From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 28 Jan 2015 15:29:32 +0000 (+0000)
Subject: JAL-1565 automatically mark query sequence as the sequence reference and hide any... 
X-Git-Tag: Jalview_2_9~102
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c04c777442ae43144dcefdae182b9fe5bded6607;p=jalview.git

JAL-1565 automatically mark query sequence as the sequence reference and hide any insertions to it
---

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index dab649e..e022c73 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -2024,6 +2024,12 @@ public class JalviewLite extends Applet implements
                     param, protocol);
             JnetAnnotationMaker.add_annotation(predictions,
                     newAlignFrame.viewport.getAlignment(), 0, false); // false==do
+            SequenceI repseq = newAlignFrame.viewport.getAlignment()
+                    .getSequenceAt(0);
+            newAlignFrame.viewport.getAlignment().setSeqrep(repseq);
+            ColumnSelection cs = new ColumnSelection();
+            cs.hideInsertionsFor(repseq);
+            newAlignFrame.viewport.setColumnSelection(cs);
             // not
             // add
             // sequence