JAL-2629 hmmalign now correctly creates a new frame

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

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index 2876893..c5e1816 100644 (file)
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -58,7 +58,11 @@ public class HMMBuildThread implements Runnable
     try
     {
         hmmSeqs = alignment.getHMMConsensusSequences(true);
-        cmds.exportData(alignment, stoTemp, null, null);
+        if (!alignment.isAligned())
+        {
+          alignment.padGaps();
+        }
+        cmds.exportData(alignment.getSequencesArray(), stoTemp, null, null);
     } catch (FileNotFoundException e)
     {
       // TODO Auto-generated catch block