Merge branch 'release/Version-4.43' into develop

copasi/CopasiDataModel/CDataModel.cpp

@@ -82,12 +82,12 @@ LIBCOMBINE_CPP_NAMESPACE_USE
 
 // static
 const CEnumAnnotation< std::string, CDataModel::ContentType >
-CDataModel::ContentTypeNames( {"COPASI",
-  "GEPASI",
-  "SBML",
-  "SED-ML",
-  "OMEX"
-});
+CDataModel::ContentTypeNames({"COPASI",
+                              "GEPASI",
+                              "SBML",
+                              "SED-ML",
+                              "OMEX"
+                             });
 
 // static
 CDataModel::ContentType CDataModel::contentType(std::istream & content)
@@ -257,11 +257,6 @@ CDataModel::~CDataModel()
   CRegisteredCommonName::setEnabled(true);
 }
 
-CRegisteredCommonName CDataModel::registeredCN(const std::string & CN) const
-{
-  return CRegisteredCommonName(CN, this);
-}
-
 bool CDataModel::loadFromString(const std::string & content,
                                 std::string referenceDir,
                                 CProcessReport * pProcessReport,
@@ -717,9 +712,9 @@ bool CDataModel::loadModelParameterSets(const std::string & fileName,
   CDataVectorN< CModelParameterSet > & loadedSet = parameterSetModel->getModelParameterSets();
   CCommonName loadedModelCn = parameterSetModel->getStringCN();
 
-for (CModelParameterSet & set : loadedSet)
+  for (CModelParameterSet & set : loadedSet)
     {
-for (CModelParameter * current : dynamic_cast< CModelParameterGroup & >(set))
+      for (CModelParameter * current : dynamic_cast< CModelParameterGroup & >(set))
         {
           replaceCnInGroup(current, loadedModelCn, thisModelsCn);
         }
@@ -762,7 +757,7 @@ void CDataModel::replaceCnInGroup(CModelParameter * pParam,
   if (!group)
     return;
 
-for (CModelParameter * element : *group)
+  for (CModelParameter * element : *group)
     {
       CModelParameterGroup * inside = dynamic_cast< CModelParameterGroup * >(element);
 
@@ -2047,7 +2042,7 @@ void addMessages(const std::string & title, std::stringstream & messageStream, c
 
   messageStream << "\n";
 
-for (auto & message : messages)
+  for (auto & message : messages)
     {
       auto startPos = message.getText().find_first_of("\n");
       auto text = message.getText().substr(startPos + 1);
@@ -2783,7 +2778,7 @@ CReportDefinition * CDataModel::addReport(const CTaskEnum::Task & taskType)
         pReport->getFooterAddr()->push_back(CRegisteredCommonName("CN=Root,Vector=TaskList[Optimization],Object=Result", this));
         break;
 
-        //**************************************************************************
+      //**************************************************************************
       case CTaskEnum::Task::parameterFitting:
         pReport = new CReportDefinition(CTaskEnum::TaskName[taskType]);
         pReport->setTaskType(taskType);
@@ -2812,7 +2807,7 @@ CReportDefinition * CDataModel::addReport(const CTaskEnum::Task & taskType)
         pReport->getFooterAddr()->push_back(CRegisteredCommonName("CN=Root,Vector=TaskList[Parameter Estimation],Object=Result", this));
         break;
 
-        //**************************************************************************
+      //**************************************************************************
       case CTaskEnum::Task::lyap:
         pReport = new CReportDefinition(CTaskEnum::TaskName[taskType]);
         pReport->setTaskType(taskType);
@@ -2829,7 +2824,7 @@ CReportDefinition * CDataModel::addReport(const CTaskEnum::Task & taskType)
         pReport->getFooterAddr()->push_back(CRegisteredCommonName("CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Result", this));
         break;
 
