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JAL-2629 fix HMMER validation fail due to checking for HMM incorrectly
authorTZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Mon, 28 Aug 2017 10:27:30 +0000 (11:27 +0100)
committerTZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Mon, 28 Aug 2017 10:33:28 +0000 (11:33 +0100)
src/jalview/gui/Preferences.java patch | blob | history

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)
     {