2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.NJTree;
25 import jalview.commands.CommandI;
26 import jalview.commands.OrderCommand;
27 import jalview.datamodel.Alignment;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.AlignmentView;
30 import jalview.datamodel.BinaryNode;
31 import jalview.datamodel.ColumnSelection;
32 import jalview.datamodel.DBRefEntry;
33 import jalview.datamodel.NodeTransformI;
34 import jalview.datamodel.SequenceFeature;
35 import jalview.datamodel.SequenceI;
36 import jalview.datamodel.SequenceNode;
37 import jalview.io.JalviewFileChooser;
38 import jalview.io.JalviewFileView;
39 import jalview.io.NewickFile;
40 import jalview.jbgui.GTreePanel;
41 import jalview.util.MessageManager;
44 import java.awt.Graphics;
45 import java.awt.event.ActionEvent;
46 import java.awt.event.ActionListener;
47 import java.awt.image.BufferedImage;
48 import java.beans.PropertyChangeEvent;
49 import java.io.FileOutputStream;
50 import java.util.ArrayList;
51 import java.util.List;
53 import javax.imageio.ImageIO;
54 import javax.swing.ButtonGroup;
55 import javax.swing.JMenuItem;
56 import javax.swing.JRadioButtonMenuItem;
58 import org.jibble.epsgraphics.EpsGraphics2D;
66 public class TreePanel extends GTreePanel
72 TreeCanvas treeCanvas;
79 * Creates a new TreePanel object.
94 public TreePanel(AlignmentPanel ap, String type, String pwtype)
97 initTreePanel(ap, type, pwtype, null, null);
99 // We know this tree has distances. JBPNote TODO: prolly should add this as
100 // a userdefined default
101 // showDistances(true);
105 * Creates a new TreePanel object.
118 public TreePanel(AlignmentPanel ap, String type, String pwtype,
122 initTreePanel(ap, type, pwtype, newtree, null);
125 public TreePanel(AlignmentPanel av, String type, String pwtype,
126 NewickFile newtree, AlignmentView inputData)
129 initTreePanel(av, type, pwtype, newtree, inputData);
132 public AlignmentI getAlignment()
134 return treeCanvas.av.getAlignment();
137 public AlignViewport getViewPort()
139 return treeCanvas.av;
142 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
143 NewickFile newTree, AlignmentView inputData)
148 this.pwtype = pwtype;
150 treeCanvas = new TreeCanvas(this, ap, scrollPane);
151 scrollPane.setViewportView(treeCanvas);
153 PaintRefresher.Register(this, ap.av.getSequenceSetId());
155 buildAssociatedViewMenu();
157 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
159 public void propertyChange(PropertyChangeEvent evt)
161 if (evt.getPropertyName().equals("alignment"))
165 System.out.println("tree is null");
166 // TODO: deal with case when a change event is received whilst a
167 // tree is still being calculated - should save reference for
168 // processing message later.
171 if (evt.getNewValue() == null)
174 .println("new alignment sequences vector value is null");
177 tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
178 treeCanvas.nameHash.clear(); // reset the mapping between canvas
179 // rectangles and leafnodes
185 TreeLoader tl = new TreeLoader(newTree);
186 if (inputData != null)
188 tl.odata = inputData;
194 public void viewMenu_menuSelected()
196 buildAssociatedViewMenu();
199 void buildAssociatedViewMenu()
201 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
202 .getSequenceSetId());
203 if (aps.length == 1 && treeCanvas.ap == aps[0])
205 associateLeavesMenu.setVisible(false);
209 associateLeavesMenu.setVisible(true);
211 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
213 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
216 associateLeavesMenu.removeAll();
218 JRadioButtonMenuItem item;
219 ButtonGroup buttonGroup = new ButtonGroup();
220 int i, iSize = aps.length;
221 final TreePanel thisTreePanel = this;
222 for (i = 0; i < iSize; i++)
224 final AlignmentPanel ap = aps[i];
225 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
226 buttonGroup.add(item);
227 item.addActionListener(new ActionListener()
229 public void actionPerformed(ActionEvent evt)
231 treeCanvas.applyToAllViews = false;
233 treeCanvas.av = ap.av;
234 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
238 associateLeavesMenu.add(item);
241 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
242 MessageManager.getString("label.all_views"));
243 buttonGroup.add(itemf);
244 itemf.setSelected(treeCanvas.applyToAllViews);
245 itemf.addActionListener(new ActionListener()
247 public void actionPerformed(ActionEvent evt)
249 treeCanvas.applyToAllViews = itemf.isSelected();
252 associateLeavesMenu.add(itemf);
256 class TreeLoader extends Thread
260 jalview.datamodel.AlignmentView odata = null;
262 public TreeLoader(NewickFile newtree)
264 this.newtree = newtree;
267 // Must be outside run(), as Jalview2XML tries to
268 // update distance/bootstrap visibility at the same time
269 showBootstrap(newtree.HasBootstrap());