-        //**************************************************************************
+      //**************************************************************************
       case CTaskEnum::Task::mca:
         pReport = new CReportDefinition(CTaskEnum::TaskName[taskType]);
         pReport->setTaskType(taskType);
@@ -2846,7 +2841,7 @@ CReportDefinition * CDataModel::addReport(const CTaskEnum::Task & taskType)
         pReport->getFooterAddr()->push_back(CRegisteredCommonName("CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Result", this));
         break;
 
-        //**************************************************************************
+      //**************************************************************************
       case CTaskEnum::Task::lna:
         pReport = new CReportDefinition(CTaskEnum::TaskName[taskType]);
         pReport->setTaskType(taskType);
@@ -2863,7 +2858,7 @@ CReportDefinition * CDataModel::addReport(const CTaskEnum::Task & taskType)
         pReport->getFooterAddr()->push_back(CRegisteredCommonName("CN=Root,Vector=TaskList[Linear Noise Approximation],Object=Result", this));
         break;
 
-        //**************************************************************************
+      //**************************************************************************
       case CTaskEnum::Task::sens:
         pReport = new CReportDefinition(CTaskEnum::TaskName[taskType]);
         pReport->setTaskType(taskType);
@@ -2880,7 +2875,7 @@ CReportDefinition * CDataModel::addReport(const CTaskEnum::Task & taskType)
         pReport->getFooterAddr()->push_back(CRegisteredCommonName("CN=Root,Vector=TaskList[Sensitivities],Object=Result", this));
         break;
 
-        //**************************************************************************
+      //**************************************************************************
       case CTaskEnum::Task::tssAnalysis:
         pReport = new CReportDefinition(CTaskEnum::TaskName[taskType]);
         pReport->setTaskType(taskType);

copasi/CopasiDataModel/CDataModel.h

@@ -191,16 +191,6 @@ class CDataModel: public CDataContainer, public COutputHandler
 
   virtual ~CDataModel();
 
-  /**
-   * resolves the given CN string in this dataModel to a
-   * registered common name
-   *
-   * @param CN the CN to resolve
-   *
-   * @return a registered common name for the CN
-   */
-  CRegisteredCommonName registeredCN(const std::string & CN) const;
-
   /**
    * Load the model from the content which may be any supported type
    * @param const std::string & content

copasi/UI/CQBrowserPaneDM.cpp

@@ -738,7 +738,7 @@ bool CQBrowserPaneDM::slotNotify(ListViews::ObjectType objectType, ListViews::Ac
       pNode = findNodeFromCN(cn);
     }
 
-  std::string NewCN = pNode != NULL ? pNode->getCN() : cn;
+  CRegisteredCommonName NewCN = pNode != NULL ? pNode->getCN() : cn;
 
   if (cn != NewCN)
     {

copasi/UI/CQEventWidget1.cpp

@@ -501,7 +501,7 @@ void CQEventWidget1::slotSelectObject()
   if (pObject == NULL)
     return;
 
-  if (mAssignments[mCurrentTarget].setTargetCN(pObject->getStringCN()))
+  if (mAssignments[mCurrentTarget].setTargetCN(pObject->getCN()))
     {
       // If the target key change was successful we need to update the label.
       mpLBTarget->item((int) mCurrentTarget)->setText(FROM_UTF8(pObject->getObjectDisplayName()));

copasi/UI/CQExperimentData.cpp

@@ -1554,7 +1554,7 @@ bool CQExperimentData::saveTable(CExperiment * pExperiment)
 
       if (ObjectMap.getObjectCN(i) != TO_UTF8(mpTable->item((int) i, COL_OBJECT_HIDDEN)->text()))
         {
-          ObjectMap.setObjectCN(i, TO_UTF8(mpTable->item((int) i, COL_OBJECT_HIDDEN)->text()));
+          ObjectMap.setObjectCN(i, CRegisteredCommonName(TO_UTF8(mpTable->item((int) i, COL_OBJECT_HIDDEN)->text()), mpDataModel));
           Changed = true;
         }
 

copasi/UI/CQFittingItemWidget.cpp

@@ -149,14 +149,14 @@ void CQFittingItemWidget::slotCheckLowerInf(bool checked)
       mpCheckLowerInf->setStyleSheet(QString(mpCheckLowerInf->metaObject()->className()) + " {background-color:" + mSavedColor.name() + ";}");
     }
 
