diff --git a/uk/ac/sanger/artemis/components/AlignmentViewer.java b/uk/ac/sanger/artemis/components/AlignmentViewer.java
index efd35575662cc9782b9effe36ff46e7ba8e2351b..81c72ae3278098340dfedd8b41825f3f052d899b 100644
--- a/uk/ac/sanger/artemis/components/AlignmentViewer.java
+++ b/uk/ac/sanger/artemis/components/AlignmentViewer.java
@@ -20,14 +20,16 @@
* 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 1.9 2004-11-01 15:41:12 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/AlignmentViewer.java,v 1.10 2004-12-15 13:48:56 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.*;
-import uk.ac.sanger.artemis.sequence.*;
-
+import uk.ac.sanger.artemis.sequence.Strand;
+import uk.ac.sanger.artemis.sequence.Bases;
+import uk.ac.sanger.artemis.sequence.SequenceChangeListener;
+import uk.ac.sanger.artemis.sequence.SequenceChangeEvent;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.util.StringVector;
import uk.ac.sanger.artemis.io.Range;
@@ -36,7 +38,6 @@ import uk.ac.sanger.artemis.io.RangeVector;
import java.awt.*;
import java.awt.event.*;
import java.util.Vector;
-
import javax.swing.*;
/**
@@ -44,13 +45,12 @@ import javax.swing.*;
* ComparisonData object.
*
* @author Kim Rutherford
- * @version $Id: AlignmentViewer.java,v 1.9 2004-11-01 15:41:12 tjc Exp $
+ * @version $Id: AlignmentViewer.java,v 1.10 2004-12-15 13:48:56 tjc Exp $
**/
public class AlignmentViewer extends CanvasPanel
implements SequenceChangeListener
{
-
/** Comparison data that will be displayed in this component. */
final private ComparisonData comparison_data;
@@ -139,12 +139,12 @@ public class AlignmentViewer extends CanvasPanel
private int maximum_score = 99999999;
/**
- * Matches with percent identity values below this number will not be shown.
+ * Matches with percent id values below this number will not be shown.
**/
private int minimum_percent_id = 0;
/**
- * Matches with percent identity values above this number will not be shown.
+ * Matches with percent id values above this number will not be shown.
**/
private int maximum_percent_id = 100;
@@ -228,7 +228,7 @@ public class AlignmentViewer extends CanvasPanel
public void selectionChanged (SelectionChangeEvent event)
{
final RangeVector ranges = query_selection.getSelectionRanges ();
- selectFromQueryRanges (ranges);
+ selectFromQueryRanges(ranges);
}
};
@@ -263,7 +263,7 @@ public class AlignmentViewer extends CanvasPanel
if(isMenuTrigger(event))
return;
- if (!modifiersForLockToggle(event))
+ if(!modifiersForLockToggle(event))
{
if(!event.isShiftDown())
{
@@ -277,7 +277,7 @@ public class AlignmentViewer extends CanvasPanel
scroll_bar = new JScrollBar(Scrollbar.VERTICAL);
scroll_bar.setValues(1, 1, 1, 1000);
- scroll_bar.setBlockIncrement (10);
+ scroll_bar.setBlockIncrement(10);
scroll_bar.addAdjustmentListener(new AdjustmentListener()
{
@@ -313,38 +313,39 @@ public class AlignmentViewer extends CanvasPanel
return;
selected_matches = null;
+ final int all_matches_length = all_matches.length;
+ final int select_ranges_size = select_ranges.size();
+
+ final Strand current_subject_fwd_strand =
+ getSubjectForwardStrand();
- for(int range_index = 0; range_index < select_ranges.size();
+ final int subject_length =
+ current_subject_fwd_strand.getSequenceLength();
+
+ for(int range_index = 0; range_index < select_ranges_size;
++range_index)
{
+ final Range select_range = select_ranges.elementAt(range_index);
+ final int select_range_start = select_range.getStart();
+ final int select_range_end = select_range.getEnd();
- final Range select_range = select_ranges.elementAt (range_index);
-
- for(int match_index = 0 ;
- match_index < all_matches.length ;
+
+ for(int match_index = 0; match_index < all_matches_length;
++match_index)
{
- final AlignMatch this_match = all_matches [match_index];
+ final AlignMatch this_match = all_matches[match_index];
if(!isVisible(this_match))
continue;
- final Strand current_subject_forward_strand =
- getSubjectForwardStrand();
-
- final int subject_length =
- current_subject_forward_strand.getSequenceLength();
-
int subject_sequence_start =
- getRealSubjectSequenceStart(this_match,
- subject_length,
+ getRealSubjectSequenceStart(this_match, subject_length,
