JAL-1466 don't include empty columns if no upstream sequence data available for align...

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 5bbdc4a..85699a4 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -28,7 +28,7 @@ public class AlignmentUtils
     for (SequenceI s:core.getSequences())
     {
       SequenceI newSeq = s.deriveSequence();
-      if (newSeq.getStart()>maxoffset)
+      if (newSeq.getStart()>maxoffset && newSeq.getDatasetSequence().getStart()<s.getStart())
       {
         maxoffset = newSeq.getStart();
       }