlobalQuantityData()
, mFirstTime(true)
{
CCopasiDataModel * pDataModel = pGlobalQuantityDM->getDataModel();
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
assert(pModel != NULL);
QModelIndexList::const_iterator i;
for (i = rows.begin(); i != rows.end(); ++i)
{
CModelValue* pModelValue = &pModel->getModelValues()[i->row()];
if (pGlobalQuantityDM->isDefaultRow(*i) || pModelValue == NULL)
continue;
UndoGlobalQuantityData *data = new UndoGlobalQuantityData(pModelValue);
mpGlobalQuantityData.append(data);
}
setText(QObject::tr(": Removed Global Quantity"));
}
void CCopasiTask::initObjects()
{
addObjectReference("Output counter", mOutputCounter, CCopasiObject::ValueInt);
new CCopasiTimer(CCopasiTimer::WALL, this);
new CCopasiTimer(CCopasiTimer::PROCESS, this);
CCopasiDataModel *pDataModel = getObjectDataModel();
if (pDataModel != NULL)
{
if (pDataModel->getModel() != NULL)
{
setMathContainer(&pDataModel->getModel()->getMathContainer());
}
}
}
RemoveAllReactionRowsCommand::RemoveAllReactionRowsCommand(CQReactionDM * pReaDM, const QModelIndex&)
{
mpReactionDM = pReaDM;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
assert(pModel != NULL);
for (int i = 0; i != pReaDM->rowCount() - 1; ++i)
{
UndoReactionData *data = new UndoReactionData();
CReactionInterface* ri = new CReactionInterface((*CCopasiRootContainer::getDatamodelList())[0]->getModel());
if (pModel->getReactions()[i])
{
data->setName(pModel->getReactions()[i]->getObjectName());
ri->initFromReaction(pModel->getReactions()[i]->getKey());
data->setRi(ri);
mpReaData.append(data);
}
}
mType = REACTIONREMOVEALL;
setEntityType("Reaction");
this->setText(removeAllReactionRowsText());
}
void CCopasiSelectionDialog::setFilter(const CQSimpleSelectionTree::ObjectClasses & classes)
{
CCopasiDataModel * pDataModel = ListViews::dataModel(this);
assert(pDataModel != NULL);
this->mpSelectionWidget->populateTree(pDataModel->getModel(), classes);
}
void insertReactionRowsCommand::redo()
{
mpReactionDM->insertNewReactionRow(mPosition, mRows, QModelIndex());
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
assert(pModel != NULL);
mpReaction = pModel->getReactions()[mPosition];
std::string sName = mpReaction->getObjectName();
if (mpReactionData != NULL)
mpReactionData->setName(sName);
CReactionInterface* ri = new CReactionInterface((*CCopasiRootContainer::getDatamodelList())[0]->getModel());
ri->initFromReaction(mpReaction);
if (mpReactionData != NULL)
mpReactionData->setRi(ri);
setUndoState(true);
setAction("Add to list");
if (mpReactionData != NULL)
setName(mpReactionData->getName());
else setName(sName);
}
void InsertCompartmentRowsCommand::redo()
{
if (firstTime)
{
mpCompartmentDM->insertNewCompartmentRow(mPosition, mRows, QModelIndex());
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
assert(pModel != NULL);
CCompartment *pCompartment = pModel->getCompartments()[mPosition];
mpCompartmentData->setName(pCompartment->getObjectName());
mpCompartmentData->setStatus(pCompartment->getStatus());
mpCompartmentData->setInitialValue(pCompartment->getInitialValue());
firstTime = false;
}
else
{
mpCompartmentDM->addCompartmentRow(mpCompartmentData);
}
setUndoState(true);
setAction("Add to list");
setName(mpCompartmentData->getName());
}
void test000046::test_stoichiometricExpression()
{
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(MODEL_STRING));
CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getQuantityUnitEnum() == CModel::mMol);
CPPUNIT_ASSERT(pModel->getVolumeUnitEnum() == CModel::ml);
CPPUNIT_ASSERT(pModel->getTimeUnitEnum() == CModel::s);
CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
const CCompartment* pCompartment = pModel->getCompartments()[0];
CPPUNIT_ASSERT(pCompartment != NULL);
CPPUNIT_ASSERT(pCompartment->getStatus() == CModelEntity::FIXED);
