From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 13 Apr 2016 20:31:42 +0000 (+0100)
Subject: JAL-2046 fix: patched SeqsetUtils so sequence features aren’t duplicated when reinsta... 
X-Git-Tag: Release_2_10_0~249^2~29
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=4b10dbcd48c997447eece2ded18b4b6393d10eec

JAL-2046 fix: patched SeqsetUtils so sequence features aren’t duplicated when reinstating sequence details
---

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 40bedad..b0ecfde 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -59,13 +59,19 @@ public class SeqsetUtils
         sfeat.addElement(sfarray[i]);
       }
     }
-    sqinfo.put("SeqFeatures", sfeat);
-    sqinfo.put("PdbId",
+    if (seq.getDatasetSequence() == null)
+    {
+      sqinfo.put("SeqFeatures", sfeat);
+      sqinfo.put("PdbId",
             (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
                     : new Vector<PDBEntry>());
-    sqinfo.put("datasetSequence",
+    }
+    else
+    {
+      sqinfo.put("datasetSequence",
             (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
                     : new Sequence("THISISAPLACEHOLDER", ""));
+    }
     return sqinfo;
   }
 
@@ -129,6 +135,11 @@ public class SeqsetUtils
             && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds
                     .getLength() == 0))
     {
+      if (sfeatures!=null)
+      {
+        System.err
+                .println("Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
+      }
       sq.setDatasetSequence(seqds);
     }