Merge branch 'features/mchmmer' of https://source.jalview.org/git/jalview.git into...

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

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index b99ad2e..3c3bd40 100644 (file)
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -188,6 +188,8 @@ public class HMMBuild extends HmmerCommand
       boolean ran = runCommand(alignmentFile, hmmFile, ac);
       if (!ran)
       {
+        JvOptionPane.showInternalMessageDialog(af, MessageManager
+                .formatMessage("warn.command_failed", "hmmbuild"));
         return;
       }
       importData(hmmFile, ac);
@@ -215,8 +217,8 @@ public class HMMBuild extends HmmerCommand
    */
   void deleteHmmSequences(AnnotatedCollectionI ac)
   {
-    SequenceI hmmSeq = ac.getHmmConsensus();
-    if (hmmSeq != null)
+    List<SequenceI> hmmSeqs = ac.getHmmSequences();
+    for (SequenceI hmmSeq : hmmSeqs)
     {
       if (ac instanceof SequenceGroup)
       {
@@ -359,17 +361,10 @@ public class HMMBuild extends HmmerCommand
       alignment.insertSequenceAt(topIndex, hmmSeq);
       ac.setSeqrep(hmmSeq);
       grp.addSequence(hmmSeq, false);
-      grp.setHmmConsensus(hmmSeq);
     }
     else
     {
       alignment.insertSequenceAt(0, hmmSeq);
-      alignment.setHmmConsensus(hmmSeq);
-    }
-
-    if (af.getSelectedHMM() == null)
-    {
-      af.setSelectedHMMSequence(hmmSeq);
     }
   }
 }