From 1b7b206cae69001c80bad8d17bb0c42f5a01e576 Mon Sep 17 00:00:00 2001
From: "Frank T. Bergmann" <fbergman@caltech.edu>
Date: Wed, 4 Dec 2013 15:51:36 +0100
Subject: [PATCH] - for now flip order on load, as the simulator is still the
 old one

---
 SpatialSBML/spatialsimulator.cpp | 50 ++++++++++++++++++++++++++++++++
 SpatialSBML/spatialsimulator.h   |  7 +++++
 SpatialUI/geometryeditwidget.cpp | 48 ++----------------------------
 SpatialUI/spatialmainwidget.cpp  |  3 +-
 4 files changed, 61 insertions(+), 47 deletions(-)

diff --git a/SpatialSBML/spatialsimulator.cpp b/SpatialSBML/spatialsimulator.cpp
index b614972..7a3e6c9 100644
--- a/SpatialSBML/spatialsimulator.cpp
+++ b/SpatialSBML/spatialsimulator.cpp
@@ -3597,6 +3597,56 @@ const Model* SpatialSimulator::getModel() const
   return model;
 }
 
+struct sort_pair
+{
+  bool operator() (std::pair<int, int> i, std::pair<int, int> j) 
+  {
+    return (i.second < j.second);
+  }
+} sorter;
+
+
+void flipOrder(AnalyticGeometry& geometry)
+{
+  if (geometry.getNumAnalyticVolumes() == 0) return;
+
+  std::vector<std::pair<int, int>> list;
+  for (size_t i = 0; i < geometry.getNumAnalyticVolumes(); ++i)
+  {
+    AnalyticVolume* current = geometry.getAnalyticVolume(i);
+    list.push_back(std::pair<int, int>((int)i, (int)current->getOrdinal()));
+  }
+
+  std::sort(list.begin(), list.end(), sorter);
+
+  for (std::vector<std::pair<int, int>>::iterator it=list.begin(); it!=list.end(); ++it)
+  {
+    AnalyticVolume* current = geometry.getAnalyticVolume(it->first);
+    current->setOrdinal((geometry.getNumAnalyticVolumes()-1)-it->second);
+  }
+
+
+}
+
+void SpatialSimulator::flipVolumeOrder()
+{    
+  if (model == NULL)
+    return;
+  SpatialModelPlugin* plugin = dynamic_cast<SpatialModelPlugin*>(model->getPlugin("spatial"));
+  if (plugin == NULL)
+    return;
+
+  Geometry* geometry = plugin->getGeometry();
+
+  for (size_t i = 0; i < geometry->getNumGeometryDefinitions(); ++i)
+  {
+    AnalyticGeometry* definition = dynamic_cast<AnalyticGeometry*>(geometry->getGeometryDefinition(i));
+    if (definition == NULL) 
+      continue;
+    flipOrder(*definition);    
+  }
+}
+
 int SpatialSimulator::getIndexForPosition(double x, double y)
 {
     for (int Y = 0; Y < Yindex; Y += 2 ) {
diff --git a/SpatialSBML/spatialsimulator.h b/SpatialSBML/spatialsimulator.h
index c2abf66..3322f81 100644
--- a/SpatialSBML/spatialsimulator.h
+++ b/SpatialSBML/spatialsimulator.h
@@ -185,6 +185,13 @@ class SpatialSimulator
    */ 
   const Model* getModel() const;
 
+  /**
+   * flips the order of analytic volumes
+   */ 
+  void flipVolumeOrder();
+  
+
+
   /**
    * Sets the specified value uniformly on the provided variable info
    * structure. 
diff --git a/SpatialUI/geometryeditwidget.cpp b/SpatialUI/geometryeditwidget.cpp
index e4938ff..d2df1e2 100644
--- a/SpatialUI/geometryeditwidget.cpp
+++ b/SpatialUI/geometryeditwidget.cpp
@@ -267,57 +267,13 @@ void GeometryEditWidget::handleButtons(QAbstractButton * button)
 
 }
 
-struct sort_pair
-{
-  bool operator() (std::pair<int, int> i, std::pair<int, int> j) 
-  {
-    return (i.second < j.second);
-  }
-} sorter;
-
-void flipOrder(AnalyticGeometry& geometry)
-{
-  if (geometry.getNumAnalyticVolumes() == 0) return;
-
-  std::vector<std::pair<int, int>> list;
-  for (size_t i = 0; i < geometry.getNumAnalyticVolumes(); ++i)
-  {
-    AnalyticVolume* current = geometry.getAnalyticVolume(i);
-    list.push_back(std::pair<int, int>((int)i, (int)current->getOrdinal()));
-  }
-
-  std::sort(list.begin(), list.end(), sorter);
-
-  for (std::vector<std::pair<int, int>>::iterator it=list.begin(); it!=list.end(); ++it)
-  {
-    AnalyticVolume* current = geometry.getAnalyticVolume(it->first);
-    current->setOrdinal((geometry.getNumAnalyticVolumes()-1)-it->second);
-  }
-
-
-}
 
 void GeometryEditWidget::flipVolumeOrder()
 {
   if (mpSimulator == NULL) 
     return;
-  Model* model = const_cast<Model*>(mpSimulator->getModel());
-  if (model == NULL)
-    return;
-  SpatialModelPlugin* plugin = dynamic_cast<SpatialModelPlugin*>(model->getPlugin("spatial"));
-  if (plugin == NULL)
-    return;
-
-  Geometry* geometry = plugin->getGeometry();
-
-  for (size_t i = 0; i < geometry->getNumGeometryDefinitions(); ++i)
-  {
-    AnalyticGeometry* definition = dynamic_cast<AnalyticGeometry*>(geometry->getGeometryDefinition(i));
-    if (definition == NULL) 
-      continue;
-    flipOrder(*definition);
-    mNeedReload = true;
-  }
+  mpSimulator->flipVolumeOrder();
+  mNeedReload = true;
 }
 
 void GeometryEditWidget::updateUI()
diff --git a/SpatialUI/spatialmainwidget.cpp b/SpatialUI/spatialmainwidget.cpp
index db20e95..7307f78 100644
--- a/SpatialUI/spatialmainwidget.cpp
+++ b/SpatialUI/spatialmainwidget.cpp
@@ -535,7 +535,6 @@ void SpatialMainWindow::loadFromDocument(SBMLDocument* toLoad)
     return;
   }
 
-
   lstSpecies->clear();
   ui->lstDose->clear();
 
@@ -573,6 +572,8 @@ void SpatialMainWindow::loadFromDocument(SBMLDocument* toLoad)
 
 
 
+  restart();
+  thread->mpSimulator->flipVolumeOrder();
   restart();
 
   ui->tblParameters->clear();