JAL-2629 fix HMMER validation fail due to checking for HMM incorrectly

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index bb226a0..7c0ac95 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1316,7 +1316,7 @@ public class Preferences extends GPreferences
   {
     HMMBuildThread hmmbuild = new HMMBuildThread(alignment);
     hmmbuild.hmmbuildWaitTillComplete();
-    SequenceI hmmSeq = alignment.getSequenceAt(1);
+    SequenceI hmmSeq = alignment.getSequenceAt(0);
     HiddenMarkovModel hmm;
     if (hmmSeq.isHMMConsensusSequence() && hmmSeq.getHMM() != null)
     {