From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 13 May 2016 15:08:10 +0000 (+0100)
Subject: JAL-2103 propagate inserts only used for reconstructing profile view, currently
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Ffeatures%2FJAL-2103;p=jalview.git

JAL-2103 propagate inserts only used for reconstructing profile view, currently
---

diff --git a/src/jalview/ws/jws1/JPredWSUtils.java b/src/jalview/ws/jws1/JPredWSUtils.java
index afdd21f..42f0268 100644
--- a/src/jalview/ws/jws1/JPredWSUtils.java
+++ b/src/jalview/ws/jws1/JPredWSUtils.java
@@ -205,32 +205,22 @@ public class JPredWSUtils
         {
           al.setDataset(null);
         }
-        if (fullAlignment != null)
-        {
-          // map gapMap from positions in visible sequence to positions in
-          // original sequence
-          if (predMap != null)
-          {
-
-          }
-        }
         jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
                 FirstSeq, true, predMap);
         SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.
         if (fullAlignment == null)
         {
           alignToProfileSeq(al, profileseq);
-        }
-        if (fullAlignment == null && predMap != null)
-        {
-          // Adjust input view for gaps
-          // propagate insertions into profile
-          alcsel = ColumnSelection.propagateInsertions(profileseq, al,
-                  input);
+          if (predMap != null)
+          {
+            // Adjust input view for gaps
+            // propagate insertions into profile
+            alcsel = ColumnSelection.propagateInsertions(profileseq, al,
+                    input);
+          }
         }
       }
     }
-
     // transfer to dataset
     for (AlignmentAnnotation alant : al.getAlignmentAnnotation())
     {