- sort SBW interface, so non-spatial models can be send to editor if …

…found

CMakeLists.txt

@@ -106,11 +106,25 @@ endif()
 
 ###############################################################################
 #
-# SBW Integration
+# SBW Integration 
 #
 option(ENABLE_SBW   "Enable SBW Integration."     ON)
+SET(USE_SBW_INTEGRATION 0)
 if (ENABLE_SBW)
 
+SET(USE_SBW_INTEGRATION 1)
+add_definitions(-DUSE_SBW_INTEGRATION)
+
+
+if (APPLE)
+add_definitions(-DDARWIN)
+endif()
+
+if (UNIX)
+add_definitions(-DLINUX)
+endif()
+
+
 find_library(SBW_LIBRARY
   NAMES SBW-static.lib SBW-static SBW
   PATHS /usr/lib /usr/local/lib /usr/lib64 /usr/local/lib64

SpatialSBML/setInfoFunction.cpp

@@ -513,7 +513,7 @@ normalUnitVector* setNormalAngle(vector<GeometryInfo*> &geoInfoList, double Xsiz
 								//X = X;
 								Y = Y - 2;
 								preD = S;
-							} else if (isD[Z * Yindex * Xindex + (Y - 1) * Xindex + (X - 1)] == 1 && preD != NE) {//southwest
+							} else if ((Y - 1) >= 0 && isD[Z * Yindex * Xindex + (Y - 1) * Xindex + (X - 1)] == 1 && preD != NE) {//southwest
 								X = X - 1;
 								Y = Y - 1;
 								preD = SW;

SpatialUI/CMakeLists.txt

@@ -11,7 +11,7 @@ cmake_policy(SET CMP0020 NEW)
 
 
 if (PREFIX_PATH)
-set (CMAKE_PREFIX_PATH "${PREFIX_PATH}")
+set (CMAKE_PREFIX_PATH "${PREFIX_PATH}") 
 endif()
 
 include(${CMAKE_CURRENT_SOURCE_DIR}/ChooseQtVersion.cmake)
@@ -70,20 +70,6 @@ set(MACOSX_BUNDLE_COPYRIGHT ${MACOSX_BUNDLE_INFO_STRING})
 
 endif(APPLE)
 
-if (ENABLE_SBW)
-
-include_directories(${SBW_INCLUDE_DIR})
-add_definitions(-DUSE_SBW_INTEGRATION)
-
-if (APPLE)
-add_definitions(-DDARWIN)
-endif()
-
-if (UNIX)
-add_definitions(-DLINUX)
-endif()
-endif()
-
 
 add_executable(SpatialUI ${EXECUTABLE_FLAGS} ${CPP_FILES}
 	${H_FILES}
@@ -98,6 +84,8 @@ QT_BIND_TO_TARGET(SpatialUI)
 target_link_libraries(SpatialUI ${EXTRA_LIBS} SpatialSBML)
 
 if (ENABLE_SBW)
+  include_directories(${SBW_INCLUDE_DIR})
+  #set_target_properties(SpatialUI PROPERTIES AUTOMOC_MOC_OPTIONS -DUSE_SBW_INTEGRATION)
   target_link_libraries(SpatialUI ${EXTRA_LIBS} SpatialSBML ${SBW_LIBRARY})
 
   if (WIN32)
@@ -106,7 +94,6 @@ if (ENABLE_SBW)
 
 endif()
 
-
 file(GLOB PALETTE_FILES palettes/*.txt )
 file(COPY ${PALETTE_FILES} DESTINATION  ${CMAKE_CURRENT_BINARY_DIR})
 

SpatialUI/spatialmainwidget.cpp

@@ -41,7 +41,15 @@
 using namespace std;
 LIBSBML_CPP_NAMESPACE_USE;
 
-SpatialMainWindow::SpatialMainWindow() : thread(NULL), updating(false), pickerX(0), pickerY(0), maxX(501), maxY(501)
+SpatialMainWindow::SpatialMainWindow() 
+  : thread(NULL)
+  , doc(NULL)
+  , updating(false)
+  , pickerX(0)
+  , pickerY(0)
+  , maxX(501)
+  , maxY(501)
+  , mHaveEdit(false)
 #ifdef USE_SBW_INTEGRATION
   , mpSBWModule(NULL)
   , mSBWAnalyzerModules()
@@ -90,7 +98,7 @@ SpatialMainWindow::SpatialMainWindow() : thread(NULL), updating(false), pickerX(
 
