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 f3a4a1c..798875f 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -29,7 +29,6 @@ import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
@@ -426,33 +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);
-              SequenceGroup sg = viewport.getSelectionGroup();
-              if (sg != null)
-              {
-                seq.insertCharAt(0, sg.getStartRes(), '-');
-                seq.insertCharAt(sg.getEndRes() + 1,
-                        alignment.getWidth() - sg.getEndRes(), '-');
-                SequenceI topSeq = sg.getSequencesInOrder(alignment)[0];
-                int topIndex = alignment.findIndex(topSeq);
-                alignment.insertSequenceAt(topIndex, seq);
-                sg.setSeqrep(seq);
-                viewport.getSelectionGroup().addSequence(seq, false);
-              }
-              else
+              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();
-              if (viewport.getAlignPanel().alignFrame
-                      .getSelectedHMM() == null)
-              {
-                viewport.getAlignPanel().alignFrame
-                        .setSelectedHMMSequence(seq);
-              }
-
             }
           }
           else
@@ -666,18 +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();
-  }
-
 }