/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*/
package jalview.gui;
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
-
-import jalview.util.*;
+import java.util.*;
import java.awt.*;
import java.awt.event.*;
import java.awt.print.*;
-
-import java.util.*;
-
import javax.swing.*;
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.util.*;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class TreeCanvas extends JPanel implements MouseListener, Runnable,
+public class TreeCanvas
+ extends JPanel implements MouseListener, Runnable,
Printable, MouseMotionListener
{
/** DOCUMENT ME!! */
scrollPane = scroller;
addMouseListener(this);
addMouseMotionListener(this);
- PaintRefresher.Register(tp, ap.av.getSequenceSetId());
ToolTipManager.sharedInstance().registerComponent(this);
}
SequenceGroup selected = av.getSelectionGroup();
if ( (selected != null) &&
- selected.getSequences(false).contains( (SequenceI) node.element()))
+ selected.getSequences(null).contains( (SequenceI) node.element()))
{
g.setColor(Color.gray);
// Draw horizontal line
g.drawLine(xstart, ypos, xend, ypos);
if (node == highlightNode)
+ {
g.fillRect(xend - 3, ypos - 3, 6, 6);
+ }
else
+ {
g.fillRect(xend - 2, ypos - 2, 4, 4);
+ }
int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) +
offy;
}
else
+ {
cs = ColourSchemeProperty.getColour(sequences,
av.alignment.getWidth(),
ColourSchemeProperty.
getColourName(
av.getGlobalColourScheme()));
+ }
cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
av.getIgnoreGapsConsensus());
}
SequenceGroup sg = new SequenceGroup(sequences,
- "TreeGroup", cs, true, true, false,
+ null, cs, true, true, false,
0,
av.alignment.getWidth() - 1);
+ sg.setName("JTreeGroup:" + sg.hashCode());
+
AlignmentPanel[] aps = getAssociatedPanels();
for (int a = 0; a < aps.length; a++)
{
{
Conservation c = new Conservation("Group",
ResidueProperties.propHash, 3,
- sg.getSequences(false),
+ sg.getSequences(null),
sg.getStartRes(), sg.getEndRes());
c.calculate();
return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
}
else
- return new AlignmentPanel[]{ap};
+ {
+ return new AlignmentPanel[]
+ {
+ ap};
+ }
}
}