JAL-2110 test demonstrating limitation of current implementation of alignAs (simple...

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 7264cd2..5e04d31 100644 (file)
--- 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());