/*
* 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!! */
public static final String PLACEHOLDER = " * ";
NJTree tree;
JScrollPane scrollPane;
+ TreePanel tp;
AlignViewport av;
AlignmentPanel ap;
Font font;
* @param scroller DOCUMENT ME!
* @param label DOCUMENT ME!
*/
- public TreeCanvas(AlignmentPanel ap, JScrollPane scroller)
+ public TreeCanvas(TreePanel tp,
+ AlignmentPanel ap,
+ JScrollPane scroller)
{
+ this.tp = tp;
this.av = ap.av;
this.ap = ap;
font = av.getFont();
scrollPane = scroller;
addMouseListener(this);
addMouseMotionListener(this);
- PaintRefresher.Register(this, ap.av.getSequenceSetId());
ToolTipManager.sharedInstance().registerComponent(this);
}
nodeLabel = nodeLabel + " : ";
}
- nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
+ nodeLabel = nodeLabel + String.valueOf(node.bootstrap);
}
if (!nodeLabel.equals(""))
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;
g.drawLine( (int) (height * scale) + offx, ystart,
(int) (height * scale) + offx, yend);
+ String nodeLabel = "";
+
if (showDistances && (node.dist > 0))
{
- g.drawString(new Format("%-.2f").form(node.dist).trim(), xstart + 2,
- ypos - 2);
+ nodeLabel = new Format("%-.2f").form(node.dist);
+ }
+
+ if (showBootstrap)
+ {
+ if (showDistances)
+ {
+ nodeLabel = nodeLabel + " : ";
+ }
+
+ nodeLabel = nodeLabel + String.valueOf(node.bootstrap);
+ }
+
+ if (!nodeLabel.equals(""))
+ {
+ g.drawString(nodeLabel, xstart + 2, ypos - 2);
}
}
}
return;
}
- if ( (node.left() == null) && (node.right() == null))
+ if ( (node.left() == null) && (node.right() == null)) // TODO: internal node
{
node.color = c;
{
Color col = JColorChooser.showDialog(this, "Select Sub-Tree Colour",
highlightNode.color);
-
- setColor(highlightNode, col);
+ if (col!=null)
+ {
+ setColor(highlightNode, col);
+ }
}
else
if (evt.getClickCount() > 1)
}
}
- PaintRefresher.Refresh(this, av.getSequenceSetId());
+ PaintRefresher.Refresh(tp, av.getSequenceSetId());
repaint();
}
}
if (ob instanceof SequenceI)
{
treeSelectionChanged( (Sequence) ob);
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+ PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
repaint();
return;
}
colourGroups();
}
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+ PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
repaint();
}
}
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};
+ }
}
}