(getOrigSubjectForwardStrand () !=
- current_subject_forward_strand));
+ current_subject_fwd_strand));
int subject_sequence_end =
- getRealSubjectSequenceEnd(this_match,
- subject_length,
+ getRealSubjectSequenceEnd(this_match, subject_length,
(getOrigSubjectForwardStrand () !=
- current_subject_forward_strand));
+ current_subject_fwd_strand));
if(subject_sequence_end < subject_sequence_start)
{
@@ -353,19 +354,19 @@ public class AlignmentViewer extends CanvasPanel
subject_sequence_end = tmp;
}
- if(select_range.getStart () < subject_sequence_start &&
- select_range.getEnd () < subject_sequence_start)
+ if(select_range_start < subject_sequence_start &&
+ select_range_end < subject_sequence_start)
continue;
- if(select_range.getStart() > subject_sequence_end &&
- select_range.getEnd() > subject_sequence_end)
+ if(select_range_start > subject_sequence_end &&
+ select_range_end > subject_sequence_end)
continue;
if(selected_matches == null)
selected_matches = new AlignMatchVector();
- if(!selected_matches.contains (this_match))
- selected_matches.add (this_match);
+ if(!selected_matches.contains(this_match))
+ selected_matches.add(this_match);
}
}
@@ -381,37 +382,35 @@ public class AlignmentViewer extends CanvasPanel
return;
selected_matches = null;
+ final int select_ranges_size = select_ranges.size();
+ final int all_matches_length = all_matches.length;
+ final Strand current_query_forward_strand = getQueryForwardStrand();
+ final int query_length =
+ current_query_forward_strand.getSequenceLength();
- for(int range_index = 0 ;
- range_index < select_ranges.size () ;
+ for(int range_index = 0; range_index < select_ranges_size;
++range_index)
{
- final Range select_range = select_ranges.elementAt (range_index);
+ final Range select_range = select_ranges.elementAt(range_index);
+ final int select_range_start = select_range.getStart();
+ final int select_range_end = select_range.getEnd();
- for(int match_index = 0 ;
- match_index < all_matches.length ;
+ for(int match_index = 0; match_index < all_matches_length;
++match_index)
{
- final AlignMatch this_match = all_matches [match_index];
+ final AlignMatch this_match = all_matches[match_index];
if(!isVisible (this_match))
continue;
- final Strand current_query_forward_strand = getQueryForwardStrand();
-
- final int query_length =
- current_query_forward_strand.getSequenceLength();
-
int query_sequence_start =
- getRealQuerySequenceStart(this_match,
- query_length,
- (getOrigQueryForwardStrand () !=
- current_query_forward_strand));
+ getRealQuerySequenceStart(this_match, query_length,
+ (getOrigQueryForwardStrand() !=
+ current_query_forward_strand));
int query_sequence_end =
- getRealQuerySequenceEnd(this_match,
- query_length,
- (getOrigQueryForwardStrand () !=
- current_query_forward_strand));
+ getRealQuerySequenceEnd(this_match, query_length,
+ (getOrigQueryForwardStrand() !=
+ current_query_forward_strand));
if(query_sequence_end < query_sequence_start)
{
@@ -420,19 +419,19 @@ public class AlignmentViewer extends CanvasPanel
query_sequence_end = tmp;
}
- if(select_range.getStart () < query_sequence_start &&
- select_range.getEnd () < query_sequence_start)
+ if(select_range_start < query_sequence_start &&
+ select_range_end < query_sequence_start)
continue;
- if(select_range.getStart () > query_sequence_end &&
- select_range.getEnd () > query_sequence_end)
+ if(select_range_start > query_sequence_end &&
+ select_range_end > query_sequence_end)
continue;
if(selected_matches == null)
- selected_matches = new AlignMatchVector ();
+ selected_matches = new AlignMatchVector();
- if(!selected_matches.contains (this_match))
- selected_matches.add (this_match);
+ if(!selected_matches.contains(this_match))
+ selected_matches.add(this_match);
}
}
@@ -445,7 +444,7 @@ public class AlignmentViewer extends CanvasPanel
public void setSelection(final AlignMatch match)
{
selected_matches = new AlignMatchVector();
- selected_matches.add (match);
+ selected_matches.add(match);
selectionChanged();
}
@@ -482,10 +481,10 @@ public class AlignmentViewer extends CanvasPanel
* Return true if and only if the given MouseEvent (a mouse press) should
* pop up a JPopupMenu.
