fix for zoom to selection

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9478 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/AlignmentViewer.java

@@ -20,7 +20,7 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  *
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/AlignmentViewer.java,v 1.42 2008-06-26 09:47:18 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/AlignmentViewer.java,v 1.43 2008-11-28 17:51:09 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.components;
@@ -48,12 +48,14 @@ import java.io.IOException;
  *  ComparisonData object.
  *
  *  @author Kim Rutherford
- *  @version $Id: AlignmentViewer.java,v 1.42 2008-06-26 09:47:18 tjc Exp $
+ *  @version $Id: AlignmentViewer.java,v 1.43 2008-11-28 17:51:09 tjc Exp $
  **/
 
 public class AlignmentViewer extends CanvasPanel
     implements SequenceChangeListener 
 {
+  private static final long serialVersionUID = 1L;
+
   private Image offscreen;
 
   /** Comparison data that will be displayed in this component. */
@@ -942,7 +944,9 @@ public class AlignmentViewer extends CanvasPanel
     final boolean query_flipped   = queryIsRevComp();
 
     final int all_matches_length = all_matches.length;
-    final float base_width = last_subject_event.getBaseWidth();
+    final float base_width       = last_subject_event.getBaseWidth();
+    final float query_base_width = last_query_event.getBaseWidth();
+    
     final int subject_start = last_subject_event.getStart();
     final int query_start   = last_query_event.getStart();
     final boolean subject_is_rev_comp = subjectIsRevComp();
@@ -957,7 +961,7 @@ public class AlignmentViewer extends CanvasPanel
       is_rev_match = this_match.isRevMatch();
       match_x_positions =
         getMatchCoords(canvas_width, this_match, subject_length, query_length,
-                       subject_flipped, query_flipped, base_width, subject_start, 
+                       subject_flipped, query_flipped, base_width, query_base_width, subject_start, 
                        query_start, subject_is_rev_comp, query_is_rev_comp, is_rev_match);
 
       if(match_x_positions == null) 
@@ -1375,7 +1379,9 @@ public class AlignmentViewer extends CanvasPanel
     final boolean subject_flipped = subjectIsRevComp();
     final boolean query_flipped   = queryIsRevComp();
 
-    final float base_width = last_subject_event.getBaseWidth();
+    final float base_width       = last_subject_event.getBaseWidth();
+    final float query_base_width = last_query_event.getBaseWidth();
+    
     final int subject_start = last_subject_event.getStart();
     final int query_start   = last_query_event.getStart();
     final boolean subject_is_rev_comp = subjectIsRevComp();
@@ -1392,7 +1398,7 @@ public class AlignmentViewer extends CanvasPanel
       is_rev_match = this_match.isRevMatch();
       match_x_positions =
         getMatchCoords(canvas_width, this_match, subject_length, query_length,
-                       subject_flipped, query_flipped, base_width, subject_start, 
+                       subject_flipped, query_flipped, base_width, query_base_width, subject_start, 
                        query_start, subject_is_rev_comp, query_is_rev_comp, is_rev_match);
 
       if(match_x_positions == null) 
@@ -1761,9 +1767,9 @@ public class AlignmentViewer extends CanvasPanel
 
     int match_start;
     int match_end;
-    int delete_overlaps = -1;
+    //int delete_overlaps = -1;
 
-    Vector removals = new Vector();
+    //Vector removals = new Vector();
 
     for(int i = 0; i < all_matches.length; ++i)
     {
@@ -2048,7 +2054,8 @@ public class AlignmentViewer extends CanvasPanel
   private int[] getMatchCoords(final int canvas_width, final AlignMatch this_match,
                                final int subject_length, final int query_length,
                                final boolean subject_flipped, final boolean query_flipped,
-                               final float base_width, final int subject_start, final int query_start,
+                               final float base_width, final float query_base_width,
+                               final int subject_start, final int query_start,
                                final boolean subject_is_rev_comp, final boolean query_is_rev_comp,
                                final boolean is_rev_match)
   {
@@ -2083,9 +2090,9 @@ public class AlignmentViewer extends CanvasPanel
     final int subject_end_x   = getScreenPosition(base_width, subject_sequence_end,
                                                   subject_start);
 
-    final int query_start_x = getScreenPosition(base_width, query_sequence_start,
+    final int query_start_x = getScreenPosition(query_base_width, query_sequence_start,
                                                 query_start);
-    final int query_end_x   = getScreenPosition(base_width, query_sequence_end,
+    final int query_end_x   = getScreenPosition(query_base_width, query_sequence_end,
                                                 query_start);
 
     boolean subject_off_left  = false;
@@ -2139,22 +2146,6 @@ public class AlignmentViewer extends CanvasPanel
     return getQueryEntryGroup().getBases().getForwardStrand();
   }
 
-  /**
-   *  Return the current reverse Strand of the subject EntryGroup.
-   **/
-  private Strand getSubjectReverseStrand() 
-  {
-    return getSubjectEntryGroup().getBases().getReverseStrand();
-  }
-
-  /**
-   *  Return the current reverse Strand of the query EntryGroup.
-   **/
-  private Strand getQueryReverseStrand() 
-  {
-    return getQueryEntryGroup().getBases().getReverseStrand();
-  }
-
   /**
    *  Return the subject EntryGroup that was passed to the constructor.
    **/
@@ -2421,6 +2412,7 @@ public class AlignmentViewer extends CanvasPanel
   public class ColorChooserShades extends JPanel
                               implements javax.swing.event.ChangeListener
   {
+    private static final long serialVersionUID = 1L;
     private JPanel bannerPanel = new JPanel(new BorderLayout());
     private JColorChooser tcc;
     private Color definedColour[] = new Color[NUMBER_OF_SHADES];
@@ -2476,7 +2468,7 @@ public class AlignmentViewer extends CanvasPanel
 
     private void colourBox()
     {
-      Dimension d = new Dimension(20, 35);
+      //Dimension d = new Dimension(20, 35);
       for(int i = 0; i < NUMBER_OF_SHADES; ++i)
       {
         banner[i].setBackground(definedColour[i]);