JAL-1759 merge from develop

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 2434b00..be56292 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -3344,9 +3344,8 @@ public class Jalview2XML
           String sessionState = ss.getViewerState();
           String tempStateFile = copyJarEntry(jprovider, sessionState,
                   "varna");
-          RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped,
-                  tempStateFile);
-          appVarna.addModel(rna, rnaTitle);
+          RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
+          appVarna.addModelSession(rna, rnaTitle, tempStateFile);
         }
         appVarna.setInitialSelection(viewer.getSelectedRna());
       }
@@ -3807,23 +3806,16 @@ public class Jalview2XML
       newFileLoc.append(";");
     }
 
-    if (newFileLoc.length() == 0)
+    if (newFileLoc.length() > 0)
     {
-      return;
-    }
-    int histbug = newFileLoc.indexOf("history = ");
-    if (histbug > -1)
-    {
-      /*
-       * change "history = [true|false];" to "history = [1|0];"
-       */
+      int histbug = newFileLoc.indexOf("history = ");
       histbug += 10;
       int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
       String val = (diff == -1) ? null : newFileLoc
               .substring(histbug, diff);
       if (val != null && val.length() >= 4)
       {
-        if (val.contains("e")) // eh? what can it be?
+        if (val.contains("e"))
         {
           if (val.trim().equals("true"))
           {
@@ -3836,53 +3828,53 @@ public class Jalview2XML
           newFileLoc.replace(histbug, diff, val);
         }
       }
-    }
 
-    final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
-            .size()]);
-    final String[] id = pdbids.toArray(new String[pdbids.size()]);
-    final SequenceI[][] sq = seqmaps
-            .toArray(new SequenceI[seqmaps.size()][]);
-    final String fileloc = newFileLoc.toString();
-    final String sviewid = viewerData.getKey();
-    final AlignFrame alf = af;
-    final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
-            svattrib.getWidth(), svattrib.getHeight());
-    try
-    {
-      javax.swing.SwingUtilities.invokeAndWait(new Runnable()
+      final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
+              .size()]);
+      final String[] id = pdbids.toArray(new String[pdbids.size()]);
+      final SequenceI[][] sq = seqmaps
+              .toArray(new SequenceI[seqmaps.size()][]);
+      final String fileloc = newFileLoc.toString();
+      final String sviewid = viewerData.getKey();
+      final AlignFrame alf = af;
+      final Rectangle rect = new Rectangle(svattrib.getX(),
+              svattrib.getY(), svattrib.getWidth(), svattrib.getHeight());
+      try
       {
-        @Override
-        public void run()
+        javax.swing.SwingUtilities.invokeAndWait(new Runnable()
         {
-          JalviewStructureDisplayI sview = null;
-          try
-          {
-            sview = new StructureViewer(alf.alignPanel
-                    .getStructureSelectionManager()).createView(
-                    StructureViewer.ViewerType.JMOL, pdbf, id, sq,
-                    alf.alignPanel, svattrib, fileloc, rect, sviewid);
-            addNewStructureViewer(sview);
-          } catch (OutOfMemoryError ex)
+          @Override
+          public void run()
           {
-            new OOMWarning("restoring structure view for PDB id " + id,
-                    (OutOfMemoryError) ex.getCause());
-            if (sview != null && sview.isVisible())
+            JalviewStructureDisplayI sview = null;
+            try
+            {
+              sview = new StructureViewer(alf.alignPanel
+                      .getStructureSelectionManager()).createView(
+                      StructureViewer.ViewerType.JMOL, pdbf, id, sq,
+                      alf.alignPanel, svattrib, fileloc, rect, sviewid);
+              addNewStructureViewer(sview);
+            } catch (OutOfMemoryError ex)
             {
-              sview.closeViewer(false);
-              sview.setVisible(false);
-              sview.dispose();
+              new OOMWarning("restoring structure view for PDB id " + id,
+                      (OutOfMemoryError) ex.getCause());
+              if (sview != null && sview.isVisible())
+              {
+                sview.closeViewer(false);
+                sview.setVisible(false);
+                sview.dispose();
+              }
             }
           }
-        }
-      });
-    } catch (InvocationTargetException ex)
-    {
-      warn("Unexpected error when opening Jmol view.", ex);
+        });
+      } catch (InvocationTargetException ex)
+      {
+        warn("Unexpected error when opening Jmol view.", ex);
 
-    } catch (InterruptedException e)
-    {
-      // e.printStackTrace();
+      } catch (InterruptedException e)
+      {
+        // e.printStackTrace();
+      }
     }
   }