2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
23 import javax.imageio.*;
26 import java.awt.event.*;
27 import java.awt.image.*;
30 import org.jibble.epsgraphics.*;
31 import jalview.analysis.*;
32 import jalview.commands.OrderCommand;
33 import jalview.datamodel.*;
35 import jalview.jbgui.*;
43 public class TreePanel extends GTreePanel
49 TreeCanvas treeCanvas;
56 * Creates a new TreePanel object.
71 public TreePanel(AlignmentPanel ap, String type, String pwtype)
74 initTreePanel(ap, type, pwtype, null, null);
76 // We know this tree has distances. JBPNote TODO: prolly should add this as
77 // a userdefined default
78 // showDistances(true);
82 * Creates a new TreePanel object.
95 public TreePanel(AlignmentPanel ap, String type, String pwtype,
99 initTreePanel(ap, type, pwtype, newtree, null);
102 public TreePanel(AlignmentPanel av, String type, String pwtype,
103 NewickFile newtree, AlignmentView inputData)
106 initTreePanel(av, type, pwtype, newtree, inputData);
109 public AlignmentI getAlignment()
111 return treeCanvas.av.getAlignment();
114 public AlignViewport getViewPort()
116 return treeCanvas.av;
119 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
120 NewickFile newTree, AlignmentView inputData)
125 this.pwtype = pwtype;
127 treeCanvas = new TreeCanvas(this, ap, scrollPane);
128 scrollPane.setViewportView(treeCanvas);
130 PaintRefresher.Register(this, ap.av.getSequenceSetId());
132 buildAssociatedViewMenu();
134 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
136 public void propertyChange(PropertyChangeEvent evt)
138 if (evt.getPropertyName().equals("alignment"))
142 System.out.println("tree is null");
143 // TODO: deal with case when a change event is received whilst a
144 // tree is still being calculated - should save reference for
145 // processing message later.
148 if (evt.getNewValue() == null)
151 .println("new alignment sequences vector value is null");
154 tree.UpdatePlaceHolders((Vector) evt.getNewValue());
155 treeCanvas.nameHash.clear(); // reset the mapping between canvas
156 // rectangles and leafnodes
162 TreeLoader tl = new TreeLoader(newTree);
163 if (inputData != null)
165 tl.odata = inputData;
171 public void viewMenu_menuSelected()
173 buildAssociatedViewMenu();
176 void buildAssociatedViewMenu()
178 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
179 .getSequenceSetId());
180 if (aps.length == 1 && treeCanvas.ap == aps[0])
182 associateLeavesMenu.setVisible(false);
186 associateLeavesMenu.setVisible(true);
188 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
190 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
193 associateLeavesMenu.removeAll();
195 JRadioButtonMenuItem item;
196 ButtonGroup buttonGroup = new ButtonGroup();
197 int i, iSize = aps.length;
198 final TreePanel thisTreePanel = this;
199 for (i = 0; i < iSize; i++)
201 final AlignmentPanel ap = aps[i];
202 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
203 buttonGroup.add(item);
204 item.addActionListener(new ActionListener()
206 public void actionPerformed(ActionEvent evt)
208 treeCanvas.applyToAllViews = false;
210 treeCanvas.av = ap.av;
211 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
215 associateLeavesMenu.add(item);
218 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
219 buttonGroup.add(itemf);
220 itemf.setSelected(treeCanvas.applyToAllViews);
221 itemf.addActionListener(new ActionListener()
223 public void actionPerformed(ActionEvent evt)
225 treeCanvas.applyToAllViews = itemf.isSelected();
228 associateLeavesMenu.add(itemf);
232 class TreeLoader extends Thread
236 jalview.datamodel.AlignmentView odata = null;
238 public TreeLoader(NewickFile newtree)
240 this.newtree = newtree;
243 // Must be outside run(), as Jalview2XML tries to
244 // update distance/bootstrap visibility at the same time
245 showBootstrap(newtree.HasBootstrap());
246 showDistances(newtree.HasDistances());
257 tree = new NJTree(av.alignment.getSequencesArray(), newtree);
261 tree = new NJTree(av.alignment.getSequencesArray(), odata,
264 if (!tree.hasOriginalSequenceData())
266 allowOriginalSeqData(false);
273 AlignmentView seqStrings = av.getAlignmentView(av
274 .getSelectionGroup() != null);
275 if (av.getSelectionGroup() == null)
278 end = av.alignment.getWidth();
279 seqs = av.alignment.getSequencesArray();
283 start = av.getSelectionGroup().getStartRes();
284 end = av.getSelectionGroup().getEndRes() + 1;
285 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
288 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
292 tree.reCount(tree.getTopNode());
293 tree.findHeight(tree.getTopNode());
294 treeCanvas.setTree(tree);
295 treeCanvas.repaint();
296 av.setCurrentTree(tree);
297 if (av.getSortByTree())
299 sortByTree_actionPerformed(null);
304 public void showDistances(boolean b)
306 treeCanvas.setShowDistances(b);
307 distanceMenu.setSelected(b);
310 public void showBootstrap(boolean b)
312 treeCanvas.setShowBootstrap(b);
313 bootstrapMenu.setSelected(b);
316 public void showPlaceholders(boolean b)
318 placeholdersMenu.setState(b);
319 treeCanvas.setMarkPlaceholders(b);
322 private void allowOriginalSeqData(boolean b)
324 originalSeqData.setVisible(b);
330 * @return DOCUMENT ME!
