JAL-2629 adjust placement and optionality of arguments/options

[jalview.git] / src / jalview / io / FileLoader.java

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 73fbc88..798875f 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -425,12 +425,16 @@ public class FileLoader implements Runnable
               AlignmentI alignment = viewport.getAlignment();
               SequenceI seq = alignment
                       .getSequenceAt(alignment.getAbsoluteHeight() - 1);
-              seq.setIsHMMConsensusSequence(true);
-              alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
-              alignment.insertSequenceAt(0, seq);
+              if (seq.hasHMMProfile())
+              {
+                /* 
+                 * fudge: move HMM consensus sequence from last to first
+                 */
+                alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+                alignment.insertSequenceAt(0, seq);
+              }
               viewport.getAlignPanel().adjustAnnotationHeight();
               viewport.updateSequenceIdColours();
-
             }
           }
           else
@@ -644,18 +648,4 @@ public class FileLoader implements Runnable
     return tempStructFile.toString();
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see java.lang.Object#finalize()
-   */
-  @Override
-  protected void finalize() throws Throwable
-  {
-    source = null;
-    alignFrame = null;
-    viewport = null;
-    super.finalize();
-  }
-
 }