270 showDistances(newtree.HasDistances());
281 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
285 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
288 if (!tree.hasOriginalSequenceData())
290 allowOriginalSeqData(false);
297 boolean selview = av.getSelectionGroup() != null
298 && av.getSelectionGroup().getSize() > 1;
299 AlignmentView seqStrings = av.getAlignmentView(selview);
303 end = av.getAlignment().getWidth();
304 seqs = av.getAlignment().getSequencesArray();
308 start = av.getSelectionGroup().getStartRes();
309 end = av.getSelectionGroup().getEndRes() + 1;
310 seqs = av.getSelectionGroup().getSequencesInOrder(
314 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
318 tree.reCount(tree.getTopNode());
319 tree.findHeight(tree.getTopNode());
320 treeCanvas.setTree(tree);
321 treeCanvas.repaint();
322 av.setCurrentTree(tree);
323 if (av.getSortByTree())
325 sortByTree_actionPerformed();
330 public void showDistances(boolean b)
332 treeCanvas.setShowDistances(b);
333 distanceMenu.setSelected(b);
336 public void showBootstrap(boolean b)
338 treeCanvas.setShowBootstrap(b);
339 bootstrapMenu.setSelected(b);
342 public void showPlaceholders(boolean b)
344 placeholdersMenu.setState(b);
345 treeCanvas.setMarkPlaceholders(b);
348 private void allowOriginalSeqData(boolean b)
350 originalSeqData.setVisible(b);
356 * @return DOCUMENT ME!
358 public NJTree getTree()
369 public void textbox_actionPerformed(ActionEvent e)
371 CutAndPasteTransfer cap = new CutAndPasteTransfer();
373 StringBuffer buffer = new StringBuffer();
375 if (type.equals("AV"))
377 buffer.append("Average distance tree using ");
381 buffer.append("Neighbour joining tree using ");
384 if (pwtype.equals("BL"))
386 buffer.append("BLOSUM62");
390 buffer.append("PID");
393 jalview.io.NewickFile fout = new jalview.io.NewickFile(
397 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
398 tree.isHasRootDistance()));
399 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
400 } catch (OutOfMemoryError oom)
402 new OOMWarning("generating newick tree file", oom);
414 public void saveAsNewick_actionPerformed(ActionEvent e)
416 JalviewFileChooser chooser = new JalviewFileChooser(
417 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
418 chooser.setFileView(new JalviewFileView());
419 chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
420 chooser.setToolTipText(MessageManager.getString("action.save"));
422 int value = chooser.showSaveDialog(null);
424 if (value == JalviewFileChooser.APPROVE_OPTION)
426 String choice = chooser.getSelectedFile().getPath();
427 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
428 .getSelectedFile().getParent());
432 jalview.io.NewickFile fout = new jalview.io.NewickFile(
434 String output = fout.print(tree.isHasBootstrap(),
435 tree.isHasDistances(), tree.isHasRootDistance());
436 java.io.PrintWriter out = new java.io.PrintWriter(
437 new java.io.FileWriter(choice));
440 } catch (Exception ex)
442 ex.printStackTrace();
453 public void printMenu_actionPerformed(ActionEvent e)
455 // Putting in a thread avoids Swing painting problems
456 treeCanvas.startPrinting();
459 public void originalSeqData_actionPerformed(ActionEvent e)
461 if (!tree.hasOriginalSequenceData())
463 jalview.bin.Cache.log
464 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
467 // decide if av alignment is sufficiently different to original data to
468 // warrant a new window to be created
469 // create new alignmnt window with hidden regions (unhiding hidden regions
470 // yields unaligned seqs)
471 // or create a selection box around columns in alignment view
472 // test Alignment(SeqCigar[])
476 // we try to get the associated view's gap character
477 // but this may fail if the view was closed...
478 gc = av.getGapCharacter();
480 } catch (Exception ex)
484 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
486 if (alAndColsel != null && alAndColsel[0] != null)
488 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
490 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
491 Alignment dataset = (av != null && av.getAlignment() != null) ? av
492 .getAlignment().getDataset() : null;
495 al.setDataset(dataset);
501 AlignFrame af = new AlignFrame(al,
502 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
503 AlignFrame.DEFAULT_HEIGHT);
505 // >>>This is a fix for the moment, until a better solution is
507 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
509 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
512 Desktop.addInternalFrame(af, MessageManager.formatMessage(
513 "label.original_data_for_params", new String[]
514 { this.title }), AlignFrame.DEFAULT_WIDTH,
515 AlignFrame.DEFAULT_HEIGHT);
526 public void fitToWindow_actionPerformed(ActionEvent e)
528 treeCanvas.fitToWindow = fitToWindow.isSelected();
533 * sort the associated alignment view by the current tree.