CPPUNIT_ASSERT(pModel->getMetabolites().size() == 2);
CMetab* pA = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pA != NULL);
CPPUNIT_ASSERT(pA->getStatus() == CModelEntity::REACTIONS);
const CMetab* pB = pModel->getMetabolites()[1];
CPPUNIT_ASSERT(pB != NULL);
CPPUNIT_ASSERT(pB->getStatus() == CModelEntity::REACTIONS);
CPPUNIT_ASSERT(pModel->getModelValues().size() == 1);
const CModelValue* pModelValue = pModel->getModelValues()[0];
CPPUNIT_ASSERT(pModelValue != NULL);
CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::FIXED);
CPPUNIT_ASSERT(fabs((pModelValue->getInitialValue() - 3.7) / 3.7) < 1e-3);
CPPUNIT_ASSERT(pModel->getReactions().size() == 1);
const CReaction* pReaction1 = pModel->getReactions()[0];
CPPUNIT_ASSERT(pReaction1 != NULL);
CPPUNIT_ASSERT(pReaction1->isReversible() == true);
// check the kinetic law
const CFunction* pKineticFunction = pReaction1->getFunction();
CPPUNIT_ASSERT(pKineticFunction != NULL);
const CMassAction* pMassAction = dynamic_cast<const CMassAction*>(pKineticFunction);
CPPUNIT_ASSERT(pMassAction != NULL);
const CChemEq* pChemEq = &pReaction1->getChemEq();
CPPUNIT_ASSERT(pChemEq != NULL);
CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
const CChemEqElement* pElement = pChemEq->getSubstrates()[0];
CPPUNIT_ASSERT(pElement != NULL);
CPPUNIT_ASSERT(fabs((pElement->getMultiplicity() - 1.85) / 1.85) < 1e-3);
CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
pElement = pChemEq->getProducts()[0];
CPPUNIT_ASSERT(pElement != NULL);
CPPUNIT_ASSERT(fabs((pElement->getMultiplicity() - 3.35) / 3.35) / 3.35 < 1e-3);
CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
//CPPUNIT_ASSERT(CCopasiMessage::size() == 5);
CCopasiMessage message = CCopasiMessage::getLastMessage();
CPPUNIT_ASSERT(message.getType() == CCopasiMessage::WARNING);
std::string s = message.getText();
CPPUNIT_ASSERT(!s.empty());
CPPUNIT_ASSERT(s.find(std::string("One or more stoichiometric expressions were evaluated and converted to constants values.")) != std::string::npos);
// the other four messages are libSBML unit warnings I don't care about right
// now.
}
void test000047::test_delay()
{
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(MODEL_STRING));
CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getQuantityUnitEnum() == CUnit::mMol);
CPPUNIT_ASSERT(pModel->getVolumeUnitEnum() == CUnit::ml);
CPPUNIT_ASSERT(pModel->getTimeUnitEnum() == CUnit::s);
CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
const CCompartment* pCompartment = pModel->getCompartments()[0];
CPPUNIT_ASSERT(pCompartment != NULL);
CPPUNIT_ASSERT(pCompartment->getStatus() == CModelEntity::FIXED);
CPPUNIT_ASSERT(pModel->getMetabolites().size() == 2);
const CMetab* pB = pModel->getMetabolites()[1];
CPPUNIT_ASSERT(pB != NULL);
CPPUNIT_ASSERT(pB->getStatus() == CModelEntity::FIXED);
CMetab* pA = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pA != NULL);
CPPUNIT_ASSERT(pA->getStatus() == CModelEntity::ASSIGNMENT);
const CExpression* pExpr = pA->getExpressionPtr();
CPPUNIT_ASSERT(pExpr != NULL);
const CEvaluationNode* pNode = pExpr->getRoot();
CPPUNIT_ASSERT(pNode != NULL);
const CEvaluationNodeDelay* pDelayNode = dynamic_cast<const CEvaluationNodeDelay*>(pNode);
CPPUNIT_ASSERT(pDelayNode != NULL);
const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pDelayNode->getChild());
CPPUNIT_ASSERT(pObjectNode != NULL);
CCopasiObjectName objectCN = pObjectNode->getObjectCN();
CPPUNIT_ASSERT(!objectCN.empty());
std::vector<CCopasiContainer*> listOfContainers;
listOfContainers.push_back(pModel);
const CCopasiObject* pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, objectCN);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isReference() == true);