**/
- private boolean isMenuTrigger (final MouseEvent event)
+ private boolean isMenuTrigger(final MouseEvent event)
{
- if( event.isPopupTrigger () ||
- (event.getModifiers () & InputEvent.BUTTON3_MASK) != 0)
+ if( event.isPopupTrigger() ||
+ (event.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
return true;
else
return false;
@@ -496,7 +495,7 @@ public class AlignmentViewer extends CanvasPanel
**/
private void popupMenu(final MouseEvent event)
{
- final JPopupMenu popup = new JPopupMenu ();
+ final JPopupMenu popup = new JPopupMenu();
final JMenuItem alignmatch_list_item =
new JMenuItem("View Selected Matches");
@@ -517,13 +516,13 @@ public class AlignmentViewer extends CanvasPanel
final AlignMatchViewer viewer =
new AlignMatchViewer(AlignmentViewer.this, matches);
- viewer.setVisible (true);
+ viewer.setVisible(true);
}
}
});
final JMenuItem flip_subject_item =
- new JMenuItem ("Flip Subject Sequence");
+ new JMenuItem("Flip Subject Sequence");
popup.add (flip_subject_item);
@@ -531,10 +530,10 @@ public class AlignmentViewer extends CanvasPanel
{
public void actionPerformed(ActionEvent _)
{
- if(getSubjectDisplay().isRevCompDisplay ())
- getSubjectDisplay().setRevCompDisplay (false);
+ if(getSubjectDisplay().isRevCompDisplay())
+ getSubjectDisplay().setRevCompDisplay(false);
else
- getSubjectDisplay().setRevCompDisplay (true);
+ getSubjectDisplay().setRevCompDisplay(true);
}
});
@@ -554,32 +553,7 @@ public class AlignmentViewer extends CanvasPanel
}
});
- final JMenuItem lock_item = new JMenuItem("Lock Sequences");
-
- popup.add(lock_item);
-
- lock_item.addActionListener(new ActionListener ()
- {
- public void actionPerformed(ActionEvent _)
- {
- lockDisplays ();
- }
- });
-
- final JMenuItem unlock_item = new JMenuItem("Unlock Sequences");
-
- popup.add(unlock_item);
-
- unlock_item.addActionListener(new ActionListener ()
- {
- public void actionPerformed(ActionEvent _)
- {
- unlockDisplays ();
- }
- });
-
final JMenuItem cutoffs_item = new JMenuItem("Set Score Cutoffs ...");
-
popup.add(cutoffs_item);
cutoffs_item.addActionListener(new ActionListener()
@@ -597,7 +571,7 @@ public class AlignmentViewer extends CanvasPanel
};
final ScoreChangeListener maximum_listener =
- new ScoreChangeListener ()
+ new ScoreChangeListener()
{
public void scoreChanged(final ScoreChangeEvent event)
{
@@ -618,7 +592,6 @@ public class AlignmentViewer extends CanvasPanel
final JMenuItem percent_id_cutoffs_item =
new JMenuItem("Set Percent ID Cutoffs ...");
-
popup.add(percent_id_cutoffs_item);
percent_id_cutoffs_item.addActionListener(new ActionListener ()
@@ -654,6 +627,22 @@ public class AlignmentViewer extends CanvasPanel
