From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 9 Mar 2015 12:54:38 +0000 (+0000)
Subject: Merge branch 'features/JAL-1565_jpred4' into develop
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6e514532a128c47d099985375d6126111ef548cb;p=jalview.git

Merge branch 'features/JAL-1565_jpred4' into develop
---

6e514532a128c47d099985375d6126111ef548cb
diff --cc src/jalview/gui/AlignFrame.java
index 09d3594,7e451aa..71cbcaf
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -5263,9 -5211,13 +5263,14 @@@ public class AlignFrame extends GAlignF
            {
              jalview.io.JPredFile predictions = new jalview.io.JPredFile(
                      file, protocol);
 -            new JnetAnnotationMaker().add_annotation(predictions,
 +            new JnetAnnotationMaker();
 +            JnetAnnotationMaker.add_annotation(predictions,
                      viewport.getAlignment(), 0, false);
+             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
+             viewport.getAlignment().setSeqrep(repseq);
+             ColumnSelection cs = new ColumnSelection();
+             cs.hideInsertionsFor(repseq);
+             viewport.setColumnSelection(cs);
              isAnnotation = true;
            }
            else