X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=d58cb5ad784492b37a9173899e6eadaa373b9290;hb=7d722306ebba9a2d6562849c598a91d867f7d00e;hp=75ddba56a4df0749fa8220be6e9ec72d323b71b0;hpb=fee1b781ca14aadea5d112fc554fe14879c787c5;p=jalview.git

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 75ddba5..d58cb5a 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.VamsasAppDatastore;
@@ -43,7 +44,6 @@ import java.util.IdentityHashMap;
 import java.util.Iterator;
 
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 
 import uk.ac.vamsas.client.ClientHandle;
 import uk.ac.vamsas.client.IClient;
@@ -821,7 +821,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               {
                 // TODO: rationalise : can only clear a selection over a
                 // referred to object
-                ssm.sendSelection(null, null, me);
+                ssm.sendSelection(null, null, null, me);
                 return;
               }
               Class type = null;
@@ -955,7 +955,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               }
               if (send)
               {
-                ssm.sendSelection(jselection, colsel, me);
+                ssm.sendSelection(jselection, colsel, null, me);
               }
               // discard message.
               for (int c = 0; c < jvobjs.length; c++)
@@ -1004,7 +1004,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource
 
           @Override
           public void selection(SequenceGroup seqsel,
-                  ColumnSelection colsel, SelectionSource source)
+                  ColumnSelection colsel, HiddenColumns hidden,
+                  SelectionSource source)
           {
             if (vobj2jv == null)
             {
@@ -1079,7 +1080,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   }
                   else
                   {
-                    int[] intervals = colsel.getVisibleContigs(
+                    // int[] intervals = colsel.getVisibleContigs(
+                    // seqsel.getStartRes(), seqsel.getEndRes() + 1);
+                    int[] intervals = hidden.getVisibleContigs(
                             seqsel.getStartRes(), seqsel.getEndRes() + 1);
                     for (int iv = 0; iv < intervals.length; iv += 2)
                     {