}
});
+
+ final JCheckBoxMenuItem lock_item = new JCheckBoxMenuItem("Lock Sequences");
+ lock_item.setSelected(displaysAreLocked());
+ popup.add(lock_item);
+
+ lock_item.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ if(lock_item.isSelected())
+ lockDisplays();
+ else
+ unlockDisplays();
+ }
+ });
+
popup.addSeparator();
final JCheckBoxMenuItem sameColour =
@@ -752,13 +741,11 @@ public class AlignmentViewer extends CanvasPanel
ColorChooserShades newContentPane = new ColorChooserShades(title,initialColour);
Object[] possibleValues = { "OK", "CANCEL" };
- int select = JOptionPane.showOptionDialog(null,
- newContentPane,
+ int select = JOptionPane.showOptionDialog(null, newContentPane,
"Colour Selection",
JOptionPane.DEFAULT_OPTION,
JOptionPane.QUESTION_MESSAGE,null,
possibleValues, possibleValues[0]);
-
if(select == 0)
return newContentPane;
@@ -766,7 +753,6 @@ public class AlignmentViewer extends CanvasPanel
}
-
/**
* Handle a mouse press event on the drawing canvas - select on click,
* select and broadcast it on double click.
@@ -777,9 +763,9 @@ public class AlignmentViewer extends CanvasPanel
return;
if(event.getClickCount() == 2)
- handleCanvasDoubleClick (event);
+ handleCanvasDoubleClick(event);
else
- handleCanvasSingleClick (event);
+ handleCanvasSingleClick(event);
repaint();
}
@@ -789,12 +775,9 @@ public class AlignmentViewer extends CanvasPanel
**/
private void handleCanvasDoubleClick(final MouseEvent event)
{
+ // there should be only one match in the array
if(selected_matches != null)
- {
- // there should be only one match in the array because
- // handleCanvasSingleClick () has been called
- alignAt(selected_matches.elementAt (0));
- }
+ alignAt(selected_matches.elementAt(0));
}
/**
@@ -832,7 +815,7 @@ public class AlignmentViewer extends CanvasPanel
if(!event.isShiftDown())
selected_matches = null;
- toggleSelection (event.getPoint ());
+ toggleSelection(event.getPoint());
}
}
@@ -853,19 +836,18 @@ public class AlignmentViewer extends CanvasPanel
}
else
{
- if (selected_matches.contains (clicked_align_match)) {
- selected_matches.remove (clicked_align_match);
- if (selected_matches.size () == 0) {
+ if(selected_matches.contains(clicked_align_match))
+ {
+ selected_matches.remove(clicked_align_match);
+ if(selected_matches.size() == 0)
selected_matches = null;
- }
- } else {
- selected_matches.add (clicked_align_match);
}
+ else
+ selected_matches.add(clicked_align_match);
}
-
}
- selectionChanged ();
+ selectionChanged();
}
/**
@@ -873,7 +855,7 @@ public class AlignmentViewer extends CanvasPanel
* no match at that point. The alignment_data_array is searched in reverse
* order.