CPPUNIT_ASSERT(pObject->getObjectName() == std::string("Concentration"));
CPPUNIT_ASSERT(pObject->getObjectParent() == pB);
const CEvaluationNodeNumber* pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pObjectNode->getSibling());
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(((CEvaluationNodeNumber::SubType)CEvaluationNode::subType(pNumberNode->getType())) == CEvaluationNodeNumber::DOUBLE);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 0.5) / 0.5) < 1e-3);
CPPUNIT_ASSERT(pNumberNode->getSibling() == NULL);
CPPUNIT_ASSERT(pModel->getModelValues().size() == 1);
const CModelValue* pModelValue = pModel->getModelValues()[0];
CPPUNIT_ASSERT(pModelValue != NULL);
CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::FIXED);
CPPUNIT_ASSERT(pModel->getReactions().size() == 0);
//CPPUNIT_ASSERT(CCopasiMessage::size() == 2);
CCopasiMessage message = CCopasiMessage::getLastMessage();
CPPUNIT_ASSERT(message.getType() == CCopasiMessage::WARNING);
std::string s = message.getText();
CPPUNIT_ASSERT(!s.empty());
CPPUNIT_ASSERT(s.find(std::string("COPASI does not support time delays. Calculations on this model will most likely lead to unusable results.")) != std::string::npos);
// right now, we don't care about the last message since it is a units
// warning from libSBML
}
void CQEventWidget1::deleteEvent()
{
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
CModel * pModel = pDataModel->getModel();
if (pModel == NULL)
return;
pDataModel->getModel()->removeEvent(mKey);
mpEvent = NULL;
protectedNotify(ListViews::EVENT, ListViews::DELETE, mKey);
mpListView->switchToOtherWidget(116, "");
}
void test000052::test_bug988()
{
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(MODEL_STRING));
CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getQuantityUnitEnum() == CModel::mMol);
CPPUNIT_ASSERT(pModel->getVolumeUnitEnum() == CModel::ml);
CPPUNIT_ASSERT(pModel->getTimeUnitEnum() == CModel::s);
CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
const CCompartment* pCompartment = pModel->getCompartments()[0];
CPPUNIT_ASSERT(pCompartment != NULL);
CPPUNIT_ASSERT(pCompartment->getStatus() == CModelEntity::FIXED);
CPPUNIT_ASSERT(pModel->getMetabolites().size() == 1);
CMetab* pA = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pA != NULL);
CPPUNIT_ASSERT(pA->getStatus() == CModelEntity::ASSIGNMENT);
const CExpression* pExpr = pA->getExpressionPtr();
// check the expression
const CEvaluationNode* pNode = pExpr->getRoot();
CPPUNIT_ASSERT(pNode != NULL);
const CEvaluationNodeChoice* pChoiceNode = dynamic_cast<const CEvaluationNodeChoice*>(pNode);
CPPUNIT_ASSERT(pChoiceNode != NULL);
pNode = dynamic_cast<const CEvaluationNode*>(pChoiceNode->getChild());
CPPUNIT_ASSERT(pNode != NULL);
const CEvaluationNodeLogical* pLogicalNode = dynamic_cast<const CEvaluationNodeLogical*>(pNode);
CPPUNIT_ASSERT(pLogicalNode != NULL);
CPPUNIT_ASSERT(((CEvaluationNodeLogical::SubType)CEvaluationNode::subType(pLogicalNode->getType())) == CEvaluationNodeLogical::LT);
const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pLogicalNode->getChild());
CPPUNIT_ASSERT(pObjectNode != NULL);
CCopasiObjectName objectCN = pObjectNode->getObjectCN();
CPPUNIT_ASSERT(!objectCN.empty());
std::vector<CCopasiContainer*> listOfContainers;
listOfContainers.push_back(pModel);
const CCopasiObject* pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, objectCN);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isReference() == true);
CPPUNIT_ASSERT(pObject->getObjectName() == std::string("Time"));
CPPUNIT_ASSERT(pObject->getObjectParent() == pModel);
const CEvaluationNodeNumber* pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pObjectNode->getSibling());