   sbwConnect();
   sbwRegister();
-    
+
 #endif // USE_SBW_INTEGRATION
 
 
@@ -937,10 +945,44 @@ bool SpatialMainWindow::loadFromDocument(SBMLDocument* toLoad)
 
   if (!haveSpatial)
   {
+#if USE_SBW_INTEGRATION
+    if (mHaveEdit)
+    {
+      if (QMessageBox::question(this, tr("Spatial UI"),
+      tr("It would seem that the given model '%1' does not use the spatial package. Would you like to add a spatial description to it?\n")
+      .arg(curFile), QMessageBox::Yes | QMessageBox::Default , QMessageBox::No) == 
+      QMessageBox::Yes)
+      {
+        try
+        {
+          int nModule = SBWLowLevel::getModuleInstance("EditSpatial");
+          int nService = SBWLowLevel::moduleFindServiceByName(nModule, "analysis");
+          int nMethod = SBWLowLevel::serviceGetMethod(nModule, nService, "void doAnalysis(string)");
+
+          DataBlockWriter args;
+          args << writeSBMLToString(doc);
+          SBWLowLevel::methodSend(nModule, nService, nMethod, args);
+
+        }
+
+        catch (SBWException * pE)
+        {
+          QMessageBox::critical(this, "SBW Error",
+            pE->getMessage().c_str(),
+            QMessageBox::Ok | QMessageBox::Default,
+            QMessageBox::NoButton);
+        }
+      }
+
+    }
+    else
+#endif
+    {
     QMessageBox::critical(this, tr("Spatial UI"),
       tr("It would seem that the given model '%1' does not use the spatial package. Please load one that does. \n")
       .arg(curFile)
       );
+    }
     return false;
   }
 
@@ -1016,13 +1058,20 @@ void SpatialMainWindow::loadFromString(const std::string& sbml)
   updating = true;
   stop();
 
-  doc = readSBMLFromString(sbml.c_str());
+  QString current = curFile;
 
   setCurrentFile("fromSBW.xml");
+  doc = readSBMLFromString(sbml.c_str());
+
   if (loadFromDocument(doc))
+  {
     statusBar()->showMessage(tr("File loaded"), 2000);
+  }
   else
+  {
     statusBar()->showMessage(tr("File could not be loaded"), 2000);
+    setCurrentFile("invalid.xml");
+  }
 
   updating = false;
 
@@ -1043,16 +1092,17 @@ void SpatialMainWindow::loadFile(const QString &fileName)
   }
 
   lastDir = QFileInfo(fileName).absoluteDir().absolutePath();
+  setCurrentFile(fileName);
   doc = readSBMLFromFile(fileName.toStdString().c_str());
 
   if (loadFromDocument(doc))
   {
     statusBar()->showMessage(tr("File loaded"), 2000);
-    setCurrentFile(fileName);
   }
   else
   {
     statusBar()->showMessage(tr("File could not be loaded"), 2000);
+    setCurrentFile("invalid.xml");
   }
 
   updating = false;  
@@ -1456,6 +1506,8 @@ void SpatialMainWindow::sbwRefreshMenu()
                 }
             }
 
+          mHaveEdit |= mHaveEdit || ModuleName == "EditSpatial";
+
           SortedNames[MenuName.c_str()] = i++;
           ModuleList.append(ModuleName.c_str());
           ServiceList.append(ServiceName.c_str());
@@ -1479,11 +1531,13 @@ void SpatialMainWindow::sbwRefreshMenu()
           mSBWAnalyzerModules.append(ModuleList[itMap.value()]);
           mSBWAnalyzerServices.append(ServiceList[itMap.value()]);
 
-          pAction = new QAction(itMap.key(), mpSBWActionGroup);
+          pAction = mpSBWActionGroup->addAction(itMap.key());
           mpSBWMenu->addAction(pAction);
           mSBWActionMap[pAction] = i;
+
         }
 
+
       if (mSBWAnalyzerModules.empty())
         Visible = false;
     }
@@ -1505,6 +1559,7 @@ void SpatialMainWindow::sbwSlotMenuTriggeredFinished(bool success)
 
 void SpatialMainWindow::sbwSlotMenuTriggered(QAction * pAction)
 {
+  if (doc == NULL) return;
 
   mSBWActionId = mSBWActionMap[pAction];
 

SpatialUI/spatialmainwidget.h

@@ -173,6 +173,8 @@ private slots:;
   int maxX;
   int maxY;
 
+  bool mHaveEdit;
+
   std::vector<ConcentrationPalette*> palettes;
   std::vector<DisplayItem*> displayItems;