/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
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)
if (tree == null)
{
System.out.println("tree is null");
+ // TODO: deal with case when a change event is received whilst a
+ // tree is still being calculated - should save reference for
+ // processing message later.
+ return;
}
if (evt.getNewValue() == null)
{
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)
{
buffer.append("PID");
}
- Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
.getTopNode());
- cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
+ try {
+ cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
tree.isHasRootDistance()));
+ Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("generating newick tree file",oom);
+ cap.dispose();
+ }
+
}
/**
* 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)
{
ex.printStackTrace();
}
}
+
+ /**
+ * change node labels to the annotation referred to by labelClass TODO:
+ * promote to a datamodel modification that can be undone TODO: make argument
+ * one case of a generic transformation function ie { undoStep = apply(Tree,
+ * TransformFunction)};
+ *
+ * @param labelClass
+ */
+ public void changeNames(final String labelClass)
+ {
+ tree.applyToNodes(new NodeTransformI()
+ {
+
+ public void transform(BinaryNode node)
+ {
+ if (node instanceof SequenceNode
+ && !((SequenceNode) node).isPlaceholder()
+ && !((SequenceNode) node).isDummy())
+ {
+ String newname = null;
+ SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+ if (sq != null)
+ {
+ // search dbrefs, features and annotation
+ DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(sq
+ .getDBRef(), new String[]
+ { labelClass.toUpperCase() });
+ if (refs != null)
+ {
+ for (int i = 0; i < refs.length; i++)
+ {
+ if (newname == null)
+ {
+ newname = new String(refs[i].getAccessionId());
+ }
+ else
+ {
+ newname = newname + "; " + refs[i].getAccessionId();
+ }
+ }
+ }
+ if (newname == null)
+ {
+ SequenceFeature sf[] = sq.getSequenceFeatures();
+ for (int i = 0; sf != null && i < sf.length; i++)
+ {
+ if (sf[i].getType().equals(labelClass))
+ {
+ if (newname == null)
+ {
+ newname = new String(sf[i].getDescription());
+ }
+ else
+ {
+ newname = newname + "; " + sf[i].getDescription();
+ }
+ }
+ }
+ }
+ }
+ if (newname != null)
+ {
+ String oldname = ((SequenceNode) node).getName();
+ // TODO : save in the undo object for this modification.
+ ((SequenceNode) node).setName(newname);
+ }
+ }
+ }
+ });
+ }
}
git://source.jalview.org / jalview.git / blobdiff