JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls...

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 8a7cd23..f133f20 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -20,7 +20,6 @@
  */
 package jalview.ext.jmol;
 
-import java.awt.Color;
 import java.awt.Container;
 import java.awt.event.ComponentEvent;
 import java.awt.event.ComponentListener;
@@ -32,6 +31,8 @@ import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
+import javax.swing.SwingUtilities;
+
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolSelectionListener;
@@ -90,8 +91,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     setStructureCommands(new JmolCommands());
     /*
      * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
-     * "jalviewJmol", ap.av.applet .getDocumentBase(),
-     * ap.av.applet.getCodeBase(), "", this);
+     * "jalviewJmol", ap.av.applet .getDocumentBase(), ap.av.applet.getCodeBase(),
+     * "", this);
      * 
      * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
      */
@@ -121,9 +122,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   private String jmolScript(String script)
   {
-    Cache.log.debug(">>Jmol>> " + script);
+    Cache.debug(">>Jmol>> " + script);
     String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
-    Cache.log.debug("<<Jmol<< " + s);
+    Cache.debug("<<Jmol<< " + s);
 
     return s;
   }
@@ -208,8 +209,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       for (int i = 0; i < modelCount; ++i)
       {
         /*
-         * defensive check for null as getModelFileName can return null
-         * even when model count ms.mc is > 0
+         * defensive check for null as getModelFileName can return null even when model
+         * count ms.mc is > 0
          */
         filePath = jmolViewer.ms.getModelFileName(i);
         if (filePath != null && !mset.contains(filePath))
@@ -402,8 +403,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
 
     /*
-     * highlight position on alignment(s); if some text is returned, 
-     * show this as a second line on the structure hover tooltip
+     * highlight position on alignment(s); if some text is returned, show this as a
+     * second line on the structure hover tooltip
      */
     String label = getSsm().mouseOverStructure(pdbResNum, chainId,
             pdbfilename);
@@ -439,8 +440,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   /*
    * { if (history != null && strStatus != null &&
-   * !strStatus.equals("Script completed")) { history.append("\n" + strStatus);
-   * } }
+   * !strStatus.equals("Script completed")) { history.append("\n" + strStatus); }
+   * }
    */
 
   public void notifyAtomPicked(int atomIndex, String strInfo,
@@ -501,6 +502,28 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   @Override
   public void notifyCallback(CBK type, Object[] data)
   {
+    /*
+     * ensure processed in AWT thread to avoid risk of deadlocks
+     */
+    SwingUtilities.invokeLater(new Runnable()
+    {
+
+      @Override
+      public void run()
+      {
+        processCallback(type, data);
+      }
+    });
+  }
+
+  /**
+   * Processes one callback notification from Jmol
+   * 
+   * @param type
+   * @param data
+   */
+  protected void processCallback(CBK type, Object[] data)
+  {
     try
     {
       switch (type)
@@ -749,14 +772,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       FeatureRenderer fr = getFeatureRenderer(null);
       if (fr != null)
       {
-        // JAL-1842 ensure FeatureRenderer knows about RESNUM
-        fr.featuresAdded();
-        // ... apply feature settings (e.g. to hide RESNUM)
         FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme();
         ((AppJmol) getViewer()).getAlignmentPanel().av
                 .applyFeaturesStyle(colours);
-        // ... and refresh again to ensure FeatureSettings is in synch!
-        fr.notifyFeaturesChanged();
       }
       refreshGUI();
       loadNotifiesHandled++;
@@ -785,8 +803,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public abstract void sendConsoleEcho(String strEcho); /*
                                                          * { showConsole(true);
                                                          * 
-                                                         * history.append("\n" +
-                                                         * strEcho); }
+                                                         * history.append("\n" + strEcho); }
                                                          */
 
   // /End JmolStatusListener