Merge branch 'develop' into feature/JAL-3551Pymol

[jalview.git] / src / jalview / gui / AppJmolBinding.java

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 75b98bc..3298509 100644 (file)
--- 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;
@@ -29,32 +39,16 @@ 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 javajs.util.BS;
 
 public class AppJmolBinding extends JalviewJmolBinding
 {
-  protected AppJmol appJmolWindow;
-
   public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
           PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
           DataSourceType protocol)
   {
     super(sSm, pdbentry, sequenceIs, protocol);
-    appJmolWindow = appJmol;
-  }
-
-  @Override
-  protected IProgressIndicator getIProgressIndicator()
-  {
-    return appJmolWindow.progressBar;
+    setViewer(appJmol);
   }
 
   @Override
@@ -105,30 +99,15 @@ public class AppJmolBinding extends JalviewJmolBinding
       @Override
       public void run()
       {
-        appJmolWindow.updateTitleAndMenus();
-        // initiates a colourbySequence
-        // via seqColour_ActionPerformed.
-        appJmolWindow.revalidate();
+        JalviewStructureDisplayI theViewer = getViewer();
+        // invokes colourbySequence() via seqColour_ActionPerformed()
+        theViewer.updateTitleAndMenus();
+        ((JComponent) theViewer).revalidate();
       }
     });
   }
 
   @Override
-  public void updateColours(Object source)
-  {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    // ignore events from panels not used to colour this view
-    if (!appJmolWindow.isUsedforcolourby(ap))
-    {
-      return;
-    }
-    if (!isLoadingFromArchive())
-    {
-      colourBySequence(ap);
-    }
-  }
-
-  @Override
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
     // todo - script termination doesn't happen ?
@@ -152,35 +131,28 @@ 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
   public void showConsole(boolean b)
   {
-    appJmolWindow.showConsole(b);
+    getViewer().showConsole(b);
   }
 
   @Override
   protected JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow)
   {
-    viewer.setJmolCallbackListener(this);
-    return null;//BH can't do this yet. new AppConsole(viewer, consolePanel, buttonsToShow);
+    jmolViewer.setJmolCallbackListener(this);
+    // BH comment: can't do this yet [for JS only, or generally?]
+    return Platform.isJS() ? null
+            : new AppConsole(jmolViewer, consolePanel, buttonsToShow);
   }
 
   @Override
   protected void releaseUIResources()
   {
-    appJmolWindow = null;
+    setViewer(null);
     closeConsole();
   }
 
@@ -189,7 +161,7 @@ public class AppJmolBinding extends JalviewJmolBinding
   {
     if (svl instanceof SeqPanel)
     {
-      appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
+      getViewer().removeAlignmentPanel(((SeqPanel) svl).ap);
     }
   }
 
@@ -200,27 +172,6 @@ public class AppJmolBinding extends JalviewJmolBinding
     return null;
   }
 
-  @Override
-  public JalviewStructureDisplayI getViewer()
-  {
-    return appJmolWindow;
-  }
-
-  @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment)
-  {
-    AlignmentPanel ap = (alignment == null)
-            ? appJmolWindow.getAlignmentPanel()
-            : (AlignmentPanel) alignment;
-    if (ap.av.isShowSequenceFeatures())
-    {
-      return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;
-    }
-
-    return null;
-  }
-
   @SuppressWarnings("unused")
   public void cacheFiles(List<File> files)
   {