JAL-2629 hmmalign now correctly creates a new frame

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 91529de..39dad15 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -168,7 +168,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   boolean autoAlignNewSequences;
 
-  boolean recurring;
 
   /*
    * The currently displayed panel (selected tabbed view if more than one)
@@ -340,11 +339,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     init();
   }
 
-  public void setIsRecurring(boolean status)
-  {
-    recurring = status;
-  }
-
   /**
    * initalise the alignframe from the underlying viewport data and the
    * configurations
@@ -4743,7 +4737,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType));
             HiddenMarkovModel hmm = hmmFile.getHMM();
             SequenceI hmmSeq = hmm.initHMMSequence(this, 0);
-            getViewport().initInformation(hmmSeq);
+            getViewport().initInformation();
             getViewport().updateInformation(alignPanel);
             getViewport().alignmentChanged(alignPanel);
             isAnnotation = true;
@@ -4773,10 +4767,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           else
           {
             new FileLoader().LoadFile(viewport, file, sourceType, format);
-            if (autoAlignNewSequences && !recurring)
-            {
-              new Thread(new HMMAlignThread(this, false)).start();
-            }
           }
         }
       }