import org.jibble.epsgraphics.*;
import jalview.analysis.*;
+import jalview.commands.OrderCommand;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.jbgui.*;
* Creates a new TreePanel object.
*
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seqVector
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pwtype
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public TreePanel(AlignmentPanel ap, String type, String pwtype)
{
* Creates a new TreePanel object.
*
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seqVector
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param newtree
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pwtype
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public TreePanel(AlignmentPanel ap, String type, String pwtype,
NewickFile newtree)
tree.UpdatePlaceHolders((Vector) evt.getNewValue());
treeCanvas.nameHash.clear(); // reset the mapping between canvas
- // rectangles and leafnodes
+ // rectangles and leafnodes
repaint();
}
}
treeCanvas.setTree(tree);
treeCanvas.repaint();
av.setCurrentTree(tree);
-
+ if (av.getSortByTree())
+ {
+ sortByTree_actionPerformed(null);
+ }
}
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void textbox_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void saveAsNewick_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void printMenu_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void fitToWindow_actionPerformed(ActionEvent e)
{
}
/**
+ * sort the associated alignment view by the current tree.
+ * @param e
+ */
+ public void sortByTree_actionPerformed(ActionEvent e)
+ {
+ AlignmentPanel ap = av.getAlignPanel();
+ SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByTree(av.getAlignment(), tree);
+
+ ap.alignFrame
+ .addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
+ av.alignment));
+
+ ap.paintAlignment(true);
+
+ }
+
+ /**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void font_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void distanceMenu_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void epsTree_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void pngTree_actionPerformed(ActionEvent e)
{