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;
42 import jalview.viewmodel.AlignmentViewport;
45 import java.awt.Graphics;
46 import java.awt.event.ActionEvent;
47 import java.awt.event.ActionListener;
48 import java.awt.image.BufferedImage;
49 import java.beans.PropertyChangeEvent;
50 import java.io.FileOutputStream;
51 import java.util.ArrayList;
52 import java.util.List;
54 import javax.imageio.ImageIO;
55 import javax.swing.ButtonGroup;
56 import javax.swing.JMenuItem;
57 import javax.swing.JRadioButtonMenuItem;
59 import org.jibble.epsgraphics.EpsGraphics2D;
67 public class TreePanel extends GTreePanel
73 TreeCanvas treeCanvas;
80 * Creates a new TreePanel object.
95 public TreePanel(AlignmentPanel ap, String type, String pwtype)
98 initTreePanel(ap, type, pwtype, null, null);
100 // We know this tree has distances. JBPNote TODO: prolly should add this as
101 // a userdefined default
102 // showDistances(true);
106 * Creates a new TreePanel object.
119 public TreePanel(AlignmentPanel ap, String type, String pwtype,
123 initTreePanel(ap, type, pwtype, newtree, null);
126 public TreePanel(AlignmentPanel av, String type, String pwtype,
127 NewickFile newtree, AlignmentView inputData)
130 initTreePanel(av, type, pwtype, newtree, inputData);
133 public AlignmentI getAlignment()
135 return treeCanvas.av.getAlignment();
138 public AlignmentViewport getViewPort()
140 return treeCanvas.av;
143 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
144 NewickFile newTree, AlignmentView inputData)
149 this.pwtype = pwtype;
151 treeCanvas = new TreeCanvas(this, ap, scrollPane);
152 scrollPane.setViewportView(treeCanvas);
154 PaintRefresher.Register(this, ap.av.getSequenceSetId());
156 buildAssociatedViewMenu();
158 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
160 public void propertyChange(PropertyChangeEvent evt)
162 if (evt.getPropertyName().equals("alignment"))
166 System.out.println("tree is null");
167 // TODO: deal with case when a change event is received whilst a
168 // tree is still being calculated - should save reference for
169 // processing message later.
172 if (evt.getNewValue() == null)
175 .println("new alignment sequences vector value is null");
178 tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
179 treeCanvas.nameHash.clear(); // reset the mapping between canvas
180 // rectangles and leafnodes
186 TreeLoader tl = new TreeLoader(newTree);
187 if (inputData != null)
189 tl.odata = inputData;
195 public void viewMenu_menuSelected()
197 buildAssociatedViewMenu();
200 void buildAssociatedViewMenu()
202 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
203 .getSequenceSetId());
204 if (aps.length == 1 && treeCanvas.ap == aps[0])
206 associateLeavesMenu.setVisible(false);
210 associateLeavesMenu.setVisible(true);
212 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
214 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
217 associateLeavesMenu.removeAll();
219 JRadioButtonMenuItem item;
220 ButtonGroup buttonGroup = new ButtonGroup();
221 int i, iSize = aps.length;
222 final TreePanel thisTreePanel = this;
223 for (i = 0; i < iSize; i++)
225 final AlignmentPanel ap = aps[i];
226 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
227 buttonGroup.add(item);
228 item.addActionListener(new ActionListener()
230 public void actionPerformed(ActionEvent evt)
232 treeCanvas.applyToAllViews = false;
234 treeCanvas.av = ap.av;
235 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
239 associateLeavesMenu.add(item);
242 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
243 MessageManager.getString("label.all_views"));
244 buttonGroup.add(itemf);
245 itemf.setSelected(treeCanvas.applyToAllViews);
246 itemf.addActionListener(new ActionListener()
248 public void actionPerformed(ActionEvent evt)
250 treeCanvas.applyToAllViews = itemf.isSelected();
253 associateLeavesMenu.add(itemf);
257 class TreeLoader extends Thread
261 jalview.datamodel.AlignmentView odata = null;
263 public TreeLoader(NewickFile newtree)
265 this.newtree = newtree;
268 // Must be outside run(), as Jalview2XML tries to
269 // update distance/bootstrap visibility at the same time
270 showBootstrap(newtree.HasBootstrap());
271 showDistances(newtree.HasDistances());
282 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
286 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
289 if (!tree.hasOriginalSequenceData())
291 allowOriginalSeqData(false);
298 boolean selview = av.getSelectionGroup() != null
299 && av.getSelectionGroup().getSize() > 1;
300 AlignmentView seqStrings = av.getAlignmentView(selview);
304 end = av.getAlignment().getWidth();
305 seqs = av.getAlignment().getSequencesArray();
309 start = av.getSelectionGroup().getStartRes();
310 end = av.getSelectionGroup().getEndRes() + 1;
311 seqs = av.getSelectionGroup().getSequencesInOrder(
315 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
319 tree.reCount(tree.getTopNode());
320 tree.findHeight(tree.getTopNode());
321 treeCanvas.setTree(tree);
322 treeCanvas.repaint();
323 av.setCurrentTree(tree);
324 if (av.getSortByTree())
326 sortByTree_actionPerformed();
331 public void showDistances(boolean b)
333 treeCanvas.setShowDistances(b);
334 distanceMenu.setSelected(b);
337 public void showBootstrap(boolean b)
339 treeCanvas.setShowBootstrap(b);
340 bootstrapMenu.setSelected(b);
343 public void showPlaceholders(boolean b)
345 placeholdersMenu.setState(b);
346 treeCanvas.setMarkPlaceholders(b);
349 private void allowOriginalSeqData(boolean b)
351 originalSeqData.setVisible(b);
357 * @return DOCUMENT ME!
