Use \n instead of std::endl to avoid flushing of stream.

copasi/MIRIAM/CMIRIAMResource.cpp

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 - 2022 by Pedro Mendes, Rector and Visitors of the
+// Copyright (C) 2019 - 2025 by Pedro Mendes, Rector and Visitors of the
 // University of Virginia, University of Heidelberg, and University
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -31,9 +31,12 @@
 #include "CRDFTriplet.h"
 #include "CRDFNode.h"
 
+#include "copasi/commandline/COptions.h"
 #include "copasi/utilities/CCopasiException.h"
+#include "copasi/utilities/CDirEntry.h"
 #include "copasi/core/CRootContainer.h"
 #include "copasi/commandline/CConfigurationFile.h"
+#include "copasi/xml/CGroupXML.h"
 
 #include <sbml/xml/XMLNode.h>
 #include <sbml/xml/XMLAttributes.h>
@@ -298,6 +301,31 @@ const CMIRIAMResources & CMIRIAMResources::operator=(const CCopasiParameterGroup
   return *this;
 }
 
+bool CMIRIAMResources::save()
+{
+  std::string FileName = COptions::getConfigDir() + CDirEntry::Separator + "MIRIAMResources.xml";
+  CGroupXML XML(*this);
+
+  bool success = XML.CCopasiXMLInterface::save(FileName, CDirEntry::dirName(FileName));
+
+  return success;
+}
+
+bool CMIRIAMResources::load()
+{
+  std::string FileName = COptions::getConfigDir() + CDirEntry::Separator + "MIRIAMResources.xml";
+
+  CMIRIAMResource Loaded;
+  CGroupXML XML(Loaded);
+
+  bool success = XML.CCopasiXMLInterface::save(FileName, CDirEntry::dirName(FileName));
+
+  if (success)
+    *this = Loaded;
+
+  return success;
+}
+
 void CMIRIAMResources::createDisplayNameMap()
 {
   mDisplayName2Resource.clear();

copasi/MIRIAM/CMIRIAMResource.h

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the
+// Copyright (C) 2019 - 2025 by Pedro Mendes, Rector and Visitors of the
 // University of Virginia, University of Heidelberg, and University
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -263,6 +263,18 @@ class CMIRIAMResources : public CCopasiParameterGroup
    */
   virtual bool elevateChildren();
 
+  /**
+   * Save the configuration file.
+   * @return bool success
+   */
+  virtual bool save();
+
+  /**
+   * Load the configuration file.
+   * @return bool success
+   */
+  virtual bool load();
+
   /**
    * Assignment operator
    * @param const CCopasiParameterGroup & rhs

copasi/MIRIAM/CRDFPredicate.cpp

@@ -1,22 +1,22 @@
-// 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. 
-
-// Copyright (C) 2010 - 2016 by Pedro Mendes, Virginia Tech Intellectual 
-// Properties, Inc., University of Heidelberg, and The University 
-// of Manchester. 
-// All rights reserved. 
-
-// Copyright (C) 2008 - 2009 by Pedro Mendes, Virginia Tech Intellectual 
-// Properties, Inc., EML Research, gGmbH, University of Heidelberg, 
-// and The University of Manchester. 
-// All rights reserved. 
+// Copyright (C) 2019 - 2025 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.
+
+// Copyright (C) 2010 - 2016 by Pedro Mendes, Virginia Tech Intellectual
+// Properties, Inc., University of Heidelberg, and The University
+// of Manchester.
+// All rights reserved.
+
+// Copyright (C) 2008 - 2009 by Pedro Mendes, Virginia Tech Intellectual
+// Properties, Inc., EML Research, gGmbH, University of Heidelberg,
+// and The University of Manchester.
+// All rights reserved.
 
 #include "copasi/copasi.h"
 
@@ -149,7 +149,6 @@ const std::string CRDFPredicate::PredicatePrefix[] =
     "end"    // end
 };
 
-
 // static
 std::map< std::string, CRDFPredicate::ePredicateType > CRDFPredicate::URI2Predicate;
 
@@ -627,7 +626,7 @@ std::string CRDFPredicate::getElementNameForType(ePredicateType type)
 {
   if (type < copasi_encodes || type >= unknown)
     return std::string();
-  
+
   return PredicatePrefix[type];
 }
 
@@ -822,15 +821,15 @@ std::ostream & operator << (std::ostream & os, const CRDFPredicate::Path & path)
   for (; it != end; ++it)
     os << *it << " ";
 