-  std::string Number;
+  CRegisteredCommonName Number;
 
   if (checked)
-    Number = "-inf";
+    Number = CRegisteredCommonName("-inf", nullptr);
   else if (isNumber(TO_UTF8(mpEditLower->text())))
-    Number = TO_UTF8(mpEditLower->text());
+    Number = CRegisteredCommonName(TO_UTF8(mpEditLower->text()), nullptr);
   else if (mpLowerObject)
-    Number = mpLowerObject->getStringCN();
+    Number = mpLowerObject->getCN();
   else return;
 
   std::set< size_t >::const_iterator it = mSelection.begin();
@@ -185,14 +185,14 @@ void CQFittingItemWidget::slotCheckUpperInf(bool checked)
       mpCheckUpperInf->setStyleSheet(QString(mpCheckUpperInf->metaObject()->className()) + " {background-color:" + mSavedColor.name() + ";}");
     }
 
-  std::string Number;
+  CRegisteredCommonName Number;
 
   if (checked)
-    Number = "inf";
+    Number = CRegisteredCommonName("inf", nullptr);
   else if (isNumber(TO_UTF8(mpEditUpper->text())))
-    Number = TO_UTF8(mpEditUpper->text());
+    Number = CRegisteredCommonName(TO_UTF8(mpEditUpper->text()), nullptr);
   else if (mpUpperObject)
-    Number = mpUpperObject->getStringCN();
+    Number = mpUpperObject->getCN();
   else return;
 
   std::set< size_t >::const_iterator it = mSelection.begin();
@@ -245,7 +245,7 @@ void CQFittingItemWidget::slotLowerEdit()
       std::set< size_t >::const_iterator it = mSelection.begin();
       std::set< size_t >::const_iterator end = mSelection.end();
       mpLowerObject = pObject;
-      CCommonName CN = mpLowerObject->getStringCN();
+      CRegisteredCommonName CN = mpLowerObject->getCN();
 
       for (; it != end; ++it)
         {
@@ -299,7 +299,7 @@ void CQFittingItemWidget::slotUpperEdit()
       std::set< size_t >::const_iterator it = mSelection.begin();
       std::set< size_t >::const_iterator end = mSelection.end();
       mpUpperObject = pObject;
-      CCommonName CN = mpUpperObject->getStringCN();
+      CRegisteredCommonName CN = mpUpperObject->getCN();
 
       for (; it != end; ++it)
         {
@@ -419,7 +419,7 @@ void CQFittingItemWidget::slotParamEdit()
 
       for (; it != end; ++it)
         {
-          (*mpItemsCopy)[*it]->setObjectCN(Selection[0]->getStringCN());
+          (*mpItemsCopy)[*it]->setObjectCN(Selection[0]->getCN());
           setTableText((int) *it, (*mpItemsCopy)[*it]);
         }
 
@@ -449,7 +449,7 @@ void CQFittingItemWidget::slotParamEdit()
                 break;
             }
 
-          pItem->setObjectCN(Selection[i]->getStringCN());
+          pItem->setObjectCN(Selection[i]->getCN());
           // Add the new item to the list.
           mpItemsCopy->insert(mpItemsCopy->begin() + current + i, pItem);
           // Update the table
@@ -1430,14 +1430,14 @@ void CQFittingItemWidget::saveSelection()
       pItem = (*mpItemsCopy)[*it];
 