359 public NJTree getTree()
370 public void textbox_actionPerformed(ActionEvent e)
372 CutAndPasteTransfer cap = new CutAndPasteTransfer();
374 StringBuffer buffer = new StringBuffer();
376 if (type.equals("AV"))
378 buffer.append("Average distance tree using ");
382 buffer.append("Neighbour joining tree using ");
385 if (pwtype.equals("BL"))
387 buffer.append("BLOSUM62");
391 buffer.append("PID");
394 jalview.io.NewickFile fout = new jalview.io.NewickFile(
398 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
399 tree.isHasRootDistance()));
400 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
401 } catch (OutOfMemoryError oom)
403 new OOMWarning("generating newick tree file", oom);
415 public void saveAsNewick_actionPerformed(ActionEvent e)
417 JalviewFileChooser chooser = new JalviewFileChooser(
418 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
419 chooser.setFileView(new JalviewFileView());
420 chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
421 chooser.setToolTipText(MessageManager.getString("action.save"));
423 int value = chooser.showSaveDialog(null);
425 if (value == JalviewFileChooser.APPROVE_OPTION)
427 String choice = chooser.getSelectedFile().getPath();
428 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
429 .getSelectedFile().getParent());
433 jalview.io.NewickFile fout = new jalview.io.NewickFile(
435 String output = fout.print(tree.isHasBootstrap(),
436 tree.isHasDistances(), tree.isHasRootDistance());
437 java.io.PrintWriter out = new java.io.PrintWriter(
438 new java.io.FileWriter(choice));
441 } catch (Exception ex)
443 ex.printStackTrace();
454 public void printMenu_actionPerformed(ActionEvent e)
456 // Putting in a thread avoids Swing painting problems
457 treeCanvas.startPrinting();
460 public void originalSeqData_actionPerformed(ActionEvent e)
462 if (!tree.hasOriginalSequenceData())
464 jalview.bin.Cache.log
465 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
468 // decide if av alignment is sufficiently different to original data to
469 // warrant a new window to be created
470 // create new alignmnt window with hidden regions (unhiding hidden regions
471 // yields unaligned seqs)
472 // or create a selection box around columns in alignment view
473 // test Alignment(SeqCigar[])
477 // we try to get the associated view's gap character
478 // but this may fail if the view was closed...
479 gc = av.getGapCharacter();
481 } catch (Exception ex)
485 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
487 if (alAndColsel != null && alAndColsel[0] != null)
489 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
491 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
492 Alignment dataset = (av != null && av.getAlignment() != null) ? av
493 .getAlignment().getDataset() : null;
496 al.setDataset(dataset);
502 AlignFrame af = new AlignFrame(al,
503 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
504 AlignFrame.DEFAULT_HEIGHT);
506 // >>>This is a fix for the moment, until a better solution is
508 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
510 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
513 Desktop.addInternalFrame(af, MessageManager.formatMessage(
514 "label.original_data_for_params", new String[]
515 { this.title }), AlignFrame.DEFAULT_WIDTH,
516 AlignFrame.DEFAULT_HEIGHT);
527 public void fitToWindow_actionPerformed(ActionEvent e)
529 treeCanvas.fitToWindow = fitToWindow.isSelected();
534 * sort the associated alignment view by the current tree.