538 public void sortByTree_actionPerformed()
541 if (treeCanvas.applyToAllViews)
543 final ArrayList<CommandI> commands = new ArrayList<CommandI>();
544 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
545 .getSequenceSetId()))
547 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
549 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
553 public void undoCommand(AlignmentI[] views)
555 for (CommandI tsort : commands)
557 tsort.undoCommand(views);
564 return commands.size();
568 public String getDescription()
570 return "Tree Sort (many views)";
574 public void doCommand(AlignmentI[] views)
577 for (CommandI tsort : commands)
579 tsort.doCommand(views);
583 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
584 .getSequenceSetId()))
586 // ensure all the alignFrames refresh their GI after adding an undo item
587 ap.alignFrame.updateEditMenuBar();
592 treeCanvas.ap.alignFrame
593 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
598 public CommandI sortAlignmentIn(AlignmentPanel ap)
600 AlignViewport av = ap.av;
601 SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
602 AlignmentSorter.sortByTree(av.getAlignment(), tree);
604 undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
606 ap.paintAlignment(true);
616 public void font_actionPerformed(ActionEvent e)
618 if (treeCanvas == null)
623 new FontChooser(this);
626 public Font getTreeFont()
628 return treeCanvas.font;
631 public void setTreeFont(Font font)
633 if (treeCanvas != null)
635 treeCanvas.setFont(font);
645 public void distanceMenu_actionPerformed(ActionEvent e)
647 treeCanvas.setShowDistances(distanceMenu.isSelected());
656 public void bootstrapMenu_actionPerformed(ActionEvent e)
658 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
667 public void placeholdersMenu_actionPerformed(ActionEvent e)
669 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
678 public void epsTree_actionPerformed(ActionEvent e)
680 boolean accurateText = true;
682 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
685 // If we need to prompt, and if the GUI is visible then
686 // Prompt for EPS rendering style
687 if (renderStyle.equalsIgnoreCase("Prompt each time")
688 && !(System.getProperty("java.awt.headless") != null && System
689 .getProperty("java.awt.headless").equals("true")))
691 EPSOptions eps = new EPSOptions();
692 renderStyle = eps.getValue();
694 if (renderStyle == null || eps.cancelled)
701 if (renderStyle.equalsIgnoreCase("text"))
703 accurateText = false;
706 int width = treeCanvas.getWidth();
707 int height = treeCanvas.getHeight();
711 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
712 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
713 { "eps" }, new String[]
714 { "Encapsulated Postscript" }, "Encapsulated Postscript");
715 chooser.setFileView(new jalview.io.JalviewFileView());
716 chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
717 chooser.setToolTipText(MessageManager.getString("action.save"));
719 int value = chooser.showSaveDialog(this);
721 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
726 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
727 .getSelectedFile().getParent());
729 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
730 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
732 pg.setAccurateTextMode(accurateText);
734 treeCanvas.draw(pg, width, height);
738 } catch (Exception ex)
740 ex.printStackTrace();
750 public void pngTree_actionPerformed(ActionEvent e)
752 int width = treeCanvas.getWidth();
753 int height = treeCanvas.getHeight();
757 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
758 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
759 { "png" }, new String[]
760 { "Portable network graphics" }, "Portable network graphics");
762 chooser.setFileView(new jalview.io.JalviewFileView());
763 chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
764 chooser.setToolTipText(MessageManager.getString("action.save"));
766 int value = chooser.showSaveDialog(this);
768 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
773 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
774 .getSelectedFile().getParent());
776 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
778 BufferedImage bi = new BufferedImage(width, height,
779 BufferedImage.TYPE_INT_RGB);
780 Graphics png = bi.getGraphics();
782 treeCanvas.draw(png, width, height);
784 ImageIO.write(bi, "png", out);
786 } catch (Exception ex)
788 ex.printStackTrace();
793 * change node labels to the annotation referred to by labelClass TODO:
794 * promote to a datamodel modification that can be undone TODO: make argument
795 * one case of a generic transformation function ie { undoStep = apply(Tree,
796 * TransformFunction)};
800 public void changeNames(final String labelClass)
802 tree.applyToNodes(new NodeTransformI()
805 public void transform(BinaryNode node)
807 if (node instanceof SequenceNode
808 && !((SequenceNode) node).isPlaceholder()
809 && !((SequenceNode) node).isDummy())
811 String newname = null;
812 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
815 // search dbrefs, features and annotation
816 DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
817 sq.getDBRef(), new String[]
818 { labelClass.toUpperCase() });
821 for (int i = 0; i < refs.length; i++)
825 newname = new String(refs[i].getAccessionId());
829 newname = newname + "; " + refs[i].getAccessionId();
835 SequenceFeature sf[] = sq.getSequenceFeatures();
836 for (int i = 0; sf != null && i < sf.length; i++)
838 if (sf[i].getType().equals(labelClass))
842 newname = new String(sf[i].getDescription());
846 newname = newname + "; " + sf[i].getDescription();
854 String oldname = ((SequenceNode) node).getName();
855 // TODO : save in the undo object for this modification.
856 ((SequenceNode) node).setName(newname);