diff --git a/uk/ac/sanger/artemis/components/FeatureDisplay.java b/uk/ac/sanger/artemis/components/FeatureDisplay.java
index 06a1e73224f0cc1f08bd5b4744b6390db2cb3f90..a1a66d3607fd0bbd7615b7cefc5b1ddd87a94086 100644
--- a/uk/ac/sanger/artemis/components/FeatureDisplay.java
+++ b/uk/ac/sanger/artemis/components/FeatureDisplay.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/FeatureDisplay.java,v 1.22 2005-05-03 09:12:09 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeatureDisplay.java,v 1.23 2005-05-05 14:50:39 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -45,7 +45,7 @@ import javax.swing.JComponent;
* This component is used for displaying an Entry.
*
* @author Kim Rutherford
- * @version $Id: FeatureDisplay.java,v 1.22 2005-05-03 09:12:09 tjc Exp $
+ * @version $Id: FeatureDisplay.java,v 1.23 2005-05-05 14:50:39 tjc Exp $
**/
public class FeatureDisplay extends EntryGroupPanel
@@ -1230,7 +1230,8 @@ public class FeatureDisplay extends EntryGroupPanel
{
final FeatureVector all_features = getSelection().getAllFeatures();
- for(int i = 0 ; i < all_features.size() ; ++i)
+ final int all_features_size = all_features.size();
+ for(int i = 0 ; i < all_features_size; ++i)
raiseFeature(all_features.elementAt(i));
raise_selection_flag = false;
@@ -1258,7 +1259,8 @@ public class FeatureDisplay extends EntryGroupPanel
// add features that are in visible_features and
// real_visible_features - ie features that are still visible
- for(int i = 0 ; i < visible_features.size() ; ++i)
+ final int visible_features_size = visible_features.size();
+ for(int i = 0 ; i < visible_features_size; ++i)
{
final Feature new_feature = visible_features.elementAt(i);
if(real_visible_features.contains(new_feature))
@@ -1268,26 +1270,26 @@ public class FeatureDisplay extends EntryGroupPanel
// add features that are in real_visible_features and not currently
// in visible_features and are not selected(selected features will be
// added last so that they stay on top).
- for(int i = 0 ; i < real_visible_features.size() ; ++i)
+ final int real_visible_features_size = real_visible_features.size();
+ for(int i = 0 ; i < real_visible_features_size; ++i)
{
final Feature new_feature = real_visible_features.elementAt(i);
if(!visible_features.contains(new_feature) &&
- !getSelection().contains(new_feature)) {
+ !getSelection().contains(new_feature))
new_visible_features.addElementAtEnd(new_feature);
- }
}
final FeatureVector selection_features = getSelection().getAllFeatures();
// now add features that are in real_visible_features, are not in
- // visible_features and are selected(selected features are added last so
+ // visible_features and are selected (selected features are added last so
// that they stay on top).
- for(int i = 0 ; i < real_visible_features.size() ; ++i)
+ for(int i = 0 ; i < real_visible_features_size; ++i)
{
final Feature new_feature = real_visible_features.elementAt(i);
if(!visible_features.contains(new_feature) &&
- selection_features.contains(new_feature))
+ selection_features.contains(new_feature))
new_visible_features.addElementAtEnd(new_feature);
}
@@ -1364,7 +1366,7 @@ public class FeatureDisplay extends EntryGroupPanel
final FeatureVector filtered_features = new FeatureVector();
- // filter out low and high scoring features and(possibly) source
+ // filter out low and high scoring features and (possibly) source
// features
for(int i = features_from_entry.size() - 1 ; i >= 0 ; --i)
{
@@ -1576,7 +1578,7 @@ public class FeatureDisplay extends EntryGroupPanel
final int scale_number_y_pos = scale_line * getLineHeight();
final float bases_per_pixel =
- (float)getMaxVisibleBases() / getWidth();
+ (float)getMaxVisibleBases()/getWidth();
final int base_label_spacing;
@@ -1594,7 +1596,7 @@ public class FeatureDisplay extends EntryGroupPanel
(int)Math.ceil(MINIMUM_LABEL_SPACING * bases_per_pixel / 100) * 100;
}
- final int label_spacing =(int)(base_label_spacing / bases_per_pixel);
+ final int label_spacing = (int)(base_label_spacing / bases_per_pixel);
final int possible_index_of_first_label;
final int seq_length = getSequenceLength();
@@ -1782,49 +1784,70 @@ public class FeatureDisplay extends EntryGroupPanel
if(!getOneLinePerEntryFlag())
{
if(show_forward_lines)
- drawForwardCodons(g);
+ drawCodons(g,true);
if(show_reverse_lines)
- drawReverseCodons(g);
+ // drawReverseCodons(g);
+ drawCodons(g,false);
}
}
}
}
+
/**
* Mark the start and stop codons on the three forward frame lines.
