X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=a50de77ae95ed0b247af8b94a86d52623ccc20b3;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=99bcff41bcd6a9bd02ebee5e087321cc76ffa42c;hpb=9c5872525e4587979d60c2a7ca93d1e527fae5c1;p=jalview.git

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 99bcff4..a50de77 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.RnaViewerModel;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -64,8 +65,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
         SecondaryStructureListener, InterfaceVARNASelectionListener,
         VamsasSource
 {
-  private static final byte[] PAIRS = new byte[]
-  { '(', ')', '[', ']', '{', '}', '<', '>' };
+  private static final byte[] PAIRS = new byte[] { '(', ')', '[', ']', '{',
+      '}', '<', '>' };
 
   private AppVarnaBinding vab;
 
@@ -181,8 +182,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     String theTitle = sname
             + (aa.sequenceRef == null ? " trimmed to " + seq.getName() : "");
     theTitle = MessageManager.formatMessage("label.varna_params",
-            new String[]
-            { theTitle });
+            new String[] { theTitle });
     setTitle(theTitle);
 
     String gappedTitle = sname + " (with gaps)";
@@ -195,7 +195,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     vab.setSelectedIndex(0);
   }
 
-
   /**
    * Constructor that links the viewer to a parent panel (but has no structures
    * yet - use addModel to add them)
@@ -402,7 +401,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
 
   @Override
   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
-          SelectionSource source)
+          HiddenColumns hidden, SelectionSource source)
   {
     if (source != ap.av)
     {
@@ -677,7 +676,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     vab.setSelectedIndex(selectedIndex);
   }
 
-
   /**
    * Add a model with associated Varna session file
    * 
@@ -716,7 +714,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     }
   }
 
-
   /**
    * Replace everything except RNA secondary structure characters with a period
    *