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;
}
bool CReportDefinition::preCompileTable(const std::vector< CCopasiContainer * > & listOfContainer)
{
bool success = true;
mHeaderVector.clear();
mBodyVector.clear();
mFooterVector.clear();
std::vector<CRegisteredObjectName>::const_iterator it = mTableVector.begin();
std::vector<CRegisteredObjectName>::const_iterator end = mTableVector.end();
CCopasiDataModel* pDataModel = getObjectDataModel();
CCopasiObject * pObject;
for (; it != end; ++it)
{
pObject = pDataModel->ObjectFromName(listOfContainer, *it);
if (pObject != NULL)
{
addTableElement(pObject);
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCCopasiTask + 6, it->c_str());
}
}
return success;
}
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 CQReportDefinition::btnCopyReportClicked()
{
btnCommitClicked();
CCopasiDataModel* pDataModel = mpObject->getObjectDataModel();
if (pDataModel == NULL) return;
CReportDefinition * pRep = new CReportDefinition(*dynamic_cast<CReportDefinition*>(CCopasiRootContainer::getKeyFactory()->get(mKey)));
std::string baseName = pRep->getObjectName() + "_copy";
std::string name = baseName;
int i = 1;
while (pDataModel->getReportDefinitionList()->getIndex(name) != C_INVALID_INDEX)
{
i++;
name = baseName + TO_UTF8(QString::number(i));
}
pRep->setObjectName(name);
pDataModel->getReportDefinitionList()->add(pRep, true);
std::string key = pRep->getKey();
protectedNotify(ListViews::REPORT, ListViews::ADD, key);
enter(key);
mpListView->switchToOtherWidget(C_INVALID_INDEX, key);
}
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 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);
}
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 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);
}
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 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 CQReportDefinitionSelect::loadReportDefinitionVector()
{
CCopasiDataModel* pDataModel = mpListView->getDataModel();
assert(pDataModel != NULL);
CReportDefinitionVector* pReportDefinitionVector = pDataModel->getReportDefinitionList();
unsigned C_INT32 i;
for (i = 0; i < pReportDefinitionVector->size(); i++)
mpComboDefinition->
insertItem(mpComboDefinition->count(), FROM_UTF8(pReportDefinitionVector->operator[](i).getObjectName()));
// if it is an empty list
if (mpComboDefinition->count() == 0)
{
std::string name = "ReportDefinition_0";
pDataModel->getReportDefinitionList()->createReportDefinition(name, "");
mpComboDefinition->insertItem(mpComboDefinition->count(), FROM_UTF8(name));
mpComboDefinition->setCurrentIndex(1);
mpReport->setReportDefinition(&pDataModel->getReportDefinitionList()->operator[](0)); //first one report definition
mpReport->setAppend(mpCheckAppend->isChecked());
mpReport->setConfirmOverwrite(mpCheckConfirmOverwrite->isChecked());
mpReport->setTarget(TO_UTF8(mpEditTarget->text()));
mpListView->getDataModelGUI()->notify(ListViews::REPORT, ListViews::CHANGE, ""); //notify Table Definition to
if (CQMessageBox::question(NULL, "No Report Template Defined",
"No report definition defined, COPASI has already created a new one for you.\n Do you want to switch to the GUI to edit it?",
QMessageBox::Ok | QMessageBox::No, QMessageBox::Ok) == QMessageBox::Ok)
slotEdit();
return;
}
if (!mpReport->getReportDefinition())
{
C_INT32 row;
row = mpComboDefinition->currentIndex();
mpReport->setReportDefinition(&pReportDefinitionVector->operator[](row));
mpReport->setAppend(mpCheckAppend->isChecked());
mpReport->setConfirmOverwrite(mpCheckConfirmOverwrite->isChecked());
mpReport->setTarget(TO_UTF8(mpEditTarget->text()));
return;
}
else
{
C_INT32 i;
// no use to compare the last one
for (i = mpComboDefinition->count() - 1; i >= 1; i--)
if (mpComboDefinition->itemText(i) == FROM_UTF8(mpReport->getReportDefinition()->getObjectName()))
break;
mpComboDefinition->setCurrentIndex(i);
mpCheckAppend->setChecked(mpReport->append());
mpCheckConfirmOverwrite->setChecked(mpReport->confirmOverwrite());
mpEditTarget->setText(FROM_UTF8(mpReport->getTarget()));
}
}
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);
}
void CQReportDefinitionSelect::slotEdit()
{
CCopasiDataModel* pDataModel = mpListView->getDataModel();
assert(pDataModel != NULL);
CReportDefinitionVector* pReportDefinitionVector = pDataModel->getReportDefinitionList();
C_INT32 row;
row = mpComboDefinition->currentIndex();
mpListView->switchToOtherWidget(C_INVALID_INDEX, pReportDefinitionVector->operator[](row).getKey());
accept(); // if shown then close
mShow = false; // if not shown then close
}
/**
* Creates the Tasks for SEDML. This will always create a task running a time course
* simulation. If the parameter scan has been specified, it will be exported as well.
