X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;fp=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=5e04d31bdae19672cb2905485d932cfb008fda64;hb=fbc1dd3e5d38efcee395a49e1774226bf45d6687;hp=7264cd2376d11a6cd3f35fdbfc79225a20989a22;hpb=856a8f8457237311c570b4abc118aadf436077bc;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 7264cd2..5e04d31 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2624,6 +2624,8 @@ public class AlignmentUtils
     Map<SequenceI, SequenceI> alignedDatasets = new HashMap<SequenceI, SequenceI>();
     for (SequenceI seq : aligned.getSequences())
     {
+      // JAL-2110: fail if two or more alignment sequences have a common dataset
+      // sequence.
       alignedDatasets.put(seq.getDatasetSequence(), seq);
     }
 
@@ -2646,6 +2648,8 @@ public class AlignmentUtils
     {
       SequenceI alignedSequence = alignedDatasets.get(seq
               .getDatasetSequence());
+      // JAL-2110: fail if two or more alignment sequences have common dataset
+      // sequence.
       // TODO: getSequenceAsString() will be deprecated in the future
       // TODO: need to leave to SequenceI implementor to update gaps
       seq.setSequence(alignedSequence.getSequenceAsString());