* @param g The object to draw into.
**/
- private void drawForwardCodons(Graphics g)
+ private void drawCodons(Graphics g, boolean fwd)
{
final Strand strand;
+ final int first_visible_base;
+ final int end_base;
+ final int direction;
- if(isRevCompDisplay())
- strand = getBases().getReverseStrand();
- else
- strand = getBases().getForwardStrand();
-
- final int first_visible_base = getForwardBaseAtLeftEdge();
+ if(fwd)
+ {
+ direction = FORWARD;
+ if(isRevCompDisplay())
+ strand = getBases().getReverseStrand();
+ else
+ strand = getBases().getForwardStrand();
+ first_visible_base = getForwardBaseAtLeftEdge();
+ // base to end translation at
+ // we + 3 to the upper bound because partial codons do not get translated
+ // by getTranslation()
+ end_base = getLastVisibleForwardBase() + 3;
+ }
+ else
+ {
+ direction = REVERSE;
+ if(isRevCompDisplay())
+ strand = getBases().getForwardStrand();
+ else
+ strand = getBases().getReverseStrand();
+ first_visible_base = getFirstVisibleReverseBase();
+ // base to end translation at
+ // we + 3 to the upper bound because partial codons do not get translated
+ // by getTranslation()
+ end_base = getLastVisibleReverseBase() + 3;
+ }
+
final int frame_shift = (first_visible_base - 1) % 3;
// base to start translation at - we start slightly off the
// left of the screen
int start_base = first_visible_base - frame_shift;
- // base to end translation at
- // we + 3 to the upper bound because partial codons do not get translated
- // by getTranslation()
- final int end_base = getLastVisibleForwardBase() + 3;
-
// not used if show_stop_codons is false
- int [][] forward_stop_codons = null;
+ int [][] stop_codons = null;
if(show_stop_codons)
{
- if(start_base < 1)
+ if(fwd && start_base < 1)
start_base = 1;
- forward_stop_codons = new int [][]
+ stop_codons = new int [][]
{
strand.getStopCodons(newRange(start_base, end_base)),
strand.getStopCodons(newRange(start_base + 1, end_base)),
@@ -1833,134 +1856,51 @@ public class FeatureDisplay extends EntryGroupPanel
}
// not used if show_start_codons is false
- int [][] forward_start_codons = null;
+ int [][] start_codons = null;
if(show_start_codons)
{
- final StringVector start_codons = Options.getOptions().getStartCodons();
+ final StringVector starts = Options.getOptions().getStartCodons();
-// if(Options.getOptions().isEukaryoticMode())
-// start_codons = Options.getOptions().getEukaryoticStartCodons();
-// else
-// start_codons = Options.getOptions().getProkaryoticStartCodons();
-
- forward_start_codons = new int [][]
+ start_codons = new int [][]
{
strand.getMatchingCodons(newRange(start_base, end_base),
- start_codons),
+ starts),
strand.getMatchingCodons(newRange(start_base + 1, end_base),
- start_codons),
+ starts),
strand.getMatchingCodons(newRange(start_base + 2, end_base),
- start_codons)
+ starts)
};
}
for(int i = 0 ; i < 3 ; ++i)
{
- final int frame_line = getFrameDisplayLine(FORWARD_FRAME_1 + i);
+ final int this_frame_line;