       if (mpCheckLowerInf->isChecked())
-        pItem->setLowerBound(CCommonName("-inf"));
+        pItem->setLowerBound(CRegisteredCommonName("-inf", nullptr));
       else if (isNumber(TO_UTF8(mpEditLower->text())))
-        pItem->setLowerBound(CCommonName(TO_UTF8(mpEditLower->text())));
+        pItem->setLowerBound(CRegisteredCommonName(TO_UTF8(mpEditLower->text()), nullptr));
 
       if (mpCheckUpperInf->isChecked())
-        pItem->setUpperBound(CCommonName("inf"));
+        pItem->setUpperBound(CRegisteredCommonName("inf", nullptr));
       else if (isNumber(TO_UTF8(mpEditUpper->text())))
-        pItem->setUpperBound(CCommonName(TO_UTF8(mpEditUpper->text())));
+        pItem->setUpperBound(CRegisteredCommonName(TO_UTF8(mpEditUpper->text()), nullptr));
 
       if (isNumber(TO_UTF8(mpEditStart->text())))
         pItem->setStartValue(mpEditStart->text().toDouble());
@@ -1508,7 +1508,7 @@ void CQFittingItemWidget::slotLowerLostFocus()
 
   for (; it != end; ++it)
     {
-      (*mpItemsCopy)[*it]->setLowerBound(Number);
+      (*mpItemsCopy)[*it]->setLowerBound(CRegisteredCommonName(Number, nullptr));
 
       if (first)
         {
@@ -1541,7 +1541,7 @@ void CQFittingItemWidget::slotUpperLostFocus()
 
   for (; it != end; ++it)
     {
-      (*mpItemsCopy)[*it]->setUpperBound(Number);
+      (*mpItemsCopy)[*it]->setUpperBound(CRegisteredCommonName(Number, nullptr));
 
       if (first)
         {

copasi/UI/CQParameterGroupView.cpp

@@ -240,7 +240,7 @@ void CQParameterGroupView::modifySelectCNs(CCopasiParameterGroup & group, const
 
   for (; itNew != endNew; ++itNew)
     {
-      group.addParameter("Reaction", CCopasiParameter::Type::CN, (*itNew)->getStringCN());
+      group.addParameter("Reaction", CCopasiParameter::Type::CN, (*itNew)->getCN());
     }
 
   mpParameterGroupDM->endResetModel();

copasi/UI/SensitivitiesWidget.cpp

@@ -323,10 +323,9 @@ SensitivitiesWidget::initCombos()
   // SubTaskChooser combo
   int i = 0;
 
-  while (CSensProblem::SubTaskName[i].length() > 0)
+  for (int i = 0; i < CSensProblem::SubTaskType::__SIZE; ++i)
     {
-      StringList.append(FROM_UTF8(CSensProblem::SubTaskName[i]));
-      ++i;
+      StringList.append(FROM_UTF8(CTaskEnum::TaskName[CSensProblem::SubTaskTypeToTask[i]]));
     }
 
   SubTaskChooser->insertItems(SubTaskChooser->count(), StringList);

copasi/analytics/CAnalyticsProblem.cpp

@@ -77,7 +77,7 @@ void CAnalyticsProblem::initializeParameter()
   mpFlagLimitOutConvergence = assertParameter("DelayOutputUntilConvergence", CCopasiParameter::Type::BOOL, false);
   mpConvergenceOutTolerance = assertParameter("OutputConvergenceTolerance", CCopasiParameter::Type::DOUBLE, (C_FLOAT64)1E-6);
   mpTriggerExpression = assertParameter("TriggerExpression", CCopasiParameter::Type::EXPRESSION, std::string(""));
-  mpSingleObjectCN = assertParameter("SingleVariable", CCopasiParameter::Type::CN, CRegisteredCommonName(""));
+  mpSingleObjectCN = assertParameter("SingleVariable", CCopasiParameter::Type::CN, CRegisteredCommonName());
   setOutputEvent(false);
 }
 

