Two bugs on AlloyParseHandler have been fixed:

1. If you click LoadSpesification and then click Cancel button without
select any .als file, Marker types was being removed. But now it
doesn't.

2. If there is an mapped marker which is a source marker (which has
MappingAnnotation type), when you load any other spesification file (als
file), the marker's annotation was not being changed as
MarkingAnnotation type. But now it is changing.

Source/eu.modelwriter.marker.command/src/eu/modelwriter/marker/command/AlloyParseHandler.java

@@ -28,12 +28,14 @@
 import org.eclipse.ui.PlatformUI;
 
 import eu.modelwriter.configuration.alloy.AlloyParser;
+import eu.modelwriter.configuration.internal.AlloyUtilities;
 import eu.modelwriter.marker.MarkerActivator;
 import eu.modelwriter.marker.Serialization;
 import eu.modelwriter.marker.internal.MarkUtilities;
 import eu.modelwriter.marker.internal.MarkerFactory;
 import eu.modelwriter.marker.internal.MarkerTypeElement;
 import eu.modelwriter.marker.ui.internal.views.visualizationview.Visualization;
+import eu.modelwriter.marker.ui.internal.wizards.mappingwizard.MappingWizard;
 import eu.modelwriter.marker.ui.internal.wizards.markerwizard.MarkerPage;
 
 public class AlloyParseHandler extends AbstractHandler {
@@ -52,8 +54,6 @@ public Object execute(final ExecutionEvent event) throws ExecutionException {
       return null;
     }
 
-    this.removeTypesFromMarkers();
-
     final FileDialog dialog =
         new FileDialog(PlatformUI.getWorkbench().getActiveWorkbenchWindow().getShell(), SWT.OPEN);
     dialog.setFilterExtensions(new String[] {"*.als", "*.mw"});
@@ -62,6 +62,8 @@ public Object execute(final ExecutionEvent event) throws ExecutionException {
       return null;
     }
 
+    this.removeTypesFromMarkers();
+
     final AlloyParser parser = new AlloyParser(result);
     final ArrayList<MarkerTypeElement> roots = parser.getTypes();
     final ArrayList<String> rels = parser.getRels();
@@ -93,9 +95,13 @@ private void removeTypesFromMarkers() {
           isClosed = true;
           ((IProject) iResource).open(new NullProgressMonitor());
         }
-        for (final IMarker iMarker : MarkerFactory.findMarkersAsArrayList(iResource)) {
+        for (IMarker iMarker : MarkerFactory.findMarkersAsArrayList(iResource)) {
           if (MarkUtilities.getType(iMarker) != null) {
+            if (MappingWizard.findTargetCount(iMarker) != 0) {
+              iMarker = MappingWizard.convertAnnotationType(iMarker, false, true);
+            }
             MarkUtilities.setType(iMarker, null);
+            AlloyUtilities.removeTypeFromMarker(iMarker);
           }
         }
         if (isClosed == true) {