X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=75b98bcd1cf9461e7b6c1523a38e6bd14fc47f28;hb=6d9ff99acf35278e6dc1c85bbc65f8e419cd91b6;hp=932517205d2a76048dad99a679419d7c1cab6239;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 9325172..75b98bc 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -28,17 +28,20 @@ import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;
 import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.Platform;
 
 import java.awt.Container;
+import java.io.File;
+import java.util.List;
 import java.util.Map;
 
 import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.java.BS;
-import org.openscience.jmol.app.jmolpanel.console.AppConsole;
+
+import javajs.util.BS;
 
 public class AppJmolBinding extends JalviewJmolBinding
 {
-  private AppJmol appJmolWindow;
+  protected AppJmol appJmolWindow;
 
   public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
           PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
@@ -49,6 +52,12 @@ public class AppJmolBinding extends JalviewJmolBinding
   }
 
   @Override
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    return appJmolWindow.progressBar;
+  }
+
+  @Override
   public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
@@ -97,6 +106,8 @@ public class AppJmolBinding extends JalviewJmolBinding
       public void run()
       {
         appJmolWindow.updateTitleAndMenus();
+        // initiates a colourbySequence
+        // via seqColour_ActionPerformed.
         appJmolWindow.revalidate();
       }
     });
@@ -163,7 +174,7 @@ public class AppJmolBinding extends JalviewJmolBinding
           Container consolePanel, String buttonsToShow)
   {
     viewer.setJmolCallbackListener(this);
-    return new AppConsole(viewer, consolePanel, buttonsToShow);
+    return null;//BH can't do this yet. new AppConsole(viewer, consolePanel, buttonsToShow);
   }
 
   @Override
@@ -209,4 +220,17 @@ public class AppJmolBinding extends JalviewJmolBinding
 
     return null;
   }
+
+  @SuppressWarnings("unused")
+  public void cacheFiles(List<File> files)
+  {
+    if (files == null)
+    {
+      return;
+    }
+    for (File f : files)
+    {
+      Platform.cacheFileData(f);
+    }
+  }
 }