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

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index bccbda8..ae3ff9e 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -59,9 +59,7 @@ import java.io.InputStream;
 import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Map;
 import java.util.Random;
-import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -183,6 +181,31 @@ public class ChimeraViewFrame extends StructureViewerBase
         // TODO Auto-generated method stub
       }
     });
+    JMenuItem writeFeatures = new JMenuItem(
+            MessageManager.getString("label.create_chimera_attributes"));
+    writeFeatures.setToolTipText(MessageManager
+            .getString("label.create_chimera_attributes_tip"));
+    writeFeatures.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sendFeaturesToChimera();
+      }
+    });
+    viewerActionMenu.add(writeFeatures);
+  }
+
+  /**
+   * Send a command to Chimera to create residue attributes for Jalview features
+   * <p>
+   * The syntax is: setattr r <attName> <attValue> <atomSpec>
+   * <p>
+   * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A
+   */
+  protected void sendFeaturesToChimera()
+  {
+    jmb.sendFeaturesToChimera(getAlignmentPanel());
   }
 
   /**
@@ -535,7 +558,11 @@ public class ChimeraViewFrame extends StructureViewerBase
         int confirm = JOptionPane.showConfirmDialog(this, prompt,
                 MessageManager.getString("label.close_viewer"),
                 JOptionPane.YES_NO_CANCEL_OPTION);
-        if (confirm == JOptionPane.CANCEL_OPTION)
+        /*
+         * abort closure if user hits escape or Cancel
+         */
+        if (confirm == JOptionPane.CANCEL_OPTION
+                || confirm == JOptionPane.CLOSED_OPTION)
         {
           return;
         }
@@ -1038,10 +1065,10 @@ public class ChimeraViewFrame extends StructureViewerBase
     setChainMenuItems(jmb.getChainNames());
 
     this.setTitle(jmb.getViewerTitle("Chimera", true));
-    if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
-    {
+    // if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
+    // {
       viewerActionMenu.setVisible(true);
-    }
+    // }
     if (!jmb.isLoadingFromArchive())
     {
       seqColour_actionPerformed(null);