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(((CEvaluationNodeNumber::SubType)CEvaluationNode::subType(pNumberNode->getType())) == CEvaluationNodeNumber::DOUBLE);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 5.0) / 5.0) < 1e-3);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pLogicalNode->getSibling());
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(((CEvaluationNodeNumber::SubType)CEvaluationNode::subType(pNumberNode->getType())) == CEvaluationNodeNumber::DOUBLE);
CPPUNIT_ASSERT(pNumberNode->getValue() < 1e-3);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pNumberNode->getSibling());
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(((CEvaluationNodeNumber::SubType)CEvaluationNode::subType(pNumberNode->getType())) == CEvaluationNodeNumber::DOUBLE);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 10.0) / 10.0) < 1e-3);
CPPUNIT_ASSERT(pModel->getModelValues().size() == 0);
CPPUNIT_ASSERT(pModel->getReactions().size() == 0);
}
// added 5/19/04
void ReactionsWidget1::slotBtnNew()
{
std::string name = "reaction";
size_t i = 0;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
while (!pDataModel->getModel()->createReaction(name))
{
i++;
name = "reaction_";
name += TO_UTF8(QString::number(i));
}
std::string key = pDataModel->getModel()->getReactions()[name]->getKey();
protectedNotify(ListViews::REACTION, ListViews::ADD, key);
enter(key);
mpListView->switchToOtherWidget(C_INVALID_INDEX, key);
}
/*! Slot to delete the active event widget */
void CQEventWidget1::slotBtnDelete()
{
#ifdef COPASI_UNDO
mpUndoStack->push(new DeleteEventCommand(this));
#else
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
CModel * pModel = pDataModel->getModel();
if (pModel == NULL)
return;
pDataModel->getModel()->removeEvent(mKey);
mpEvent = NULL;
protectedNotify(ListViews::EVENT, ListViews::DELETE, mKey);
#endif
}
bool CQUnitDM::removeRows(QModelIndexList rows, const QModelIndex&)
{
if (rows.isEmpty())
return false;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = &CCopasiRootContainer::getDatamodelList()->operator[](0);
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
if (pModel == NULL)
return false;
// Build the list of pointers to items to be deleted
// before actually deleting any item.
QList <CUnitDefinition *> pUnitDefQList;
QModelIndexList::const_iterator i;
CUnitDefinition * pUnitDef;
for (i = rows.begin(); i != rows.end(); ++i)
{
if (!isDefaultRow(*i) &&
(pUnitDef = &CCopasiRootContainer::getUnitList()->operator[](i->row())) != NULL &&
pModel->getUnitSymbolUsage(pUnitDef->getSymbol()).empty() &&
!pUnitDef->isReadOnly())//Don't delete built-ins or used units
pUnitDefQList.append(&CCopasiRootContainer::getUnitList()->operator[](i->row()));
}
for (QList <CUnitDefinition *>::const_iterator j = pUnitDefQList.begin(); j != pUnitDefQList.end(); ++j)
{
size_t delRow =
CCopasiRootContainer::getUnitList()->CCopasiVector< CUnitDefinition >::getIndex(*j);
if (delRow != C_INVALID_INDEX)
{
CCopasiObject::DataObjectSet DeletedObjects;
DeletedObjects.insert(*j);
QMessageBox::StandardButton choice =
CQMessageBox::confirmDelete(NULL, "unit",
FROM_UTF8((*j)->getObjectName()),
DeletedObjects);
if (choice == QMessageBox::Ok)
removeRow((int) delRow);
}
}
return true;
}
RemoveAllGlobalQuantityRowsCommand::RemoveAllGlobalQuantityRowsCommand(CQGlobalQuantityDM * pGlobalQuantityDM, const QModelIndex&)
{
mpGlobalQuantityDM = pGlobalQuantityDM;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
assert(pModel != NULL);
for (int i = 0; i != pGlobalQuantityDM->rowCount() - 1; ++i)
{
UndoGlobalQuantityData *data = new UndoGlobalQuantityData();
if (pModel->getModelValues()[i])
{
data->setName(pModel->getModelValues()[i]->getObjectName());
data->setStatus(pModel->getModelValues()[i]->getStatus());
if (pModel->getModelValues()[i]->getStatus() != CModelEntity::ASSIGNMENT)
{