-  return os << std::endl;
+  return os << "\n";
 }
 
 std::ostream & operator << (std::ostream & os, const CRDFPredicate::sAllowedLocation & location)
 {
-  os << "MaxOccurance: " << location.MaxOccurance << std::endl;
-  os << "ReadOnly: " << location.ReadOnly << std::endl;
-  os << "Type: " << location.Type << std::endl;
-  os << location.Location << std::endl;
+  os << "MaxOccurance: " << location.MaxOccurance << "\n";
+  os << "ReadOnly: " << location.ReadOnly << "\n";
+  os << "Type: " << location.Type << "\n";
+  os << location.Location << "\n";
 
   return os;
 }

copasi/MIRIAM/CRDFTriplet.cpp

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 by Pedro Mendes, Rector and Visitors of the
+// Copyright (C) 2019 - 2025 by Pedro Mendes, Rector and Visitors of the
 // University of Virginia, University of Heidelberg, and University
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -61,10 +61,10 @@ std::ostream & operator << (std::ostream & os, const CRDFTriplet & triplet)
     {
       os << triplet.pSubject->getSubject() << ", ";
       os << triplet.Predicate.getURI() << ", ";
-      os << triplet.pObject->getObject() << std::endl;
+      os << triplet.pObject->getObject() << "\n";
     }
   else
-    os << "Invalid Triplet" << std::endl;
+    os << "Invalid Triplet" << "\n";
 
   return os;
 }

copasi/UI/CQBrowserPaneDM.cpp

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the
+// Copyright (C) 2019 - 2025 by Pedro Mendes, Rector and Visitors of the
 // University of Virginia, University of Heidelberg, and University
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -1220,12 +1220,12 @@ int CQBrowserPaneDM::CNode::getRow() const
 
 std::ostream & operator<<(std::ostream &os, const CQBrowserPaneDM::CNode & n)
 {
-  os << "CQBrowserPaneDM::CNode:" << std::endl;
-  //os << "   mChemicalEquation:          " << d.getChemicalEquation() << std::endl;
-  //os << "   mChemicalEquationConverted: " << d.getChemicalEquationConverted() << std::endl;
+  os << "CQBrowserPaneDM::CNode:" << "\n";
+  //os << "   mChemicalEquation:          " << d.getChemicalEquation() << "\n";
+  //os << "   mChemicalEquationConverted: " << d.getChemicalEquationConverted() << "\n";
 
-  os << "   mId:          " << (size_t) n.mData.mId << std::endl;
-  os << "   mCN:          " << n.mData.mCN << std::endl;
-  os << "   mDisplayRole: " << TO_UTF8(n.mData.mDisplayRole) << std::endl;
+  os << "   mId:          " << (size_t) n.mData.mId << "\n";
+  os << "   mCN:          " << n.mData.mCN << "\n";
+  os << "   mDisplayRole: " << TO_UTF8(n.mData.mDisplayRole) << "\n";
   return os;
 }

copasi/UI/CQDifferentialEquations.cpp

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 - 2021 by Pedro Mendes, Rector and Visitors of the
+// Copyright (C) 2019 - 2025 by Pedro Mendes, Rector and Visitors of the
 // University of Virginia, University of Heidelberg, and University
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -93,13 +93,13 @@ void CQDifferentialEquations::saveMML(const QString& outfilename)
   std::ofstream ofile;
   ofile.open(CLocaleString::fromUtf8(TO_UTF8(outfilename)).c_str(), std::ios::trunc);
 
-  ofile << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" << std::endl;
-  ofile << "<!DOCTYPE math PUBLIC \"-//W3C//DTD MathML 2.0//EN\" \"http://www.w3.org/Math/DTD/mathml2/mathml2.dtd\">" << std::endl;
-  ofile << "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">" << std::endl;
+  ofile << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" << "\n";
+  ofile << "<!DOCTYPE math PUBLIC \"-//W3C//DTD MathML 2.0//EN\" \"http://www.w3.org/Math/DTD/mathml2/mathml2.dtd\">" << "\n";
+  ofile << "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">" << "\n";
 
   ofile << mml.str();
 
