JAL-3297 pad gaps in alignment to ensure hmmalign runs

[jalview.git] / src / jalview / hmmer / HMMAlign.java

diff --git a/src/jalview/hmmer/HMMAlign.java b/src/jalview/hmmer/HMMAlign.java
index 57e35e7..4642034 100644 (file)
--- a/src/jalview/hmmer/HMMAlign.java
+++ b/src/jalview/hmmer/HMMAlign.java
@@ -70,6 +70,9 @@ public class HMMAlign extends HmmerCommand
     af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
             msgId);
 
+    // ensure alignments are the same length
+    alignment.padGaps();
+
     AlignmentView msa = af.gatherSequencesForAlignment();
     SequenceI[][] subAlignments = msa.getVisibleContigs(alignment.getGapCharacter());