package jalview.appletgui;
import jalview.analysis.Conservation;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import java.awt.event.MouseMotionListener;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
public class TreeCanvas extends Panel implements MouseListener,
MouseMotionListener
{
- NJTree tree;
+ TreeModel tree;
ScrollPane scrollPane;
selected.addOrRemove(sequence, true);
}
- public void setTree(NJTree tree)
+ public void setTree(TreeModel tree2)
{
- this.tree = tree;
- tree.findHeight(tree.getTopNode());
+ this.tree = tree2;
+ tree2.findHeight(tree2.getTopNode());
// Now have to calculate longest name based on the leaves
- Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
+ Vector<SequenceNode> leaves = tree2.findLeaves(tree2.getTopNode());
boolean has_placeholders = false;
longestName = "";
threshold = (float) (x - offx)
/ (float) (getSize().width - labelLength - 2 * offx);
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(), threshold);
+ List<SequenceNode> groups = tree.groupNodes(threshold);
setColor(tree.getTopNode(), Color.black);
av.setSelectionGroup(null);
codingComplement.clearSequenceColours();
}
- colourGroups();
+ colourGroups(groups);
}
}
}
- void colourGroups()
+ void colourGroups(List<SequenceNode> groups)
{
- for (int i = 0; i < tree.getGroups().size(); i++)
+ for (int i = 0; i < groups.size(); i++)
{
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
- setColor(tree.getGroups().elementAt(i), col.brighter());
+ setColor(groups.get(i), col.brighter());
- Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
- .elementAt(i));
+ Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
Vector<SequenceI> sequences = new Vector<SequenceI>();
for (int j = 0; j < l.size(); j++)