JAL-2629 fix issue where HMM would not be added to alignment

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index fd8429b..73fbc88 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -427,6 +427,7 @@ public class FileLoader implements Runnable
                       .getSequenceAt(alignment.getAbsoluteHeight() - 1);
               seq.setIsHMMConsensusSequence(true);
               alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+              alignment.insertSequenceAt(0, seq);
               viewport.getAlignPanel().adjustAnnotationHeight();
               viewport.updateSequenceIdColours();