*/
void CSEDMLExporter::createTasks(CCopasiDataModel& dataModel, std::string & modelRef)
{
std::string modelId = modelRef.substr(0, modelRef.length() - 4);
// create time course task
std::string taskId = createTimeCourseTask(dataModel, modelId);
createDataGenerators(dataModel, taskId, (*dataModel.getTaskList())["Time-Course"]);
taskId = createScanTask(dataModel, modelId);
if (!taskId.empty())
createDataGenerators(dataModel, taskId, (*dataModel.getTaskList())["Scan"]);
}
bool HistoWidget::LoadFromCurveSpec(const CPlotItem * curve)
{
if (!curve)
{
// We need to reset the widget to defaults
mpEditTitle->setText("");
mpObjectX = NULL;
mpEditVariable->setText("");
mpEditIncrement->setText("");
mpCheckBefore->setChecked(false);
mpCheckDuring->setChecked(true);
mpCheckAfter->setChecked(false);
return true;
}
if (curve->getType() != CPlotItem::histoItem1d) return false;
if (curve->getChannels().size() != 1) return false;
//title
mpEditTitle->setText(FROM_UTF8(curve->getTitle()));
//variable
mpObjectX = NULL;
CCopasiDataModel* pDataModel = mpModel->getObjectDataModel();
assert(pDataModel != NULL);
if (curve->getChannels().size() >= 1)
mpObjectX = CObjectInterface::DataObject(pDataModel->getObjectFromCN(curve->getChannels()[0]));
if (mpObjectX == pDataModel)
{
mpObjectX = NULL;
}
if (mpObjectX != NULL)
mpEditVariable->setText(FROM_UTF8(mpObjectX->getObjectDisplayName()));
else
mpEditVariable->setText("");
//other parameters:
mpEditIncrement->setText(QString::number(curve->getValue< C_FLOAT64 >("increment")));
mpCheckBefore->setChecked(curve->getActivity() & COutputInterface::BEFORE);
mpCheckDuring->setChecked(curve->getActivity() & COutputInterface::DURING);
mpCheckAfter->setChecked(curve->getActivity() & COutputInterface::AFTER);
return true; //TODO
}
void CQReportListItem::refreshText()
{
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
const CCopasiObject * pObject = pDataModel->getDataObject(mCN);
if (pObject)
setText(FROM_UTF8(pObject->getObjectDisplayName()));
else
setText(QString("Not found: ") + FROM_UTF8(mCN));
}
// virtual
void CScanWidgetScan::load(const CCopasiParameterGroup * pItem)
{
if (pItem == NULL) return;
*mpData = *pItem;
void * tmp;
if (!(tmp = mpData->getValue("Type").pVOID)) return;
CScanProblem::Type type = *(CScanProblem::Type*)tmp;
if (type != CScanProblem::SCAN_LINEAR)
return;
if (!(tmp = mpData->getValue("Number of steps").pVOID)) return;
lineEditNumber->setText(QString::number(*(C_INT32*)tmp));
if (!(tmp = mpData->getValue("Object").pVOID)) return;
std::string tmpString = *(std::string*)tmp;
if (tmpString == "")
mpObject = NULL;
else
{
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
mpObject = pDataModel->getDataObject(tmpString);
}
if (mpObject)
lineEditObject->setText(FROM_UTF8(mpObject->getObjectDisplayName()));
else
lineEditObject->setText("");
if (!(tmp = mpData->getValue("Minimum").pVOID)) return;
lineEditMin->setText(QString::number(*(C_FLOAT64*)tmp));
if (!(tmp = mpData->getValue("Maximum").pVOID)) return;
lineEditMax->setText(QString::number(*(C_FLOAT64*)tmp));
if (!(tmp = mpData->getValue("log").pVOID)) return;
checkBoxLog->setChecked(*(bool*)tmp);
return;
}
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());
}
/**
* Set whether the steady state analysis is requested.
