JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index f3fdd67..062dbf8 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -25,6 +25,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.TreeBuilder;
 import jalview.analysis.scoremodels.PIDModel;
 import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.AlignFrameI;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
@@ -106,7 +107,6 @@ import java.awt.event.KeyListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.io.IOException;
-import java.io.UnsupportedEncodingException;
 import java.net.URL;
 import java.net.URLEncoder;
 import java.util.Arrays;
@@ -119,7 +119,8 @@ import java.util.Vector;
 
 import org.jmol.viewer.Viewer;
 
-public class AlignFrame extends EmbmenuFrame implements ActionListener,
+public class AlignFrame extends EmbmenuFrame implements AlignFrameI,
+        ActionListener,
         ItemListener, KeyListener, AlignViewControllerGuiI
 {
   public AlignViewControllerI avc;
@@ -881,7 +882,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (source == autoCalculate)
     {
-      viewport.autoCalculateConsensus = autoCalculate.getState();
+      viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
     }
     else if (source == sortByTree)
     {
@@ -1570,7 +1571,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     try
     {
       new URL(url);
-      url = URLEncoder.encode(url, "UTF-8");
+      url = URLEncoder.encode(url);
     }
     /*
      * When we finally deprecate 1.1 compatibility, we can start to use
@@ -1583,13 +1584,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       url = viewport.applet.getCodeBase() + url;
     }
-    catch (UnsupportedEncodingException ex)
-    {
-      System.err.println(
-              "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
-                      + url);
-      ex.printStackTrace();
-    }
     return url;
   }