data->setInitialValue(pModel->getModelValues()[i]->getInitialValue());
}
// set expression
if (pModel->getModelValues()[i]->getStatus() != CModelEntity::FIXED)
{
data->setExpression(pModel->getModelValues()[i]->getExpression());
}
// set initial expression
if (pModel->getModelValues()[i]->getStatus() != CModelEntity::ASSIGNMENT)
{
data->setInitialExpression(pModel->getModelValues()[i]->getInitialExpression());
}
setDependentObjects(pModel->getModelValues()[i]->getDeletedObjects());
data->setReactionDependencyObjects(getReactionData());
data->setSpecieDependencyObjects(getSpecieData());
data->setEventDependencyObjects(getEventData());
mpGlobalQuantityData.append(data);
}
}
mType = GLOBALQUANTITYREMOVEALL;
setEntityType("Global Quantity");
this->setText(removeAllGlobalQuantityRowsText());
}
// Just added 5/18/04
void ReactionsWidget1::slotBtnDelete()
{
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
if (pModel == NULL)
return;
CReaction * pReaction =
dynamic_cast< CReaction * >(CCopasiRootContainer::getKeyFactory()->get(mKey));
if (pReaction == NULL) return;
QMessageBox::StandardButton choice =
CQMessageBox::confirmDelete(NULL, "reaction",
FROM_UTF8(pReaction->getObjectName()),
pReaction->getDeletedObjects());
switch (choice)
{
case QMessageBox::Ok: // Yes or Enter
{
pDataModel->getModel()->removeReaction(mKey);
mpRi->setFunctionWithEmptyMapping("");
protectedNotify(ListViews::REACTION, ListViews::DELETE, mKey);
protectedNotify(ListViews::REACTION, ListViews::DELETE, "");//Refresh all as there may be dependencies.
break;
}
default: // No or Escape
break;
}
}
bool CSlider::setSliderObject(CCopasiObject * pObject)
{
mpSliderObject = pObject;
if (!pObject)
{
mInitialRefreshes.clear();
return false;
}
mCN = pObject->getCN();
std::set< const CCopasiObject * > ChangedObjects;
ChangedObjects.insert(pObject);
CCopasiDataModel* pDataModel = getObjectDataModel();
assert(pDataModel != NULL);
mInitialRefreshes = pDataModel->getModel()->buildInitialRefreshSequence(ChangedObjects);
if (mpSliderObject->isValueInt())
{
this->setSliderType(Integer);
}
else if (mpSliderObject->isValueDbl())
{
this->setSliderType(Float);
}
else
{
this->setSliderType(Undefined);
}
if (this->mSync) this->sync();
C_FLOAT64 value = this->getSliderValue();
this->mOriginalValue = value;
if (this->mMinValue > value)
{
this->mMinValue = value;
}
if (this->mMaxValue < value)
{
this->mMaxValue = value;
}
return true;
}
void CQCompartment::slotBtnDelete()
{
#ifdef COPASI_UNDO
mpUndoStack->push(new DeleteCompartmentCommand(this));
#else
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
if (pModel == NULL) return;
if (mpCompartment == NULL) return;
QMessageBox::StandardButton choice =
CQMessageBox::confirmDelete(this, "compartment",
FROM_UTF8(mpCompartment->getObjectName()),
mpCompartment->getDeletedObjects());
switch (choice)
{
case QMessageBox::Ok:
{
pDataModel->getModel()->removeCompartment(mKey);
protectedNotify(ListViews::COMPARTMENT, ListViews::DELETE, mKey);
protectedNotify(ListViews::COMPARTMENT, ListViews::DELETE, ""); //Refresh all as there may be dependencies.
break;
}
default:
break;
}
#endif
}
void CQPlotsWidget::slotBtnDeactivateAllClicked()
{
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
if (!pDataModel->getModel())
return;
for (size_t i = 0; i < pDataModel->getPlotDefinitionList()->size(); i++)
{
CPlotSpecification *pPS = static_cast<CPlotSpecification *>(pDataModel->getPlotDefinitionList()->operator[](i));
pPS->setActive(false);
}
mpTblPlots->doItemsLayout();
}
bool CQSpecieDM::removeRows(QModelIndexList rows, const QModelIndex&)
{
if (rows.isEmpty())
return false;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
if (pModel == NULL)
return false;
//Build the list of pointers to items to be deleted
//before actually deleting any item.
