Merge branch 'develop' into features/JAL-2295setChimeraAttributes

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

diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index 892e094..c1f15e5 100644 (file)
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -1,9 +1,30 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
 
 public class JalviewChimeraBindingModel extends JalviewChimeraBinding
@@ -12,11 +33,12 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
 
   private FeatureRenderer fr = null;
 
+
   public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
           StructureSelectionManager ssm, PDBEntry[] pdbentry,
-          SequenceI[][] sequenceIs, String[][] chains, String protocol)
+          SequenceI[][] sequenceIs, DataSourceType protocol)
   {
-    super(ssm, pdbentry, sequenceIs, chains, protocol);
+    super(ssm, pdbentry, sequenceIs, protocol);
     cvf = chimeraViewFrame;
   }
 
@@ -52,6 +74,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
   {
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         cvf.updateTitleAndMenus();
@@ -60,6 +83,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     });
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
@@ -93,6 +117,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
    * Send an asynchronous command to Chimera, in a new thread, optionally with
    * an 'in progress' message in a progress bar somewhere
    */
+  @Override
   protected void sendAsynchronousCommand(final String command,
           final String progressMsg)
   {
@@ -102,17 +127,26 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
       @Override
       public void run()
       {
-        long stm = cvf.startProgressBar(progressMsg);
+        long handle = 0;
+        if (progressMsg != null)
+        {
+          handle = cvf.startProgressBar(progressMsg);
+        }
         try
         {
           sendChimeraCommand(command, false);
         } finally
         {
-          cvf.stopProgressBar(null, stm);
+          if (progressMsg != null)
+          {
+            cvf.stopProgressBar(null, handle);
+          }
         }
       }
     });
     thread.start();
 
   }
+
+
 }