X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Farchaeopteryx%2FAptxInit.java;h=9d248d0046dd5c53ce355877ae1a96934434a8e8;hb=b39c593c3799dc8a2ec799ce015c86d201d43da7;hp=dfc438715fabe11d225be882a66dbf8c58be8886;hpb=60e7c072c017a2a8cec9cc39139b3fca8680d0eb;p=jalview.git

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index dfc4387..9d248d0 100644
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -496,7 +496,7 @@ public final class AptxInit
     MainFrame aptxApp = Archaeopteryx.createApplication(aptxTree,
             APTX_CONFIG, treeTitle);
 
-    adaptAptxGui(aptxApp);
+
     LoadedTreeSequenceAssociation bindAptxNodes = new LoadedTreeSequenceAssociation(
             jalviewAlignport.getAlignment().getSequencesArray(), aptxTree);
     bindAptxNodes.associateLeavesToSequences();
@@ -506,6 +506,7 @@ public final class AptxInit
             bindAptxNodes.getNodesWithAlignment());
     bindTreeViewFrameToJalview(aptxApp);
 
+    adaptAptxGui(aptxApp);
     return aptxApp;
   }
 
@@ -592,7 +593,22 @@ public final class AptxInit
       else if (menu.getText().contains("View"))
       {
         menu.addSeparator();
-        menu.add(new JMenuItem("Sort alignment by tree"));
+        JMenuItem sortByTree = new JMenuItem("Sort alignment by tree");
+        JMenuItem refreshJalview = new JMenuItem(
+                "Filter alignment to show only currently visible sequences");
+
+        refreshJalview.setFont(menu.getFont());
+
+        menu.add(sortByTree);
+        menu.add(refreshJalview);
+
+        sortByTree.setFont(menu.getFont());
+        sortByTree.setVisible(false); // don't show unless it's actually
+        // possible
+
+        refreshJalview.addActionListener(activeAptx.get(aptxFrame));
+
+
       }
 
     }