package jalview.gui;
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.print.PrinterJob;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
import javax.swing.JColorChooser;
/** DOCUMENT ME!! */
public static final String PLACEHOLDER = " * ";
- NJTree tree;
+ TreeModel tree;
JScrollPane scrollPane;
* @param tree
* DOCUMENT ME!
*/
- public void setTree(NJTree tree)
+ public void setTree(TreeModel tree)
{
this.tree = tree;
tree.findHeight(tree.getTopNode());
public void run()
{
PrinterJob printJob = PrinterJob.getPrinterJob();
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+ PageFormat defaultPage = printJob.defaultPage();
+ PageFormat pf = printJob.pageDialog(defaultPage);
+
+ if (defaultPage == pf)
+ {
+ /*
+ * user cancelled
+ */
+ return;
+ }
printJob.setPrintable(this, pf);
threshold = (float) (x - offx)
/ (float) (getWidth() - labelLength - (2 * offx));
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(), threshold);
+ List<SequenceNode> groups = tree.groupNodes(threshold);
setColor(tree.getTopNode(), Color.black);
AlignmentPanel[] aps = getAssociatedPanels();
aps[a].av.getCodingComplement().clearSequenceColours();
}
}
- colourGroups();
+ colourGroups(groups);
}
PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
}
- void colourGroups()
+ void colourGroups(List<SequenceNode> groups)
{
AlignmentPanel[] aps = getAssociatedPanels();
- 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>();