**/
- private AlignMatch getAlignMatchFromPosition (final Point click_point)
+ private AlignMatch getAlignMatchFromPosition(final Point click_point)
{
final int canvas_height = getSize().height;
final int canvas_width = getSize().width;
@@ -884,7 +866,9 @@ public class AlignmentViewer extends CanvasPanel
final boolean subject_flipped = subjectIsRevComp();
final boolean query_flipped = queryIsRevComp();
- for(int i = all_matches.length - 1; i >= 0 ; --i)
+ final int all_matches_length = all_matches.length;
+
+ for(int i = all_matches_length - 1; i >= 0 ; --i)
{
final AlignMatch this_match = all_matches [i];
@@ -928,38 +912,40 @@ public class AlignmentViewer extends CanvasPanel
}
/**
- * This method is called by setSelection () and others whenever the list of
- * selected/highlighted hits changes. Calls alignmentSelectionChanged ()
+ * This method is called by setSelection() and others whenever the list of
+ * selected/highlighted hits changes. Calls alignmentSelectionChanged()
* on all interested AlignmentSelectionChangeListener objects, moves the
* selected matches to the top of the display and then calls
* repaint
**/
private void selectionChanged()
{
- for(int i = 0 ; i < selection_change_listeners.size () ; ++i)
+ for(int i = 0 ; i < selection_change_listeners.size() ; ++i)
{
final AlignMatchVector matches =
- (AlignMatchVector) selected_matches.clone ();
+ (AlignMatchVector) selected_matches.clone();
final AlignmentSelectionChangeEvent ev =
- new AlignmentSelectionChangeEvent (this, matches);
+ new AlignmentSelectionChangeEvent(this, matches);
final AlignmentSelectionChangeListener listener =
- (AlignmentSelectionChangeListener) selection_change_listeners.elementAt (i);
+ (AlignmentSelectionChangeListener)selection_change_listeners.elementAt(i);
- listener.alignmentSelectionChanged (ev);
+ listener.alignmentSelectionChanged(ev);
}
- if(selected_matches != null && selected_matches.size () > 0)
+ final int selected_matches_size = selected_matches.size();
+ if(selected_matches != null && selected_matches_size > 0)
{
// a count of the number of selected matches seen so far
int seen_and_selected_count = 0;
+ final int all_matches_length = all_matches.length;
- for(int i = 0 ; i < all_matches.length ; ++i)
+ for(int i = 0 ; i < all_matches_length ; ++i)
{
final AlignMatch this_match = all_matches[i];
- if (selected_matches.contains (this_match))
+ if(selected_matches.contains(this_match))
++seen_and_selected_count;
else
{
@@ -972,10 +958,10 @@ public class AlignmentViewer extends CanvasPanel
}
// put the selected_matches at the end of all_matches
- for(int i = 0 ; i < selected_matches.size () ; ++i)
+ for(int i = 0; i < selected_matches_size; ++i)
{
- all_matches[all_matches.length - selected_matches.size () + i] =
- selected_matches.elementAt (i);
+ all_matches[all_matches_length - selected_matches_size + i] =
+ selected_matches.elementAt(i);
}
}
@@ -1101,11 +1087,11 @@ public class AlignmentViewer extends CanvasPanel
(scroll_bar.getMaximum() -
scroll_bar.getMinimum())) * canvas_height);
- if(cutoff_label_position < getFontAscent ())
- cutoff_label_position = getFontAscent ();
+ if(cutoff_label_position < getFontAscent())
+ cutoff_label_position = getFontAscent();
- final int [] cutoff_x_points =
+ final int[] cutoff_x_points =
{
canvas_width - cutoff_label_width,
canvas_width - 2,
@@ -1113,120 +1099,119 @@ public class AlignmentViewer extends CanvasPanel
canvas_width - cutoff_label_width,
};
- final int [] cutoff_y_points =
+ final int[] cutoff_y_points =
{
cutoff_label_position + 1,
cutoff_label_position + 1,
- cutoff_label_position - getFontAscent (),
- cutoff_label_position - getFontAscent (),
+ cutoff_label_position - getFontAscent(),
+ cutoff_label_position - getFontAscent(),
};
g.setColor(Color.white);
g.fillPolygon(cutoff_x_points, cutoff_y_points, 4);
g.setColor(Color.black);
-
g.drawString(cutoff_label, canvas_width - cutoff_label_width,
- cutoff_label_position);
+ cutoff_label_position);
- final int font_height = getFontAscent () + getFontDescent ();
+ final int font_height = getFontAscent() + getFontDescent();
if(selected_matches != null)
{
final String match_string_1;
- if(selected_matches.size () > 1)