QList <CMetab *> pSpecies;
QModelIndexList::const_iterator i;
for (i = rows.begin(); i != rows.end(); ++i)
{
if (!isDefaultRow(*i) && pModel->getMetabolites()[(*i).row()])
pSpecies.append(pModel->getMetabolites()[(*i).row()]);
}
QList <CMetab *>::const_iterator j;
for (j = pSpecies.begin(); j != pSpecies.end(); ++j)
{
CMetab * pSpecie = *j;
size_t delRow =
pModel->getMetabolites().CCopasiVector< CMetab >::getIndex(pSpecie);
if (delRow != C_INVALID_INDEX)
{
QMessageBox::StandardButton choice =
CQMessageBox::confirmDelete(NULL, "species",
FROM_UTF8(pSpecie->getObjectName()),
pSpecie->getDeletedObjects());
if (choice == QMessageBox::Ok)
removeRow((int) delRow);
}
}
return true;
}
RemoveEventRowsCommand::RemoveEventRowsCommand(QModelIndexList rows, CQEventDM * pEventDM, const QModelIndex&)
{
mpEventDM = pEventDM;
mRows = rows;
mFirstTime = true;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
assert(pModel != NULL);
QModelIndexList::const_iterator i;
for (i = rows.begin(); i != rows.end(); ++i)
{
UndoEventData *data = new UndoEventData();
if (!pEventDM->isDefaultRow(*i) && pModel->getEvents()[(*i).row()])
{
data->setName(pModel->getEvents()[(*i).row()]->getObjectName());
data->setPriorityExpression(pModel->getEvents()[(*i).row()]->getPriorityExpression());
data->setDelayExpression(pModel->getEvents()[(*i).row()]->getDelayExpression());
data->setTriggerExpression(pModel->getEvents()[(*i).row()]->getTriggerExpression());
CCopasiVector< CEventAssignment >::const_iterator it = pModel->getEvents()[(*i).row()]->getAssignments().begin();
CCopasiVector< CEventAssignment >::const_iterator end = pModel->getEvents()[(*i).row()]->getAssignments().end();
for (; it != end; ++it)
{
const CModelEntity * pEntity = dynamic_cast< CModelEntity * >(CCopasiRootContainer::getKeyFactory()->get((*it)->getTargetKey()));
UndoEventAssignmentData *eventAssignData = new UndoEventAssignmentData();
eventAssignData->setName(pEntity->getObjectName());
eventAssignData->setExpression((*it)->getExpression());
data->getEventAssignmentData()->append(eventAssignData);
}
mpEventData.append(data);
}
}
this->setText(removeEventRowsText());
mType = EVENTREMOVE;
setEntityType("Event");
}
/**
* Load a trajectory problem
* @param "CReadConfig &" configBuffer
*/
void CTrajectoryProblem::load(CReadConfig & configBuffer,
CReadConfig::Mode C_UNUSED(mode))
{
if (configBuffer.getVersion() < "4.0")
{
CCopasiDataModel* pDataModel = getObjectDataModel();
assert(pDataModel != NULL);
mpModel = pDataModel->getModel();
configBuffer.getVariable("EndTime", "C_FLOAT64",
mpDuration,
CReadConfig::LOOP);
configBuffer.getVariable("Points", "C_INT32",
mpStepNumber);
mStepNumberSetLast = true;
sync();
}
}
RemoveCompartmentRowsCommand::RemoveCompartmentRowsCommand(QModelIndexList rows, CQCompartmentDM * pCompartmentDM, const QModelIndex&)
{
mpCompartmentDM = pCompartmentDM;
mRows = rows;
mFirstTime = true;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
assert(pModel != NULL);
QModelIndexList::const_iterator i;
for (i = rows.begin(); i != rows.end(); ++i)
{
UndoCompartmentData *data = new UndoCompartmentData();
if (!pCompartmentDM->isDefaultRow(*i) && pModel->getCompartments()[(*i).row()])
{
