JAL-2629 choice of hmm profile now a parameter not a selection, apis simplified

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 90c509e..798875f 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -26,7 +26,6 @@ import jalview.api.FeaturesDisplayedI;
 import jalview.api.FeaturesSourceI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
-import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
@@ -426,23 +425,16 @@ public class FileLoader implements Runnable
               AlignmentI alignment = viewport.getAlignment();
               SequenceI seq = alignment
                       .getSequenceAt(alignment.getAbsoluteHeight() - 1);
-              seq.setIsHMMConsensusSequence(true);
-              AlignmentAnnotation[] annots = viewport.getAlignment()
-                      .getAlignmentAnnotation();
-              for (AlignmentAnnotation annot : annots)
+              if (seq.hasHMMProfile())
               {
-                if ("RF".equals(annot.label)
-                        || annot.label.contains("Reference"))
-                {
-                  seq.mapToReference(annot);
-                  break;
-                }
+                /* 
+                 * fudge: move HMM consensus sequence from last to first
+                 */
+                alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+                alignment.insertSequenceAt(0, seq);
               }
-              alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
-              alignment.insertSequenceAt(0, seq);
               viewport.getAlignPanel().adjustAnnotationHeight();
               viewport.updateSequenceIdColours();
-
             }
           }
           else
@@ -656,18 +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();
-  }
-
 }