* @param bool * steadyStateRequested
*/
void CLNAProblem::setSteadyStateRequested(const bool & steadyStateRequested)
{
CSteadyStateTask * pSubTask = NULL;
CCopasiDataModel* pDataModel = getObjectDataModel();
assert(pDataModel != NULL);
if (pDataModel && pDataModel->getTaskList())
pSubTask = dynamic_cast<CSteadyStateTask *>((*pDataModel->getTaskList())["Steady-State"]);
if (steadyStateRequested && pSubTask)
setValue("Steady-State", pSubTask->getKey());
else
setValue("Steady-State", std::string(""));
}
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;
}
bool CScanWidgetRandom::initFromScanItem(CCopasiParameterGroup * pg, const CModel* model)
{
if (!model) return false;
mpModel = model;
unsigned C_INT32 * tmp;
if (!(tmp = pg->getValue("Type").pUINT)) return false;
if (*(CScanProblem::Type *) tmp != CScanProblem::SCAN_RANDOM)
return false;
std::string *pString;
if (!(pString = pg->getValue("Object").pSTRING)) return false;
if (*pString == "")
mpObject = NULL;
else
{
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
mpObject = pDataModel->getObject(*pString);
}
if (mpObject)
lineEditObject->setText(FROM_UTF8(mpObject->getObjectDisplayName()));
else
lineEditObject->setText("");
if (!(tmp = pg->getValue("Distribution type").pUINT)) return false;
comboBoxType->setCurrentItem(*tmp);
changeType();
lineEditMin->setText(getParameterValue(pg, "Minimum"));
lineEditMax->setText(getParameterValue(pg, "Maximum"));
bool * pBool;
if (!(pBool = pg->getValue("log").pBOOL)) return false;
checkBoxLog->setChecked(* pBool);
return true;
}
void DataModelGUI::linkDataModelToGUI()
{
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
std::set< ListViews * >::iterator it = mListViews.begin();
std::set< ListViews * >::iterator end = mListViews.end();
for (; it != end; ++it)
{
(*it)->setDataModel(this);
}
pDataModel->deleteOldData();
}
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();
}
/**
* Creates the simulations for SEDML.
*/
std::string CSEDMLExporter::createTimeCourseTask(CCopasiDataModel& dataModel, const std::string & modelId)
{
mpTimecourse = this->mpSEDMLDocument->createUniformTimeCourse();
mpTimecourse->setId(SEDMLUtils::getNextId("sim", mpSEDMLDocument->getNumSimulations()));
//presently SEDML only supports time course
CCopasiTask* pTask = (*dataModel.getTaskList())["Time-Course"];
CTrajectoryProblem* tProblem = static_cast<CTrajectoryProblem*>(pTask->getProblem());
mpTimecourse->setInitialTime(0.0);
mpTimecourse->setOutputStartTime(tProblem->getOutputStartTime());
mpTimecourse->setOutputEndTime(tProblem->getStepNumber()*tProblem->getStepSize());
mpTimecourse->setNumberOfPoints(tProblem->getStepNumber());
// set the correct KISAO Term
SedAlgorithm* alg = mpTimecourse->createAlgorithm();
if (pTask->getMethod()->getObjectName().find("Stochastic") != std::string::npos)
alg->setKisaoID("KISAO:0000241");
else
alg->setKisaoID("KISAO:0000019");
mpTimecourseTask = this->mpSEDMLDocument->createTask();
std::string taskId = SEDMLUtils::getNextId("task", mpSEDMLDocument->getNumTasks());
mpTimecourseTask->setId(taskId);
mpTimecourseTask->setSimulationReference(mpTimecourse->getId());
mpTimecourseTask->setModelReference(modelId);
return taskId;
}
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());
}
}
}