539 public void sortByTree_actionPerformed()
542 if (treeCanvas.applyToAllViews)
544 final ArrayList<CommandI> commands = new ArrayList<CommandI>();
545 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
546 .getSequenceSetId()))
548 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
550 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
554 public void undoCommand(AlignmentI[] views)
556 for (CommandI tsort : commands)
558 tsort.undoCommand(views);
565 return commands.size();
569 public String getDescription()
571 return "Tree Sort (many views)";
575 public void doCommand(AlignmentI[] views)
578 for (CommandI tsort : commands)
580 tsort.doCommand(views);
584 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
585 .getSequenceSetId()))
587 // ensure all the alignFrames refresh their GI after adding an undo item
588 ap.alignFrame.updateEditMenuBar();
593 treeCanvas.ap.alignFrame
594 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
599 public CommandI sortAlignmentIn(AlignmentPanel ap)
601 AlignmentViewport av = ap.av;
602 SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
603 AlignmentSorter.sortByTree(av.getAlignment(), tree);
605 undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
607 ap.paintAlignment(true);
617 public void font_actionPerformed(ActionEvent e)
619 if (treeCanvas == null)
624 new FontChooser(this);
627 public Font getTreeFont()
629 return treeCanvas.font;
632 public void setTreeFont(Font font)
634 if (treeCanvas != null)
636 treeCanvas.setFont(font);
646 public void distanceMenu_actionPerformed(ActionEvent e)
648 treeCanvas.setShowDistances(distanceMenu.isSelected());
657 public void bootstrapMenu_actionPerformed(ActionEvent e)
659 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
668 public void placeholdersMenu_actionPerformed(ActionEvent e)
670 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
679 public void epsTree_actionPerformed(ActionEvent e)
681 boolean accurateText = true;
683 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
686 // If we need to prompt, and if the GUI is visible then
687 // Prompt for EPS rendering style
688 if (renderStyle.equalsIgnoreCase("Prompt each time")
689 && !(System.getProperty("java.awt.headless") != null && System
690 .getProperty("java.awt.headless").equals("true")))
692 EPSOptions eps = new EPSOptions();
693 renderStyle = eps.getValue();
695 if (renderStyle == null || eps.cancelled)
702 if (renderStyle.equalsIgnoreCase("text"))
704 accurateText = false;
707 int width = treeCanvas.getWidth();
708 int height = treeCanvas.getHeight();
712 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
713 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
714 { "eps" }, new String[]
715 { "Encapsulated Postscript" }, "Encapsulated Postscript");
716 chooser.setFileView(new jalview.io.JalviewFileView());
717 chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
718 chooser.setToolTipText(MessageManager.getString("action.save"));
720 int value = chooser.showSaveDialog(this);
722 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
727 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
728 .getSelectedFile().getParent());
730 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
731 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
733 pg.setAccurateTextMode(accurateText);
735 treeCanvas.draw(pg, width, height);
739 } catch (Exception ex)
741 ex.printStackTrace();
751 public void pngTree_actionPerformed(ActionEvent e)
753 int width = treeCanvas.getWidth();
754 int height = treeCanvas.getHeight();
758 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
759 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
760 { "png" }, new String[]
761 { "Portable network graphics" }, "Portable network graphics");
763 chooser.setFileView(new jalview.io.JalviewFileView());
764 chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
765 chooser.setToolTipText(MessageManager.getString("action.save"));
767 int value = chooser.showSaveDialog(this);
769 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
774 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
775 .getSelectedFile().getParent());
777 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
779 BufferedImage bi = new BufferedImage(width, height,
780 BufferedImage.TYPE_INT_RGB);
781 Graphics png = bi.getGraphics();
783 treeCanvas.draw(png, width, height);
785 ImageIO.write(bi, "png", out);
787 } catch (Exception ex)
789 ex.printStackTrace();
794 * change node labels to the annotation referred to by labelClass TODO:
795 * promote to a datamodel modification that can be undone TODO: make argument
796 * one case of a generic transformation function ie { undoStep = apply(Tree,
797 * TransformFunction)};
801 public void changeNames(final String labelClass)
803 tree.applyToNodes(new NodeTransformI()
806 public void transform(BinaryNode node)
808 if (node instanceof SequenceNode
809 && !((SequenceNode) node).isPlaceholder()
810 && !((SequenceNode) node).isDummy())
812 String newname = null;
813 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
816 // search dbrefs, features and annotation
817 DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
818 sq.getDBRef(), new String[]
819 { labelClass.toUpperCase() });
822 for (int i = 0; i < refs.length; i++)
826 newname = new String(refs[i].getAccessionId());
830 newname = newname + "; " + refs[i].getAccessionId();
836 SequenceFeature sf[] = sq.getSequenceFeatures();
837 for (int i = 0; sf != null && i < sf.length; i++)
839 if (sf[i].getType().equals(labelClass))
843 newname = new String(sf[i].getDescription());
847 newname = newname + "; " + sf[i].getDescription();
855 String oldname = ((SequenceNode) node).getName();
856 // TODO : save in the undo object for this modification.
857 ((SequenceNode) node).setName(newname);