JAL-3148 show/hide features on structure independent of alignment

[jalview.git] / src / jalview / appletgui / AppletJmolBinding.java

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 6ec5b4d..696a272 100644 (file)
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -24,13 +24,13 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.gui.IProgressIndicator;
+import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
 
 import java.awt.Container;
 import java.util.Map;
 
-import javajs.awt.Dimension;
-
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.console.AppletConsole;
 import org.jmol.java.BS;
@@ -45,9 +45,9 @@ class AppletJmolBinding extends 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;
   }
 
@@ -55,28 +55,7 @@ class AppletJmolBinding extends JalviewJmolBinding
   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;
-  }
-
-  @Override
-  public jalview.api.SequenceRenderer getSequenceRenderer(
-          AlignmentViewPanel alignment)
-  {
-    return new SequenceRenderer(((AlignmentPanel) alignment).av);
+    return appletJmolBinding.ap.getFeatureRenderer();
   }
 
   @Override
@@ -113,18 +92,20 @@ class AppletJmolBinding extends JalviewJmolBinding
     appletJmolBinding.updateTitleAndMenus();
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap);
+    colourBySequence(ap, ap.av.isShowSequenceFeatures());
   }
 
+  @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)
     {
     }
@@ -143,6 +124,7 @@ class AppletJmolBinding extends JalviewJmolBinding
     // do nothing.
   }
 
+  @Override
   public void selectionChanged(BS arg0)
   {
     // TODO Auto-generated method stub
@@ -183,7 +165,7 @@ class AppletJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public Dimension resizeInnerPanel(String data)
+  public int[] resizeInnerPanel(String data)
   {
     // TODO Auto-generated method stub
     return null;
@@ -195,4 +177,11 @@ class AppletJmolBinding extends JalviewJmolBinding
     // TODO Auto-generated method stub
     return null;
   }
+
+  @Override
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    // no progress indicators on the applet
+    return null;
+  }
 }