- match_string_1 = selected_matches.size () + " matches selected";
+ if(selected_matches.size() > 1)
+ match_string_1 = selected_matches.size() + " matches selected";
else
{
- final AlignMatch selected_align_match = selected_matches.elementAt (0);
+ final AlignMatch selected_align_match = selected_matches.elementAt(0);
match_string_1 =
- selected_align_match.getQuerySequenceStart () + ".." +
- selected_align_match.getQuerySequenceEnd () + " -> " +
- selected_align_match.getSubjectSequenceStart () + ".." +
- selected_align_match.getSubjectSequenceEnd ();
+ selected_align_match.getQuerySequenceStart() + ".." +
+ selected_align_match.getQuerySequenceEnd() + " -> " +
+ selected_align_match.getSubjectSequenceStart() + ".." +
+ selected_align_match.getSubjectSequenceEnd();
}
- final int match_string_1_width = fm.stringWidth (match_string_1);
+ final int match_string_1_width = fm.stringWidth(match_string_1);
- final int [] match_1_x_points =
+ final int[] match_1_x_points =
{
0, 0, match_string_1_width, match_string_1_width
};
- final int [] match_1_y_points =
+ final int[] match_1_y_points =
{
0, font_height, font_height, 0
};
- g.setColor (Color.white);
- g.fillPolygon (match_1_x_points, match_1_y_points, 4);
+ g.setColor(Color.white);
+ g.fillPolygon(match_1_x_points, match_1_y_points, 4);
- g.setColor (Color.black);
- g.drawString (match_string_1, 0, getFontAscent ());
+ g.setColor(Color.black);
+ g.drawString(match_string_1, 0, getFontAscent ());
- if (selected_matches.size () == 1)
+ if(selected_matches.size() == 1)
{
- final AlignMatch selected_align_match = selected_matches.elementAt (0);
+ final AlignMatch selected_align_match = selected_matches.elementAt(0);
final String match_string_2 = "score: " +
- selected_align_match.getScore () + " percent id: " +
- selected_align_match.getPercentID () + "%";
+ selected_align_match.getScore() + " percent id: " +
+ selected_align_match.getPercentID() + "%";
- final int match_string_2_width = fm.stringWidth (match_string_2);
+ final int match_string_2_width = fm.stringWidth(match_string_2);
- final int [] match_2_x_points =
+ final int[] match_2_x_points =
{
0, 0, match_string_2_width, match_string_2_width
};
- final int [] match_2_y_points =
+ final int[] match_2_y_points =
{
font_height, font_height * 2, font_height * 2, font_height
};
- g.setColor (Color.white);
- g.fillPolygon (match_2_x_points, match_2_y_points, 4);
+ g.setColor(Color.white);
+ g.fillPolygon(match_2_x_points, match_2_y_points, 4);
- g.setColor (Color.black);
- g.drawString (match_string_2, 0, getFontAscent () + font_height);
+ g.setColor(Color.black);
+ g.drawString(match_string_2, 0, getFontAscent() + font_height);
}
}
- final StringVector status_strings = new StringVector ();
+ final StringVector status_strings = new StringVector();
- if(displaysAreLocked ())
- status_strings.add ("LOCKED");
+ if(displaysAreLocked())
+ status_strings.add("LOCKED");
- if(getSubjectDisplay ().isRevCompDisplay ())
- status_strings.add ("Subject: Flipped");
+ if(getSubjectDisplay().isRevCompDisplay())
+ status_strings.add("Subject: Flipped");
- if(getQueryDisplay ().isRevCompDisplay ())
- status_strings.add ("Query: Flipped");
+ if(getQueryDisplay().isRevCompDisplay())
+ status_strings.add("Query: Flipped");
- if(getOrigSubjectForwardStrand () != getSubjectForwardStrand ())
- status_strings.add ("Subject: Reverse Complemented");
+ if(getOrigSubjectForwardStrand() != getSubjectForwardStrand())
+ status_strings.add("Subject: Reverse Complemented");
- if(getOrigQueryForwardStrand () != getQueryForwardStrand ())
- status_strings.add ("Query: Reverse Complemented");
+ if(getOrigQueryForwardStrand() != getQueryForwardStrand())
+ status_strings.add("Query: Reverse Complemented");
g.setColor(Color.white);
- for(int i = 0 ; i < status_strings.size () ; ++i)
+ for(int i = 0 ; i < status_strings.size() ; ++i)
{
- final String status_string = status_strings.elementAt (i);
+ final String status_string = status_strings.elementAt(i);
- final int status_string_width = fm.stringWidth (status_string);
+ final int status_string_width = fm.stringWidth(status_string);
- final int [] x_points =
+ final int[] x_points =
{
0, 0, status_string_width, status_string_width
};