+ if(fwd)
+ this_frame_line = getFrameDisplayLine(FORWARD_FRAME_1 + i);
+ else
+ this_frame_line = getFrameDisplayLine(REVERSE_FRAME_1 - i);
if(show_start_codons)
{
- final int [] this_frame_start_codons = forward_start_codons [i];
+ final int[] this_frame_start_codons = start_codons[i];
- drawCodonMarkLine(g, frame_line,
+ drawCodonMarkLine(g, this_frame_line,
this_frame_start_codons,
- FORWARD, 80);
+ direction, 80);
}
if(show_stop_codons)
{
- final int [] this_frame_stop_codons = forward_stop_codons [i];
-
- drawCodonMarkLine(g, frame_line,
- this_frame_stop_codons,
- FORWARD, 100);
- }
- }
- }
-
- /**
- * Mark the stop codons into the three reverse frame lines.
- * @param g The object to draw into.
- **/
- private void drawReverseCodons(Graphics g)
- {
- final Strand strand;
-
- if(isRevCompDisplay())
- strand = getBases().getForwardStrand();
- else
- strand = getBases().getReverseStrand();
-
- final int first_visible_base = getFirstVisibleReverseBase();
-
- final int frame_shift = (first_visible_base - 1) % 3;
-
- // base to start translation at
- final int start_base = first_visible_base - frame_shift;
-
- // base to end translation at
- // we + 3 to the upper bound because partial codons do not get translated
- // by getTranslation()
- final int end_base = getLastVisibleReverseBase() + 3;
-
- // not used if show_stop_codons is false
- int [][] reverse_stop_codons = null;
-
- if(show_stop_codons)
- {
- reverse_stop_codons = new int [][]
- {
- strand.getStopCodons(newRange(start_base, end_base)),
- strand.getStopCodons(newRange(start_base + 1, end_base)),
- strand.getStopCodons(newRange(start_base + 2, end_base))
- };
- }
-
- // not used if show_start_codons is false
- int [][] reverse_start_codons = null;
-
- if(show_start_codons)
- {
- final StringVector start_codons = Options.getOptions().getStartCodons();;
-
-// if(Options.getOptions().isEukaryoticMode())
-// start_codons = Options.getOptions().getEukaryoticStartCodons();
-// else
-// start_codons = Options.getOptions().getProkaryoticStartCodons();
-
- reverse_start_codons = new int [][]
- {
- strand.getMatchingCodons(newRange(start_base, end_base),
- start_codons),
- strand.getMatchingCodons(newRange(start_base + 1, end_base),
- start_codons),
- strand.getMatchingCodons(newRange(start_base + 2, end_base),
- start_codons)
- };
- }
+ final int[] this_frame_stop_codons = stop_codons[i];
- for(int i = 0 ; i < 3 ; ++i)
- {
- final int frame_line = getFrameDisplayLine(REVERSE_FRAME_1 - i);
-
- if(show_start_codons)
- {
- final int [] this_frame_start_codons = reverse_start_codons [i];
- drawCodonMarkLine(g, frame_line,
- this_frame_start_codons,
- REVERSE, 80);
- }
-
- if(show_stop_codons)
- {
- final int [] this_frame_stop_codons = reverse_stop_codons [i];
- drawCodonMarkLine(g, frame_line,
+ drawCodonMarkLine(g, this_frame_line,
this_frame_stop_codons,
- REVERSE, 100);
+ direction, 100);
}
}
}
+
/**
* Draw the codon letters into the three forward frame lines.