/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
SequenceNode highlightNode;
- public TreeCanvas(AlignViewport av, ScrollPane scroller)
+ AlignmentPanel ap;
+ public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
{
- this.av = av;
+ this.ap = ap;
+ this.av = ap.av;
font = av.getFont();
scrollPane = scroller;
addMouseListener(this);
}
String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
- .getName())
- : node.getName();
+ .getName()) : node.getName();
FontMetrics fm = g.getFontMetrics(font);
int charWidth = fm.stringWidth(name) + 3;
int charHeight = fm.getHeight();
PaintRefresher.Refresh(this, av.getSequenceSetId());
repaint();
+ av.sendSelection();
}
}
treeSelectionChanged((Sequence) ob);
PaintRefresher.Refresh(this, av.getSequenceSetId());
repaint();
+ av.sendSelection();
return;
}
else if (!(ob instanceof SequenceNode))
for (int i = 0; i < tree.getGroups().size(); i++)
{
- Color col = new Color((int) (Math.random() * 255), (int) (Math
- .random() * 255), (int) (Math.random() * 255));
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
- Vector l = tree.findLeaves((SequenceNode) tree.getGroups().elementAt(
- i), new Vector());
+ Vector l = tree.findLeaves(
+ (SequenceNode) tree.getGroups().elementAt(i), new Vector());
Vector sequences = new Vector();
for (int j = 0; j < l.size(); j++)
{
if (av.getGlobalColourScheme() instanceof UserColourScheme)
{
- cs = new UserColourScheme(((UserColourScheme) av
- .getGlobalColourScheme()).getColours());
+ cs = new UserColourScheme(
+ ((UserColourScheme) av.getGlobalColourScheme())
+ .getColours());
}
else
.getWidth(), ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
}
-
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(), av
- .getIgnoreGapsConsensus());
+ // cs is null if shading is an annotationColourGradient
+ if (cs!=null)
+ {
+ cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+ av.getIgnoreGapsConsensus());
+ }
}
SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
&& av.getGlobalColourScheme().conservationApplied())
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null), sg
- .getStartRes(), sg.getEndRes());
+ ResidueProperties.propHash, 3, sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());
c.calculate();
c.verdict(false, av.ConsPercGaps);
av.alignment.addGroup(sg);
}
-
+ ap.updateAnnotation();
+
}
public void setShowDistances(boolean state)