copasi/bindings/cpp_examples/example5/example5.cpp

@@ -141,12 +141,12 @@ int main()
   // now we create the optimization items
   // i.e. the model elements that have to be changed during the optimization
   // in order to get to the optimal solution
-  COptItem* pOptItem = &pOptProblem->addOptItem(CCommonName(pFixedModelValue->getObject(CCommonName("Reference=InitialValue"))->getCN()));
+  COptItem* pOptItem = &pOptProblem->addOptItem(pFixedModelValue->getObject(CCommonName("Reference=InitialValue"))->getCN());
   // we want to change the fixed model value from -100 to +100 with a start
   // value of 50
   pOptItem->setStartValue(50.0);
-  pOptItem->setLowerBound(CCommonName("-100"));
-  pOptItem->setUpperBound(CCommonName("100"));
+  pOptItem->setLowerBound(-100);
+  pOptItem->setUpperBound(100);
 
   // now we set some parameters on the method
   // these parameters are specific to the method type we set above

copasi/bindings/cpp_examples/example6/example6.cpp

@@ -1,4 +1,9 @@
-// Copyright (C) 2017 by Pedro Mendes, Virginia Tech Intellectual
+// Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the
+// University of Virginia, University of Heidelberg, and University
+// of Connecticut School of Medicine.
+// All rights reserved.
+
+// Copyright (C) 2017 - 2018 by Pedro Mendes, Virginia Tech Intellectual
 // Properties, Inc., University of Heidelberg, and University of
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -367,8 +372,8 @@ int main()
   pFitItem1->setObjectCN(pParameterReference->getCN());
   assert(pFitItem1 != NULL);
   pFitItem1->setStartValue(4.0);
-  pFitItem1->setLowerBound(CCommonName("0.00001"));
-  pFitItem1->setUpperBound(CCommonName("10"));
+  pFitItem1->setLowerBound(0.00001);
+  pFitItem1->setUpperBound(10);
   // add the fit item
   pOptimizationItemGroup->addParameter(pFitItem1);
 
@@ -385,8 +390,8 @@ int main()
   pFitItem2->setObjectCN(pParameterReference->getCN());
   assert(pFitItem2 != NULL);
   pFitItem2->setStartValue(4.0);
-  pFitItem2->setLowerBound(CCommonName("0.00001"));
-  pFitItem2->setUpperBound(CCommonName("10"));
+  pFitItem2->setLowerBound(0.00001);
+  pFitItem2->setUpperBound(10);
   // add the fit item
   pOptimizationItemGroup->addParameter(pFitItem2);
 

copasi/bindings/swig/CCopasiParameter.i

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 - 2023 by Pedro Mendes, Rector and Visitors of the 
+// Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the 
 // University of Virginia, University of Heidelberg, and University 
 // of Connecticut School of Medicine. 
 // All rights reserved. 
@@ -194,14 +194,14 @@
     return self->setValue(v);
   }
 
-  bool setCNValue(const CCommonName& v)
+  bool setCNValue(const CRegisteredCommonName & v)
   {
     return self->setValue(v);
   }
 
-  bool setCNValue(const std::string& v)
+  bool setCNValue(const std::string & v)
   {
-    return self->setValue(CCommonName(v));
+    return self->setValue(CRegisteredCommonName(v));
   }
 
   bool setKeyValue(const std::string& v)

copasi/bindings/swig/COptItem.i

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 - 2023 by Pedro Mendes, Rector and Visitors of the 
+// Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the 
 // University of Virginia, University of Heidelberg, and University 
 // of Connecticut School of Medicine. 
 // All rights reserved. 
@@ -71,6 +71,16 @@
         return v;
     }
 
+    bool setLowerBound(const std::string & v)
+    {
+      return self->setLowerBound(CRegisteredCommonName(v));
+    }
+
+    bool setUpperBound(const std::string & v)
+    {
+      return self->setUpperBound(CRegisteredCommonName(v));
+    }
+
     CFitItem* asFitItem()
     {
       return dynamic_cast<CFitItem*>($self);