X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMBuild.java;h=3c3bd4089543367e81fe591cf6ee4621e6ca480a;hb=f024e66fd13fc3c4fb251291b69c36ad9ff5c8d8;hp=c596cec1b23a1ce0a11d115fc63a6974b593acdb;hpb=820c75d483648a2208039a00580bdc257b22e5f6;p=jalview.git

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index c596cec..3c3bd40 100644
--- 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)
       {
@@ -312,8 +314,8 @@ public class HMMBuild extends HmmerCommand
       args.add(ARG_DNA);
     }
 
-    args.add(hmmFile.getAbsolutePath());
-    args.add(sequencesFile.getAbsolutePath());
+    args.add(getFilePath(hmmFile));
+    args.add(getFilePath(sequencesFile));
 
     return runCommand(args);
   }
@@ -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);
     }
   }
 }