2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 java.util.List;
25 import javax.imageio.*;
28 import java.awt.event.*;
29 import java.awt.image.*;
32 import org.jibble.epsgraphics.*;
33 import jalview.analysis.*;
34 import jalview.commands.CommandI;
35 import jalview.commands.OrderCommand;
36 import jalview.datamodel.*;
38 import jalview.jbgui.*;
46 public class TreePanel extends GTreePanel
52 TreeCanvas treeCanvas;
59 * Creates a new TreePanel object.
74 public TreePanel(AlignmentPanel ap, String type, String pwtype)
77 initTreePanel(ap, type, pwtype, null, null);
79 // We know this tree has distances. JBPNote TODO: prolly should add this as
80 // a userdefined default
81 // showDistances(true);
85 * Creates a new TreePanel object.
98 public TreePanel(AlignmentPanel ap, String type, String pwtype,
102 initTreePanel(ap, type, pwtype, newtree, null);
105 public TreePanel(AlignmentPanel av, String type, String pwtype,
106 NewickFile newtree, AlignmentView inputData)
109 initTreePanel(av, type, pwtype, newtree, inputData);
112 public AlignmentI getAlignment()
114 return treeCanvas.av.getAlignment();
117 public AlignViewport getViewPort()
119 return treeCanvas.av;
122 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
123 NewickFile newTree, AlignmentView inputData)
128 this.pwtype = pwtype;
130 treeCanvas = new TreeCanvas(this, ap, scrollPane);
131 scrollPane.setViewportView(treeCanvas);
133 PaintRefresher.Register(this, ap.av.getSequenceSetId());
135 buildAssociatedViewMenu();
137 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
139 public void propertyChange(PropertyChangeEvent evt)
141 if (evt.getPropertyName().equals("alignment"))
145 System.out.println("tree is null");
146 // TODO: deal with case when a change event is received whilst a
147 // tree is still being calculated - should save reference for
148 // processing message later.
151 if (evt.getNewValue() == null)
154 .println("new alignment sequences vector value is null");
157 tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
158 treeCanvas.nameHash.clear(); // reset the mapping between canvas
159 // rectangles and leafnodes
165 TreeLoader tl = new TreeLoader(newTree);
166 if (inputData != null)
168 tl.odata = inputData;
174 public void viewMenu_menuSelected()
176 buildAssociatedViewMenu();
179 void buildAssociatedViewMenu()
181 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
182 .getSequenceSetId());
183 if (aps.length == 1 && treeCanvas.ap == aps[0])
185 associateLeavesMenu.setVisible(false);
189 associateLeavesMenu.setVisible(true);
191 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
193 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
196 associateLeavesMenu.removeAll();
198 JRadioButtonMenuItem item;
199 ButtonGroup buttonGroup = new ButtonGroup();
200 int i, iSize = aps.length;
201 final TreePanel thisTreePanel = this;
202 for (i = 0; i < iSize; i++)
204 final AlignmentPanel ap = aps[i];
205 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
206 buttonGroup.add(item);
207 item.addActionListener(new ActionListener()
209 public void actionPerformed(ActionEvent evt)
211 treeCanvas.applyToAllViews = false;
213 treeCanvas.av = ap.av;
214 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
218 associateLeavesMenu.add(item);
221 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
222 buttonGroup.add(itemf);
223 itemf.setSelected(treeCanvas.applyToAllViews);
224 itemf.addActionListener(new ActionListener()
226 public void actionPerformed(ActionEvent evt)
228 treeCanvas.applyToAllViews = itemf.isSelected();
231 associateLeavesMenu.add(itemf);
235 class TreeLoader extends Thread
239 jalview.datamodel.AlignmentView odata = null;
241 public TreeLoader(NewickFile newtree)
243 this.newtree = newtree;
246 // Must be outside run(), as Jalview2XML tries to
247 // update distance/bootstrap visibility at the same time
248 showBootstrap(newtree.HasBootstrap());
249 showDistances(newtree.HasDistances());
260 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
264 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
267 if (!tree.hasOriginalSequenceData())
269 allowOriginalSeqData(false);
276 boolean selview = av.getSelectionGroup() != null
277 && av.getSelectionGroup().getSize() > 1;
278 AlignmentView seqStrings = av.getAlignmentView(selview);
282 end = av.getAlignment().getWidth();
283 seqs = av.getAlignment().getSequencesArray();
287 start = av.getSelectionGroup().getStartRes();
288 end = av.getSelectionGroup().getEndRes() + 1;
289 seqs = av.getSelectionGroup().getSequencesInOrder(
293 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
297 tree.reCount(tree.getTopNode());
298 tree.findHeight(tree.getTopNode());
299 treeCanvas.setTree(tree);
300 treeCanvas.repaint();
301 av.setCurrentTree(tree);
302 if (av.getSortByTree())
304 sortByTree_actionPerformed(null);
309 public void showDistances(boolean b)
311 treeCanvas.setShowDistances(b);
312 distanceMenu.setSelected(b);
315 public void showBootstrap(boolean b)
317 treeCanvas.setShowBootstrap(b);
318 bootstrapMenu.setSelected(b);
321 public void showPlaceholders(boolean b)
323 placeholdersMenu.setState(b);
324 treeCanvas.setMarkPlaceholders(b);
327 private void allowOriginalSeqData(boolean b)
329 originalSeqData.setVisible(b);
335 * @return DOCUMENT ME!
