X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=98787cbb749edd01f9eb5e9859940ba57fa9146a;hb=c38d37887ae51d63942ac4321f6769308188ed6b;hp=aa6a15923c780d8ee0f2e05ba51a3c1a00293240;hpb=f2511dd2e8e37b8e999e924f8a53d150377b21b5;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index aa6a159..98787cb 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -20,6 +20,16 @@
  */
 package jalview.gui;
 
+import java.awt.Container;
+import java.io.File;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JComponent;
+
+import org.jmol.api.JmolAppConsoleInterface;
+import org.openscience.jmol.app.jmolpanel.console.AppConsole;
+
 import jalview.api.AlignmentViewPanel;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
@@ -28,15 +38,8 @@ import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;
 import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
-
-import java.awt.Container;
-import java.util.Map;
-
-import javax.swing.JComponent;
-
-import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.java.BS;
-import org.openscience.jmol.app.jmolpanel.console.AppConsole;
+import jalview.util.Platform;
+import javajs.util.BS;
 
 public class AppJmolBinding extends JalviewJmolBinding
 {
@@ -90,6 +93,11 @@ public class AppJmolBinding extends JalviewJmolBinding
   @Override
   public void refreshGUI()
   {
+    if (getMappedStructureCount() == 0)
+    {
+      // too soon!
+      return;
+    }
     // appJmolWindow.repaint();
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
@@ -97,6 +105,7 @@ public class AppJmolBinding extends JalviewJmolBinding
       public void run()
       {
         JalviewStructureDisplayI theViewer = getViewer();
+        // invokes colourbySequence() via seqColour_ActionPerformed()
         theViewer.updateTitleAndMenus();
         ((JComponent) theViewer).revalidate();
       }
@@ -104,21 +113,6 @@ public class AppJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public void updateColours(Object source)
-  {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    // ignore events from panels not used to colour this view
-    if (!getViewer().isUsedForColourBy(ap))
-    {
-      return;
-    }
-    if (!isLoadingFromArchive())
-    {
-      colourBySequence(ap);
-    }
-  }
-
-  @Override
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
     // todo - script termination doesn't happen ?
@@ -142,15 +136,6 @@ public class AppJmolBinding extends JalviewJmolBinding
   @Override
   public void selectionChanged(BS arg0)
   {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public void refreshPdbEntries()
-  {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
@@ -164,7 +149,9 @@ public class AppJmolBinding extends JalviewJmolBinding
           Container consolePanel, String buttonsToShow)
   {
     jmolViewer.setJmolCallbackListener(this);
-    return new AppConsole(jmolViewer, consolePanel, buttonsToShow);
+    // BH comment: can't do this yet [for JS only, or generally?]
+    return Platform.isJS() ? null
+            : new AppConsole(jmolViewer, consolePanel, buttonsToShow);
   }
 
   @Override
@@ -189,4 +176,17 @@ public class AppJmolBinding extends JalviewJmolBinding
     // TODO Auto-generated method stub
     return null;
   }
+
+  @SuppressWarnings("unused")
+  public void cacheFiles(List<File> files)
+  {
+    if (files == null)
+    {
+      return;
+    }
+    for (File f : files)
+    {
+      Platform.cacheFileData(f);
+    }
+  }
 }