From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 17 Jun 2013 09:33:11 +0000 (+0100)
Subject: JAL-1318 avoid failure if SequenceI objects don't have valid dataset references
X-Git-Tag: Jalview_2_9~240^2~11
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e498cc04385671872ab98220219aaeac2ec245f2;p=jalview.git

JAL-1318 avoid failure if SequenceI objects don't have valid dataset references
---

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index f0041f6..5228413 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -131,11 +131,14 @@ public class Dna
       {
         pepseqs.addElement(newseq);
         SequenceI ds = newseq;
-        while (ds.getDatasetSequence() != null)
+        if (dataset != null)
         {
-          ds = ds.getDatasetSequence();
+          while (ds.getDatasetSequence() != null)
+          {
+            ds = ds.getDatasetSequence();
+          }
+          dataset.addSequence(ds);
         }
-        dataset.addSequence(ds);
       }
     }
     if (codons.aaWidth == 0)
@@ -676,7 +679,7 @@ public class Dna
   private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
           MapList map, Hashtable featureTypes, Hashtable featureGroups)
   {
-    SequenceFeature[] sf = dna.getDatasetSequence().getSequenceFeatures();
+    SequenceFeature[] sf = (dna.getDatasetSequence()!=null ? dna.getDatasetSequence() : dna).getSequenceFeatures();
     Boolean fgstate;
     jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
             .selectRefs(dna.getDBRef(),