final int string_offset = font_height * (status_strings.size () - i - 1);
- final int [] y_points =
+ final int[] y_points =
{
canvas_height - string_offset,
canvas_height - font_height - string_offset,
@@ -1234,19 +1219,17 @@ public class AlignmentViewer extends CanvasPanel
canvas_height - string_offset
};
- g.fillPolygon (x_points, y_points, 4);
+ g.fillPolygon(x_points, y_points, 4);
}
- g.setColor (Color.black);
-
- for(int i = 0 ; i < status_strings.size () ; ++i)
+ g.setColor(Color.black);
+ for(int i = 0; i < status_strings.size(); ++i)
{
- final String status_string = status_strings.elementAt (i);
-
- final int string_offset = font_height * (status_strings.size () - i - 1);
+ final String status_string = status_strings.elementAt(i);
+ final int string_offset = font_height * (status_strings.size() - i - 1);
g.drawString(status_string, 0,
- canvas_height - string_offset - getFontDescent ());
+ canvas_height - string_offset - getFontDescent());
}
}
@@ -1256,8 +1239,8 @@ public class AlignmentViewer extends CanvasPanel
private void drawAlignments(final Graphics g)
{
final int canvas_height = getSize().height;
- final int canvas_width = getSize().width;
- final int OFFSCREEN = 3000;
+ final int canvas_width = getSize().width;
+ final int OFFSCREEN = 3000;
final int subject_length = getSubjectForwardStrand().getSequenceLength();
final int query_length = getQueryForwardStrand().getSequenceLength();
@@ -1339,14 +1322,13 @@ public class AlignmentViewer extends CanvasPanel
g.fillPolygon(x_coords, y_coords, x_coords.length);
- if (subject_end_x - subject_start_x < 5 &&
- subject_end_x - subject_start_x > -5 ||
- subject_start_x < -OFFSCREEN ||
- subject_end_x > OFFSCREEN ||
- query_start_x < -OFFSCREEN ||
- query_end_x > OFFSCREEN)
+ if(subject_end_x - subject_start_x < 5 &&
+ subject_end_x - subject_start_x > -5 ||
+ subject_start_x < -OFFSCREEN ||
+ subject_end_x > OFFSCREEN ||
+ query_start_x < -OFFSCREEN ||
+ query_end_x > OFFSCREEN)
{
-
// match is (probably) narrow so draw the border to the same colour as
// the polygon
}
@@ -1404,9 +1386,9 @@ public class AlignmentViewer extends CanvasPanel
final boolean reverse_position)
{
if(reverse_position)
- return sequence_length - match.getSubjectSequenceStart () + 1;
+ return sequence_length - match.getSubjectSequenceStart() + 1;
else
- return match.getSubjectSequenceStart ();
+ return match.getSubjectSequenceStart();
}
/**
@@ -1420,9 +1402,9 @@ public class AlignmentViewer extends CanvasPanel
final boolean reverse_position)
{
if(reverse_position)
- return sequence_length - match.getSubjectSequenceEnd () + 1;
+ return sequence_length - match.getSubjectSequenceEnd() + 1;
else
- return match.getSubjectSequenceEnd ();
+ return match.getSubjectSequenceEnd();
}
/**
@@ -1451,10 +1433,10 @@ public class AlignmentViewer extends CanvasPanel
final int sequence_length,
final boolean reverse_position)
{
- if (reverse_position)
- return sequence_length - match.getQuerySequenceEnd () + 1;
+ if(reverse_position)
+ return sequence_length - match.getQuerySequenceEnd() + 1;
else
- return match.getQuerySequenceEnd ();
+ return match.getQuerySequenceEnd();
}
/**
@@ -1614,12 +1596,11 @@ public class AlignmentViewer extends CanvasPanel
**/
boolean subjectIsRevComp()
{
- final Strand current_subject_forward_strand = getSubjectForwardStrand ();
+ final Strand current_subject_forward_strand = getSubjectForwardStrand();
- if(getOrigSubjectForwardStrand () == current_subject_forward_strand ^
- getSubjectDisplay ().isRevCompDisplay ()) {
+ if(getOrigSubjectForwardStrand() == current_subject_forward_strand ^
+ getSubjectDisplay().isRevCompDisplay())
return false;
- }
else
return true;
}
@@ -1632,8 +1613,8 @@ public class AlignmentViewer extends CanvasPanel
{
final Strand current_query_forward_strand = getQueryForwardStrand ();
- if(getOrigQueryForwardStrand () == current_query_forward_strand ^
- getQueryDisplay ().isRevCompDisplay ())
+ if(getOrigQueryForwardStrand() == current_query_forward_strand ^
+ getQueryDisplay().isRevCompDisplay())
return false;
else
return true;
@@ -1643,7 +1624,7 @@ public class AlignmentViewer extends CanvasPanel
* Return the forward Strand of the subject EntryGroup from when the
* Comparator was created.