332 public NJTree getTree()
343 public void textbox_actionPerformed(ActionEvent e)
345 CutAndPasteTransfer cap = new CutAndPasteTransfer();
347 StringBuffer buffer = new StringBuffer();
349 if (type.equals("AV"))
351 buffer.append("Average distance tree using ");
355 buffer.append("Neighbour joining tree using ");
358 if (pwtype.equals("BL"))
360 buffer.append("BLOSUM62");
364 buffer.append("PID");
367 jalview.io.NewickFile fout = new jalview.io.NewickFile(
371 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
372 tree.isHasRootDistance()));
373 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
374 } catch (OutOfMemoryError oom)
376 new OOMWarning("generating newick tree file", oom);
388 public void saveAsNewick_actionPerformed(ActionEvent e)
390 JalviewFileChooser chooser = new JalviewFileChooser(
391 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
392 chooser.setFileView(new JalviewFileView());
393 chooser.setDialogTitle("Save tree as newick file");
394 chooser.setToolTipText("Save");
396 int value = chooser.showSaveDialog(null);
398 if (value == JalviewFileChooser.APPROVE_OPTION)
400 String choice = chooser.getSelectedFile().getPath();
401 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
402 .getSelectedFile().getParent());
406 jalview.io.NewickFile fout = new jalview.io.NewickFile(
408 String output = fout.print(tree.isHasBootstrap(),
409 tree.isHasDistances(), tree.isHasRootDistance());
410 java.io.PrintWriter out = new java.io.PrintWriter(
411 new java.io.FileWriter(choice));
414 } catch (Exception ex)
416 ex.printStackTrace();
427 public void printMenu_actionPerformed(ActionEvent e)
429 // Putting in a thread avoids Swing painting problems
430 treeCanvas.startPrinting();
433 public void originalSeqData_actionPerformed(ActionEvent e)
435 if (!tree.hasOriginalSequenceData())
437 jalview.bin.Cache.log
438 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
441 // decide if av alignment is sufficiently different to original data to
442 // warrant a new window to be created
443 // create new alignmnt window with hidden regions (unhiding hidden regions
444 // yields unaligned seqs)
445 // or create a selection box around columns in alignment view
446 // test Alignment(SeqCigar[])
450 // we try to get the associated view's gap character
451 // but this may fail if the view was closed...
452 gc = av.getGapCharacter();
454 } catch (Exception ex)
458 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
460 if (alAndColsel != null && alAndColsel[0] != null)
462 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
464 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
465 Alignment dataset = (av != null && av.getAlignment() != null) ? av
466 .getAlignment().getDataset() : null;
469 al.setDataset(dataset);
475 AlignFrame af = new AlignFrame(al,
476 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
477 AlignFrame.DEFAULT_HEIGHT);
479 // >>>This is a fix for the moment, until a better solution is
481 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
483 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
486 Desktop.addInternalFrame(af, "Original Data for " + this.title,
487 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
498 public void fitToWindow_actionPerformed(ActionEvent e)
500 treeCanvas.fitToWindow = fitToWindow.isSelected();
505 * sort the associated alignment view by the current tree.