337 public NJTree getTree()
348 public void textbox_actionPerformed(ActionEvent e)
350 CutAndPasteTransfer cap = new CutAndPasteTransfer();
352 StringBuffer buffer = new StringBuffer();
354 if (type.equals("AV"))
356 buffer.append("Average distance tree using ");
360 buffer.append("Neighbour joining tree using ");
363 if (pwtype.equals("BL"))
365 buffer.append("BLOSUM62");
369 buffer.append("PID");
372 jalview.io.NewickFile fout = new jalview.io.NewickFile(
376 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
377 tree.isHasRootDistance()));
378 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
379 } catch (OutOfMemoryError oom)
381 new OOMWarning("generating newick tree file", oom);
393 public void saveAsNewick_actionPerformed(ActionEvent e)
395 JalviewFileChooser chooser = new JalviewFileChooser(
396 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
397 chooser.setFileView(new JalviewFileView());
398 chooser.setDialogTitle("Save tree as newick file");
399 chooser.setToolTipText("Save");
401 int value = chooser.showSaveDialog(null);
403 if (value == JalviewFileChooser.APPROVE_OPTION)
405 String choice = chooser.getSelectedFile().getPath();
406 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
407 .getSelectedFile().getParent());
411 jalview.io.NewickFile fout = new jalview.io.NewickFile(
413 String output = fout.print(tree.isHasBootstrap(),
414 tree.isHasDistances(), tree.isHasRootDistance());
415 java.io.PrintWriter out = new java.io.PrintWriter(
416 new java.io.FileWriter(choice));
419 } catch (Exception ex)
421 ex.printStackTrace();
432 public void printMenu_actionPerformed(ActionEvent e)
434 // Putting in a thread avoids Swing painting problems
435 treeCanvas.startPrinting();
438 public void originalSeqData_actionPerformed(ActionEvent e)
440 if (!tree.hasOriginalSequenceData())
442 jalview.bin.Cache.log
443 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
446 // decide if av alignment is sufficiently different to original data to
447 // warrant a new window to be created
448 // create new alignmnt window with hidden regions (unhiding hidden regions
449 // yields unaligned seqs)
450 // or create a selection box around columns in alignment view
451 // test Alignment(SeqCigar[])
455 // we try to get the associated view's gap character
456 // but this may fail if the view was closed...
457 gc = av.getGapCharacter();
459 } catch (Exception ex)
463 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
465 if (alAndColsel != null && alAndColsel[0] != null)
467 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
469 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
470 Alignment dataset = (av != null && av.getAlignment() != null) ? av
471 .getAlignment().getDataset() : null;
474 al.setDataset(dataset);
480 AlignFrame af = new AlignFrame(al,
481 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
482 AlignFrame.DEFAULT_HEIGHT);
484 // >>>This is a fix for the moment, until a better solution is
486 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
488 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
491 Desktop.addInternalFrame(af, "Original Data for " + this.title,
492 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
503 public void fitToWindow_actionPerformed(ActionEvent e)
505 treeCanvas.fitToWindow = fitToWindow.isSelected();
510 * sort the associated alignment view by the current tree.
