X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmolBinding.java;h=e5767b68c8b06b8e1b10d9bc87248d6f553caaa3;hb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;hp=ff1f5b22ca1ad974011508320456795e7eb458d1;hpb=c0aaf84826ff25d510846bd1099e10809c4df711;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index ff1f5b2..e5767b6 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,16 +23,18 @@ package jalview.appletgui;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
 
 import java.awt.Container;
-import java.util.BitSet;
+import java.util.Map;
 
 import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
-import org.jmol.popup.JmolPopup;
+import org.jmol.console.AppletConsole;
+import org.jmol.java.BS;
 
-class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+class AppletJmolBinding extends JalviewJmolBinding
 {
 
   /**
@@ -42,38 +44,27 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   public AppletJmolBinding(AppletJmol appletJmol,
           StructureSelectionManager sSm, PDBEntry[] pdbentry,
-          SequenceI[][] seq, String[][] chains, String protocol)
+          SequenceI[][] seq, DataSourceType protocol)
   {
-    super(sSm, pdbentry, seq, chains, protocol);
+    super(sSm, pdbentry, seq, protocol);
     appletJmolBinding = appletJmol;
   }
 
+  @Override
   public jalview.api.FeatureRenderer getFeatureRenderer(
           AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (AlignmentPanel) alignment;
-    if (appletJmolBinding.ap.av.isShowSequenceFeatures())
-    {
-      if (appletJmolBinding.fr == null)
-      {
-        appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(
-                appletJmolBinding.ap.av);
-      }
-
-      appletJmolBinding.fr
-              .transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas
-                      .getFeatureRenderer());
-    }
-
-    return appletJmolBinding.fr;
+    return appletJmolBinding.ap.getFeatureRenderer();
   }
 
+  @Override
   public jalview.api.SequenceRenderer getSequenceRenderer(
           AlignmentViewPanel alignment)
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
 
+  @Override
   public void sendConsoleEcho(String strEcho)
   {
     if (appletJmolBinding.scriptWindow == null)
@@ -81,41 +72,46 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
       appletJmolBinding.showConsole(true);
     }
 
-    appletJmolBinding.history.append("\n" + strEcho);
+    appletJmolBinding.addToHistory(strEcho);
   }
 
+  @Override
   public void sendConsoleMessage(String strStatus)
   {
     if (appletJmolBinding.history != null && strStatus != null
             && !strStatus.equals("Script completed"))
     {
-      appletJmolBinding.history.append("\n" + strStatus);
+      appletJmolBinding.addToHistory(strStatus);
     }
   }
 
+  @Override
   public void showUrl(String url, String target)
   {
     appletJmolBinding.ap.alignFrame.showURL(url, target);
 
   }
 
+  @Override
   public void refreshGUI()
   {
     appletJmolBinding.updateTitleAndMenus();
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+    colourBySequence(ap);
   }
 
+  @Override
   public void showUrl(String url)
   {
     try
     {
-      appletJmolBinding.ap.av.applet.getAppletContext().showDocument(
-              new java.net.URL(url), "jmol");
+      appletJmolBinding.ap.av.applet.getAppletContext()
+              .showDocument(new java.net.URL(url), "jmol");
     } catch (java.net.MalformedURLException ex)
     {
     }
@@ -124,17 +120,18 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void newJmolPopup(boolean translateLocale, String menuName,
           boolean asPopup)
   {
-
-    jmolpopup = new JmolPopup();
-    jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
+    // jmolpopup = new JmolAwtPopup(); // is this used?
+    // jmolpopup.jpiInitialize((viewer), menuName);
   }
 
+  @Override
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
     // do nothing.
   }
 
-  public void selectionChanged(BitSet arg0)
+  @Override
+  public void selectionChanged(BS arg0)
   {
     // TODO Auto-generated method stub
 
@@ -153,12 +150,11 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   }
 
   @Override
-  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+  protected JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow)
   {
-    // return new org.jmol.console.AppletConsole(viewer2, consolePanel);
-    JmolAppConsoleInterface appc = new org.jmol.console.AppletConsole()
-            .getAppConsole(viewer2);
+    JmolAppConsoleInterface appc = new AppletConsole();
+    appc.start(viewer);
     return appc;
   }
 
@@ -175,9 +171,14 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   }
 
   @Override
-  public void resizeInnerPanel(String data)
+  public int[] resizeInnerPanel(String data)
   {
-    // TODO Auto-generated method stub
+    return null;
+  }
 
+  @Override
+  public Map<String, Object> getJSpecViewProperty(String arg0)
+  {
+    return null;
   }
 }