**/
- public Strand getOrigSubjectForwardStrand ()
+ public Strand getOrigSubjectForwardStrand()
{
return orig_subject_forward_strand;
}
@@ -1652,7 +1633,7 @@ public class AlignmentViewer extends CanvasPanel
* Return the forward Strand of the query EntryGroup from when the
* Comparator was created.
**/
- public Strand getOrigQueryForwardStrand ()
+ public Strand getOrigQueryForwardStrand()
{
return orig_query_forward_strand;
}
@@ -1661,7 +1642,7 @@ public class AlignmentViewer extends CanvasPanel
* Return the reverse Strand of the subject EntryGroup from when the
* Comparator was created.
**/
- public Strand getOrigSubjectReverseStrand ()
+ public Strand getOrigSubjectReverseStrand()
{
return orig_subject_reverse_strand;
}
@@ -1670,7 +1651,7 @@ public class AlignmentViewer extends CanvasPanel
* Return the reverse Strand of the query EntryGroup from when the
* Comparator was created.
**/
- public Strand getOrigQueryReverseStrand ()
+ public Strand getOrigQueryReverseStrand()
{
return orig_query_reverse_strand;
}
@@ -1678,7 +1659,7 @@ public class AlignmentViewer extends CanvasPanel
/**
* Arrange for the two FeatureDisplay objects to scroll in parallel.
**/
- public void lockDisplays ()
+ protected void lockDisplays()
{
displays_are_locked = true;
repaint();
@@ -1687,7 +1668,7 @@ public class AlignmentViewer extends CanvasPanel
/**
* Arrange for the two FeatureDisplay objects to scroll independently.
**/
- public void unlockDisplays ()
+ protected void unlockDisplays()
{
displays_are_locked = false;
repaint();
@@ -1696,7 +1677,7 @@ public class AlignmentViewer extends CanvasPanel
/**
* Return true if and only if the displays are currently locked.
**/
- public boolean displaysAreLocked ()
+ protected boolean displaysAreLocked()
{
return displays_are_locked;
}
@@ -1704,7 +1685,7 @@ public class AlignmentViewer extends CanvasPanel
/**
* Toggle whether the two displays are locked.
**/
- public void toggleDisplayLock ()
+ protected void toggleDisplayLock()
{
displays_are_locked = !displays_are_locked;
repaint();
@@ -1716,7 +1697,7 @@ public class AlignmentViewer extends CanvasPanel
* the selections of the top and bottom FeatureDisplays to be set without
* changing which AlignMatches are selected.
**/
- public void disableSelection ()
+ protected void disableSelection()
{
disable_selection_from_ranges = true;
}
@@ -1724,7 +1705,7 @@ public class AlignmentViewer extends CanvasPanel
/**
* Enable selectFromQueryRange() and selectFromSubjectRange().
**/
- public void enableSelection ()
+ protected void enableSelection()
{
disable_selection_from_ranges = false;
}
@@ -1802,7 +1783,6 @@ public class AlignmentViewer extends CanvasPanel
banner[i] = new JLabel(" "+percent_id+" ",JLabel.CENTER);
banner[i].setOpaque(true);
banner[i].setPreferredSize(d);
-// banner[i].setMaximumSize(d);
bacross.add(banner[i]);
}