514 public void sortByTree_actionPerformed(ActionEvent e)
517 if (treeCanvas.applyToAllViews)
519 final ArrayList<CommandI> commands = new ArrayList<CommandI>();
520 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
521 .getSequenceSetId()))
523 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
525 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
529 public void undoCommand(AlignmentI[] views)
531 for (CommandI tsort : commands)
533 tsort.undoCommand(views);
540 return commands.size();
544 public String getDescription()
546 return "Tree Sort (many views)";
550 public void doCommand(AlignmentI[] views)
553 for (CommandI tsort : commands)
555 tsort.doCommand(views);
559 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
560 .getSequenceSetId()))
562 // ensure all the alignFrames refresh their GI after adding an undo item
563 ap.alignFrame.updateEditMenuBar();
568 treeCanvas.ap.alignFrame
569 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
574 public CommandI sortAlignmentIn(AlignmentPanel ap)
576 AlignViewport av = ap.av;
577 SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
578 AlignmentSorter.sortByTree(av.getAlignment(), tree);
580 undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
582 ap.paintAlignment(true);
592 public void font_actionPerformed(ActionEvent e)
594 if (treeCanvas == null)
599 new FontChooser(this);
602 public Font getTreeFont()
604 return treeCanvas.font;
607 public void setTreeFont(Font font)
609 if (treeCanvas != null)
611 treeCanvas.setFont(font);
621 public void distanceMenu_actionPerformed(ActionEvent e)
623 treeCanvas.setShowDistances(distanceMenu.isSelected());
632 public void bootstrapMenu_actionPerformed(ActionEvent e)
634 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
643 public void placeholdersMenu_actionPerformed(ActionEvent e)
645 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
654 public void epsTree_actionPerformed(ActionEvent e)
656 boolean accurateText = true;
658 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
661 // If we need to prompt, and if the GUI is visible then
662 // Prompt for EPS rendering style
663 if (renderStyle.equalsIgnoreCase("Prompt each time")
664 && !(System.getProperty("java.awt.headless") != null && System
665 .getProperty("java.awt.headless").equals("true")))
667 EPSOptions eps = new EPSOptions();
668 renderStyle = eps.getValue();
670 if (renderStyle == null || eps.cancelled)
677 if (renderStyle.equalsIgnoreCase("text"))
679 accurateText = false;
682 int width = treeCanvas.getWidth();
683 int height = treeCanvas.getHeight();
687 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
688 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
689 { "eps" }, new String[]
690 { "Encapsulated Postscript" }, "Encapsulated Postscript");
691 chooser.setFileView(new jalview.io.JalviewFileView());
692 chooser.setDialogTitle("Create EPS file from tree");
693 chooser.setToolTipText("Save");
695 int value = chooser.showSaveDialog(this);
697 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
702 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
703 .getSelectedFile().getParent());
705 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
706 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
708 pg.setAccurateTextMode(accurateText);
710 treeCanvas.draw(pg, width, height);
714 } catch (Exception ex)
716 ex.printStackTrace();
726 public void pngTree_actionPerformed(ActionEvent e)
728 int width = treeCanvas.getWidth();
729 int height = treeCanvas.getHeight();
733 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
734 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
735 { "png" }, new String[]
736 { "Portable network graphics" }, "Portable network graphics");
738 chooser.setFileView(new jalview.io.JalviewFileView());
739 chooser.setDialogTitle("Create PNG image from tree");
740 chooser.setToolTipText("Save");
742 int value = chooser.showSaveDialog(this);
744 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
749 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
750 .getSelectedFile().getParent());
752 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
754 BufferedImage bi = new BufferedImage(width, height,
755 BufferedImage.TYPE_INT_RGB);
756 Graphics png = bi.getGraphics();
758 treeCanvas.draw(png, width, height);
760 ImageIO.write(bi, "png", out);
762 } catch (Exception ex)
764 ex.printStackTrace();
769 * change node labels to the annotation referred to by labelClass TODO:
770 * promote to a datamodel modification that can be undone TODO: make argument
771 * one case of a generic transformation function ie { undoStep = apply(Tree,
772 * TransformFunction)};
776 public void changeNames(final String labelClass)
778 tree.applyToNodes(new NodeTransformI()
781 public void transform(BinaryNode node)
783 if (node instanceof SequenceNode
784 && !((SequenceNode) node).isPlaceholder()
785 && !((SequenceNode) node).isDummy())
787 String newname = null;
788 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
791 // search dbrefs, features and annotation
792 DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
793 sq.getDBRef(), new String[]
794 { labelClass.toUpperCase() });
797 for (int i = 0; i < refs.length; i++)
801 newname = new String(refs[i].getAccessionId());
805 newname = newname + "; " + refs[i].getAccessionId();
811 SequenceFeature sf[] = sq.getSequenceFeatures();
812 for (int i = 0; sf != null && i < sf.length; i++)
814 if (sf[i].getType().equals(labelClass))
818 newname = new String(sf[i].getDescription());
822 newname = newname + "; " + sf[i].getDescription();
830 String oldname = ((SequenceNode) node).getName();
831 // TODO : save in the undo object for this modification.
832 ((SequenceNode) node).setName(newname);