mpSpecieData = new QList <UndoSpecieData*>();
mpReactionData = new QList <UndoReactionData*>();
mpGlobalQuantityData = new QList <UndoGlobalQuantityData*>();
mpEventData = new QList <UndoEventData*>();
data->setName(pModel->getCompartments()[(*i).row()]->getObjectName());
data->setStatus(pModel->getCompartments()[(*i).row()]->getStatus());
data->setInitialValue(pModel->getCompartments()[(*i).row()]->getInitialValue());
setDependentObjects(pModel->getCompartments()[(*i).row()]->getDeletedObjects());
data->setReactionDependencyObjects(getReactionData());
data->setSpecieDependencyObjects(getSpecieData());
data->setGlobalQuantityDependencyObjects(getGlobalQuantityData());
data->setEventDependencyObjects(getEventData());
mpCompartmentData.append(data);
}
}
this->setText(removeCompartmentRowsText());
mType = COMPARTMENTREMOVE;
setEntityType("Compartment");
}
void SliderDialog::addSlider(CSlider* pSlider)
{
if (mpParentWindow == NULL)
return;
// check if there already is a slider for this object
CCopasiDataModel * pDataModel = pSlider->getObjectDataModel();
assert(pDataModel != NULL);
SCopasiXMLGUI* pGUI = pDataModel->getGUI();
assert(pGUI);
if (!equivalentSliderExists(pSlider))
{
CObjectInterface::ContainerList listOfContainers;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
listOfContainers.push_back(pDataModel->getModel());
pSlider->compile(listOfContainers);
pGUI->getSliderList()->add(pSlider, true);
}
CopasiSlider* tmp = findCopasiSliderForCSlider(pSlider);
if (!tmp)
{
setCurrentSlider(new CopasiSlider(pSlider, mpParentWindow->getDataModel(), mpSliderBox));
mpCurrSlider->installEventFilter(this);
mpCurrSlider->setHidden(true);
mpCurrSlider->updateSliderData();
// make sure the slider points to the correct object
// for the currently set framework
this->setCorrectSliderObject(this->mpCurrSlider);
mSliderMap[mCurrentFolderId].push_back(mpCurrSlider);
QBoxLayout* layout = static_cast<QBoxLayout*>(mpSliderBox->layout());
int childCount = layout->count() - 1;
layout->insertWidget(childCount, mpCurrSlider);
connect(mpCurrSlider, SIGNAL(valueChanged(double)), this , SLOT(sliderValueChanged()));
connect(mpCurrSlider, SIGNAL(sliderReleased()), this, SLOT(sliderReleased()));
connect(mpCurrSlider, SIGNAL(sliderPressed()), this, SLOT(sliderPressed()));
connect(mpCurrSlider, SIGNAL(closeClicked(CopasiSlider*)), this, SLOT(removeSlider(CopasiSlider*)));
connect(mpCurrSlider, SIGNAL(editClicked(CopasiSlider*)), this, SLOT(editSlider(CopasiSlider*)));
mpCurrSlider->setHidden(false);
mChanged = true;
}
void CQSpeciesDetail::slotBtnNew()
{
save();
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
if (pModel == NULL)
return;
if (pModel->getCompartments().size() == 0)
pModel->createCompartment("compartment");
std::string name = "species";
int i = 0;
while (!(mpMetab = pModel->createMetabolite(name, "", 1.0, CModelEntity::REACTIONS)))
{
i++;
name = "species_";
name += TO_UTF8(QString::number(i));
}
switch (mFramework)
{
case 0:
mpMetab->setInitialConcentration(1.0);
break;
case 1:
mpMetab->setInitialValue(100.0);
break;
}
std::string key = mpMetab->getKey();
enter(key);
protectedNotify(ListViews::METABOLITE, ListViews::ADD, key);
mpListView->switchToOtherWidget(-1, key);
}