-  ofile << "</math>" << std::endl;
+  ofile << "</math>" << "\n";
 
   ofile.close();
 }

copasi/UI/CQExpressionMmlStackedWidget.cpp

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 - 2023 by Pedro Mendes, Rector and Visitors of the
+// Copyright (C) 2019 - 2025 by Pedro Mendes, Rector and Visitors of the
 // University of Virginia, University of Heidelberg, and University
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -165,7 +165,6 @@ void CQExpressionMmlStackedWidget::reset()
   mpExpressionWidget->setExpression("");
 
   updateWidget();
-
 }
 
 void CQExpressionMmlStackedWidget::init()
@@ -271,13 +270,13 @@ void CQExpressionMmlStackedWidget::saveMML(const QString& outfilename)
   std::ofstream ofile;
   ofile.open(CLocaleString::fromUtf8(TO_UTF8(outfilename)).c_str(), std::ios::trunc);
 
-  ofile << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" << std::endl;
-  ofile << "<!DOCTYPE math PUBLIC \"-//W3C//DTD MathML 2.0//EN\" \"http://www.w3.org/Math/DTD/mathml2/mathml2.dtd\">" << std::endl;
-  ofile << "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">" << std::endl;
+  ofile << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" << "\n";
+  ofile << "<!DOCTYPE math PUBLIC \"-//W3C//DTD MathML 2.0//EN\" \"http://www.w3.org/Math/DTD/mathml2/mathml2.dtd\">" << "\n";
+  ofile << "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">" << "\n";
 
   mpExpressionWidget->writeMathML(ofile);
 
-  ofile << "</math>" << std::endl;
+  ofile << "</math>" << "\n";
 
   ofile.close();
 }

copasi/UI/CQExpressionWidget.cpp

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the
+// Copyright (C) 2019 - 2025 by Pedro Mendes, Rector and Visitors of the
 // University of Virginia, University of Heidelberg, and University
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -60,11 +60,11 @@
 #ifdef DEBUG_UI
 std::ostream & operator<<(std::ostream & os, const QTextCursor & d)
 {
-  os << "Position:        " << d.position() << std::endl;
-  os << "Selection Start: " << d.selectionStart() << std::endl;
-  os << "Selection End:   " << d.selectionEnd() << std::endl;
-  os << "Anchor:          " << d.anchor() << std::endl;
-  os << "Selected Text:   " << TO_UTF8(d.selectedText()) << std::endl;
+  os << "Position:        " << d.position() << "\n";
+  os << "Selection Start: " << d.selectionStart() << "\n";
+  os << "Selection End:   " << d.selectionEnd() << "\n";
+  os << "Anchor:          " << d.anchor() << "\n";
+  os << "Selected Text:   " << TO_UTF8(d.selectedText()) << "\n";
   return os;
 }
 #endif // DEBUG_UI

copasi/UI/CQOptimizationResult.cpp

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the
+// Copyright (C) 2019 - 2025 by Pedro Mendes, Rector and Visitors of the
 // University of Virginia, University of Heidelberg, and University
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -222,38 +222,38 @@ void CQOptimizationResult::slotSave(void)
   if (file.fail()) return;
 
   // The global result and statistics
-  file << "Objective Value" << std::endl;
-  file << mpProblem->getSolutionValue() << std::endl;
+  file << "Objective Value" << "\n";
+  file << mpProblem->getSolutionValue() << "\n";
 
-  file << "Function Evaluations\tCPU Time [s]\tEvaluations/second [1/s]" << std::endl;
+  file << "Function Evaluations\tCPU Time [s]\tEvaluations/second [1/s]" << "\n";
   const size_t & FunctionEvaluations = mpProblem->getFunctionEvaluations();
   const C_FLOAT64 & ExecutionTime = mpProblem->getExecutionTime();
   file << FunctionEvaluations << "\t";
   file << ExecutionTime << "\t";
-  file << FunctionEvaluations / ExecutionTime << std::endl << std::endl;
+  file << FunctionEvaluations / ExecutionTime << "\n" << "\n";
 
   // Set up the parameters table
-  file << "Parameters:" << std::endl;
+  file << "Parameters:" << "\n";
   file << TO_UTF8(toTsvString(mpParameters->model(), true, false))
-       << std::endl;
+       << "\n";
 
   // log
   const COptMethod * pMethod = dynamic_cast<const COptMethod *>(mpTask->getMethod());
 
   if (pMethod)
     {
 
-      file << std::endl;
+      file << "\n";
 
       // Set up log output
-      file << "Method Log:" << std::endl;
+      file << "Method Log:" << "\n";
 
       file << pMethod->getMethodLog().getPlainLog().c_str();
 
-      file << std::endl;
+      file << "\n";
     }
 
-  file << std::endl;
+  file << "\n";
 }
 
 void CQOptimizationResult::slotUpdateModel()