X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=21ad1cc5832bc9cabd8771e079c61f33ee41b61a;hb=97f870ff4890ebfadcbb73e6793c83f856948658;hp=40bedad3bd03352c03f85475b41ece9a5491c963;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 40bedad..21ad1cc 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",
-            (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
-                    : new Vector<PDBEntry>());
-    sqinfo.put("datasetSequence",
-            (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
-                    : new Sequence("THISISAPLACEHOLDER", ""));
+    if (seq.getDatasetSequence() == null)
+    {
+      sqinfo.put("SeqFeatures", sfeat);
+      sqinfo.put("PdbId",
+              (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
+                      : new Vector<PDBEntry>());
+    }
+    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);
     }