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

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

diff --git a/src/jalview/hmmer/HMMAlign.java b/src/jalview/hmmer/HMMAlign.java
index 6300c4b..b5f047e 100644 (file)
--- a/src/jalview/hmmer/HMMAlign.java
+++ b/src/jalview/hmmer/HMMAlign.java
@@ -64,12 +64,7 @@ public class HMMAlign extends HmmerCommand
   @Override
   public void run()
   {
-    HiddenMarkovModel hmm = af.getSelectedHMM();
-    if (hmm == null)
-    {
-      System.err.println("Can't run hmmalign as no HMM profile selected");
-      return;
-    }
+    HiddenMarkovModel hmm = getHmmProfile();
 
     long msgId = System.currentTimeMillis();
     af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
@@ -97,8 +92,8 @@ public class HMMAlign extends HmmerCommand
         boolean ran = runCommand(modelFile, alignmentFile, resultFile);
         if (!ran)
         {
-          JvOptionPane.showInternalMessageDialog(af,
-                  MessageManager.getString("warn.hmmalign_failed"));
+          JvOptionPane.showInternalMessageDialog(af, MessageManager
+                  .formatMessage("warn.command_failed", "hmmalign"));
           return;
         }
 
@@ -212,14 +207,6 @@ public class HMMAlign extends HmmerCommand
       al.setDataset(dataset);
     }
 
-    /*
-     * hack to ensure hmm set on alignment
-     */
-    if (al.getSequenceAt(0).hasHMMProfile())
-    {
-      al.setHmmConsensus(al.getSequenceAt(0));
-    }
-
     displayInNewFrame(al, allOrders, hidden, title);
   }