Uses RemoveGapsCommand

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 27503f9..73872d0 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -44,8 +44,7 @@ import org.biojava.dasobert.eventmodel.*;
  * @author $author$
  * @version $Revision$
  */
-public class AlignFrame
-    extends GAlignFrame implements DropTargetListener, FeatureListener
+public class AlignFrame extends GAlignFrame implements DropTargetListener
 {
   /** DOCUMENT ME!! */
   public static final int DEFAULT_WIDTH = 700;
@@ -115,15 +114,14 @@ public class AlignFrame
   {
     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 
-    if (viewport.hconsensus == null)
+    if (viewport.conservation == null)
     {
-      //Out of memory calculating consensus.
       BLOSUM62Colour.setEnabled(false);
-      PIDColour.setEnabled(false);
       conservationMenuItem.setEnabled(false);
       modifyConservation.setEnabled(false);
-      abovePIDThreshold.setEnabled(false);
-      modifyPID.setEnabled(false);
+    //  PIDColour.setEnabled(false);
+    //  abovePIDThreshold.setEnabled(false);
+    //  modifyPID.setEnabled(false);
     }
 
     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
@@ -490,17 +488,6 @@ public class AlignFrame
     }
   }
 
-  public void comeBackLater(FeatureEvent evt)
-  {}
-
-  public void newFeatures(FeatureEvent evt)
-  {
-    if (evt.getFeatures().length > 0)
-    {
-      alignPanel.seqPanel.seqCanvas.fr.featuresAdded();
-      alignPanel.repaint();
-    }
-  }
 
   Hashtable progressBars;
   public void setProgressBar(String message, long id)
@@ -541,6 +528,8 @@ public class AlignFrame
   }
 
 
+
+
   /*
    Added so Castor Mapping file can obtain Jalview Version
   */
@@ -1292,8 +1281,6 @@ public class AlignFrame
     for (int i = 0; i < sg.getSize(false); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
-      int index = viewport.getAlignment().findIndex(seq);
-
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
       // If the cut affects all sequences, remove highlighted columns
@@ -1308,10 +1295,6 @@ public class AlignFrame
         viewport.getAlignment().deleteSequence(seq);
         PaintRefresher.Refresh(alignPanel,alignPanel.av.getSequenceSetId(),seq,null);
       }
-      else
-      {
-        viewport.getAlignment().getSequences().setElementAt(seq, index);
-      }
     }
 
     viewport.setSelectionGroup(null);
@@ -2759,7 +2742,7 @@ public class AlignFrame
     return ShowNewickTree(nf, title, null, w, h, x, y);
   }
   /**
-   * Add a treeviewer for the tree extracted from a newick file object to the current alignment view 
+   * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
    *
    * @param nf the tree
    * @param title tree viewer title
@@ -3224,4 +3207,4 @@ public void drop(DropTargetDropEvent evt)
   {
     return viewport;
   }
-}
\ No newline at end of file
+}