JAL-1641 updated applet version

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index ee64dda..1b1a5b8 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1313,7 +1313,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.alignment_output_command", new Object[]
             { e.getActionCommand() }), 600, 500);
-    cap.setText(new AppletFormatAdapter().formatSequences(
+
+    FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+    viewport.setFeatureRenderer(fr);
+    viewport.setIncludeHiddenRegion(false);
+    cap.setText(new AppletFormatAdapter(viewport).formatSequences(
             e.getActionCommand(), viewport.getAlignment(),
             viewport.getShowJVSuffix()));
   }
@@ -4182,9 +4186,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   @Override
   public void setShowSeqFeatures(boolean b)
   {
-    // showSeqFeatures.setSelected(b);
-    // viewport.setShowSequenceFeatures(b);
-
+    this.sequenceFeatures.setState(b);
+    viewport.setShowSequenceFeatures(b);
   }
 
   @Override