Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[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 eee48df..848eb75 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -31,6 +31,7 @@ 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;
@@ -41,10 +42,12 @@ import org.jmol.viewer.Viewer;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.SequenceRenderer;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.gui.AppJmol;
 import jalview.gui.IProgressIndicator;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
@@ -54,14 +57,15 @@ import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.ws.dbsources.Pdb;
 import javajs.util.BS;
-
 public abstract class JalviewJmolBinding extends AAStructureBindingModel
         implements JmolStatusListener, JmolSelectionListener,
         ComponentListener
 {
   private String lastMessage;
 
+
   /*
    * when true, try to search the associated datamodel for sequences that are
    * associated with any unknown structures in the Jmol view.
@@ -86,8 +90,8 @@ 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);
      */
@@ -132,6 +136,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     {
       return null;
     }
+
     String cmd = command.getCommand();
     jmolHistory(false);
     if (lastCommand == null || !lastCommand.equals(cmd))
@@ -181,6 +186,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return null;
   }
 
+
   /**
    * map between index of model filename returned from getPdbFile and the first
    * index of models from this file in the viewer. Note - this is not trimmed -
@@ -204,8 +210,8 @@ 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))
@@ -292,6 +298,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
     jmolScript(cmd.toString());
     jmolHistory(true);
+
   }
 
   private boolean debug = true;
@@ -398,8 +405,8 @@ 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);
@@ -435,8 +442,8 @@ 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,
@@ -497,6 +504,28 @@ 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)
@@ -745,7 +774,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       FeatureRenderer fr = getFeatureRenderer(null);
       if (fr != null)
       {
-        fr.featuresAdded();
+        FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme();
+        ((AppJmol) getViewer()).getAlignmentPanel().av
+                .applyFeaturesStyle(colours);
       }
       refreshGUI();
       loadNotifiesHandled++;
@@ -753,6 +784,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     setLoadingFromArchive(false);
   }
 
+
   protected IProgressIndicator getIProgressIndicator()
   {
     return null;
@@ -774,8 +806,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public abstract void sendConsoleEcho(String strEcho); /*
                                                          * { showConsole(true);
                                                          * 
-                                                         * history.append("\n" +
-                                                         * strEcho); }
+                                                         * history.append("\n" + strEcho); }
                                                          */
 
   // /End JmolStatusListener
@@ -797,6 +828,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   }
 
+
   public void showHelp()
   {
     showUrl("http://wiki.jmol.org"