509 public void sortByTree_actionPerformed(ActionEvent e)
511 AlignmentPanel ap = av.getAlignPanel();
512 SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
513 AlignmentSorter.sortByTree(av.getAlignment(), tree);
515 ap.alignFrame.addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
518 ap.paintAlignment(true);
528 public void font_actionPerformed(ActionEvent e)
530 if (treeCanvas == null)
535 new FontChooser(this);
538 public Font getTreeFont()
540 return treeCanvas.font;
543 public void setTreeFont(Font font)
545 if (treeCanvas != null)
547 treeCanvas.setFont(font);
557 public void distanceMenu_actionPerformed(ActionEvent e)
559 treeCanvas.setShowDistances(distanceMenu.isSelected());
568 public void bootstrapMenu_actionPerformed(ActionEvent e)
570 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
579 public void placeholdersMenu_actionPerformed(ActionEvent e)
581 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
590 public void epsTree_actionPerformed(ActionEvent e)
592 boolean accurateText = true;
594 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
597 // If we need to prompt, and if the GUI is visible then
598 // Prompt for EPS rendering style
599 if (renderStyle.equalsIgnoreCase("Prompt each time")
600 && !(System.getProperty("java.awt.headless") != null && System
601 .getProperty("java.awt.headless").equals("true")))
603 EPSOptions eps = new EPSOptions();
604 renderStyle = eps.getValue();
606 if (renderStyle == null || eps.cancelled)
613 if (renderStyle.equalsIgnoreCase("text"))
615 accurateText = false;
618 int width = treeCanvas.getWidth();
619 int height = treeCanvas.getHeight();
623 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
624 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
625 { "eps" }, new String[]
626 { "Encapsulated Postscript" }, "Encapsulated Postscript");
627 chooser.setFileView(new jalview.io.JalviewFileView());
628 chooser.setDialogTitle("Create EPS file from tree");
629 chooser.setToolTipText("Save");
631 int value = chooser.showSaveDialog(this);
633 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
638 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
639 .getSelectedFile().getParent());
641 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
642 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
644 pg.setAccurateTextMode(accurateText);
646 treeCanvas.draw(pg, width, height);
650 } catch (Exception ex)
652 ex.printStackTrace();
662 public void pngTree_actionPerformed(ActionEvent e)
664 int width = treeCanvas.getWidth();
665 int height = treeCanvas.getHeight();
669 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
670 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
671 { "png" }, new String[]
672 { "Portable network graphics" }, "Portable network graphics");
674 chooser.setFileView(new jalview.io.JalviewFileView());
675 chooser.setDialogTitle("Create PNG image from tree");
676 chooser.setToolTipText("Save");
678 int value = chooser.showSaveDialog(this);
680 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
685 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
686 .getSelectedFile().getParent());
688 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
690 BufferedImage bi = new BufferedImage(width, height,
691 BufferedImage.TYPE_INT_RGB);
692 Graphics png = bi.getGraphics();
694 treeCanvas.draw(png, width, height);
696 ImageIO.write(bi, "png", out);
698 } catch (Exception ex)
700 ex.printStackTrace();
705 * change node labels to the annotation referred to by labelClass TODO:
706 * promote to a datamodel modification that can be undone TODO: make argument
707 * one case of a generic transformation function ie { undoStep = apply(Tree,
708 * TransformFunction)};
712 public void changeNames(final String labelClass)
714 tree.applyToNodes(new NodeTransformI()
717 public void transform(BinaryNode node)
719 if (node instanceof SequenceNode
720 && !((SequenceNode) node).isPlaceholder()
721 && !((SequenceNode) node).isDummy())
723 String newname = null;
724 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
727 // search dbrefs, features and annotation
728 DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
729 sq.getDBRef(), new String[]
730 { labelClass.toUpperCase() });
733 for (int i = 0; i < refs.length; i++)
737 newname = new String(refs[i].getAccessionId());
741 newname = newname + "; " + refs[i].getAccessionId();
747 SequenceFeature sf[] = sq.getSequenceFeatures();
748 for (int i = 0; sf != null && i < sf.length; i++)
750 if (sf[i].getType().equals(labelClass))
754 newname = new String(sf[i].getDescription());
758 newname = newname + "; " + sf[i].getDescription();
766 String oldname = ((SequenceNode) node).getName();
767 // TODO : save in the undo object for this modification.
768 ((SequenceNode) node).setName(newname);