X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=903d9b7c53faed57f0b58f2490c44f61758de5d2;hb=931c66e5efd8c066326b6db713b4db498657ebe6;hp=54eb59975166a034d435e48395e109489a243be7;hpb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 54eb599..903d9b7 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -31,6 +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;
@@ -39,10 +41,14 @@ import org.jmol.api.JmolViewer;
 import org.jmol.c.CBK;
 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;
@@ -52,6 +58,8 @@ 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,
@@ -83,8 +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);
      */
@@ -115,7 +123,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   private String jmolScript(String script)
   {
     Cache.log.debug(">>Jmol>> " + script);
-    String s = jmolViewer.evalStringQuiet(script);
+    String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
     Cache.log.debug("<<Jmol<< " + s);
 
     return s;
@@ -201,8 +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))
@@ -210,7 +218,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           mset.add(filePath);
         }
       }
-      modelFileNames = mset.toArray(new String[mset.size()]);
+      if (!mset.isEmpty())
+      {
+        modelFileNames = mset.toArray(new String[mset.size()]);
+      }
     }
 
     return modelFileNames;
@@ -392,8 +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);
@@ -429,8 +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,
@@ -491,6 +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)
@@ -592,6 +625,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     modelFileNames = null;
     boolean notifyLoaded = false;
     String[] modelfilenames = getStructureFiles();
+    if (modelfilenames == null)
+    {
+      // Jmol is still loading files!
+      return;
+    }
     // first check if we've lost any structures
     if (oldmodels != null && oldmodels.length > 0)
     {
@@ -734,7 +772,9 @@ 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++;
@@ -763,8 +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
@@ -994,4 +1033,23 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     return ".spt";
   }
+
+  @Override
+  public void selectionChanged(BS arg0)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
+  {
+    return new jalview.gui.SequenceRenderer(avp.getAlignViewport());
+  }
+
+  @Override
+  public String getHelpURL()
+  {
+    return "http://wiki.jmol.org"; // BH 2018
+  }
 }