diff --git a/uk/ac/sanger/artemis/components/AlignmentViewer.java b/uk/ac/sanger/artemis/components/AlignmentViewer.java
index a2d1308a232871e60afd37f33f33c04a31ed4396..e8d30b680561d660fcc42fe8bfac62ab23be649e 100644
--- a/uk/ac/sanger/artemis/components/AlignmentViewer.java
+++ b/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]);