JAL-1355

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index a3ff00b..cf04ae8 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -154,7 +154,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
       _alignwith = new Vector<AlignmentPanel>();
     }
 
-    seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
+    seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
             new ItemListener()
             {
 
@@ -174,7 +174,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
             });
     viewMenu.add(seqColourBy);
     final ItemListener handler;
-    JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
+    JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
             _alignwith, handler = new ItemListener()
             {
 
@@ -586,7 +586,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
     {
       command = "";
     }
-    jmb.evalStateCommand(command);
+    jmb.evalStateCommand(command, false);
     jmb.setFinishedInit(true);
   }
 
@@ -689,9 +689,8 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
       jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
       for (int pi = 0; pi < jmb.pdbentry.length; pi++)
       {
-        String file = new File(jmb.pdbentry[pi].getFile())
-                .getAbsoluteFile().getPath();
-        if (file == null)
+        String file = null;
+        if (jmb.pdbentry[pi].getFile()==null) 
         {
           // retrieve the pdb and store it locally
           AlignmentI pdbseq = null;
@@ -734,6 +733,8 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
         }
         else
         {
+          file = new File(jmb.pdbentry[pi].getFile())
+          .getAbsoluteFile().getPath();
           if (curfiles != null && curfiles.length > 0)
           {
             addingStructures = true; // already files loaded.
@@ -844,13 +845,13 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
       // do superposition if asked to
       if (alignAddedStructures)
       {
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        new Thread(new Runnable()
         {
           public void run()
           {
             alignStructs_withAllAlignPanels();
           }
-        });
+        }).start();
         alignAddedStructures = false;
       }
       addingStructures = false;