2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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.api.analysis.ScoreModelI;
26 import jalview.api.analysis.ViewBasedAnalysisI;
27 import jalview.bin.Cache;
28 import jalview.commands.CommandI;
29 import jalview.commands.OrderCommand;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.AlignmentView;
33 import jalview.datamodel.BinaryNode;
34 import jalview.datamodel.ColumnSelection;
35 import jalview.datamodel.DBRefEntry;
36 import jalview.datamodel.NodeTransformI;
37 import jalview.datamodel.SequenceFeature;
38 import jalview.datamodel.SequenceI;
39 import jalview.datamodel.SequenceNode;
40 import jalview.io.JalviewFileChooser;
41 import jalview.io.JalviewFileView;
42 import jalview.io.NewickFile;
43 import jalview.jbgui.GTreePanel;
44 import jalview.schemes.ResidueProperties;
45 import jalview.util.DBRefUtils;
46 import jalview.util.MessageManager;
47 import jalview.viewmodel.AlignmentViewport;
50 import java.awt.Graphics;
51 import java.awt.event.ActionEvent;
52 import java.awt.event.ActionListener;
53 import java.awt.image.BufferedImage;
54 import java.beans.PropertyChangeEvent;
55 import java.io.FileOutputStream;
56 import java.util.ArrayList;
57 import java.util.List;
59 import javax.imageio.ImageIO;
60 import javax.swing.ButtonGroup;
61 import javax.swing.JMenuItem;
62 import javax.swing.JRadioButtonMenuItem;
64 import org.jibble.epsgraphics.EpsGraphics2D;
72 public class TreePanel extends GTreePanel
78 TreeCanvas treeCanvas;
85 * Creates a new TreePanel object.
100 public TreePanel(AlignmentPanel ap, String type, String pwtype)
103 initTreePanel(ap, type, pwtype, null, null);
105 // We know this tree has distances. JBPNote TODO: prolly should add this as
106 // a userdefined default
107 // showDistances(true);
111 * Creates a new TreePanel object.
124 public TreePanel(AlignmentPanel ap, String type, String pwtype,
128 initTreePanel(ap, type, pwtype, newtree, null);
131 public TreePanel(AlignmentPanel av, String type, String pwtype,
132 NewickFile newtree, AlignmentView inputData)
135 initTreePanel(av, type, pwtype, newtree, inputData);
138 public AlignmentI getAlignment()
140 return treeCanvas.av.getAlignment();
143 public AlignmentViewport getViewPort()
145 return treeCanvas.av;
148 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
149 NewickFile newTree, AlignmentView inputData)
154 this.pwtype = pwtype;
156 treeCanvas = new TreeCanvas(this, ap, scrollPane);
157 scrollPane.setViewportView(treeCanvas);
159 PaintRefresher.Register(this, ap.av.getSequenceSetId());
161 buildAssociatedViewMenu();
163 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
165 public void propertyChange(PropertyChangeEvent evt)
167 if (evt.getPropertyName().equals("alignment"))
171 System.out.println("tree is null");
172 // TODO: deal with case when a change event is received whilst a
173 // tree is still being calculated - should save reference for
174 // processing message later.
177 if (evt.getNewValue() == null)
180 .println("new alignment sequences vector value is null");
183 tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
184 treeCanvas.nameHash.clear(); // reset the mapping between canvas
185 // rectangles and leafnodes
191 TreeLoader tl = new TreeLoader(newTree);
192 if (inputData != null)
194 tl.odata = inputData;
200 public void viewMenu_menuSelected()
202 buildAssociatedViewMenu();
205 void buildAssociatedViewMenu()
207 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
208 .getSequenceSetId());
209 if (aps.length == 1 && treeCanvas.ap == aps[0])
211 associateLeavesMenu.setVisible(false);
215 associateLeavesMenu.setVisible(true);
217 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
219 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
222 associateLeavesMenu.removeAll();
224 JRadioButtonMenuItem item;
225 ButtonGroup buttonGroup = new ButtonGroup();
226 int i, iSize = aps.length;
227 final TreePanel thisTreePanel = this;
228 for (i = 0; i < iSize; i++)
230 final AlignmentPanel ap = aps[i];
231 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
232 buttonGroup.add(item);
233 item.addActionListener(new ActionListener()
235 public void actionPerformed(ActionEvent evt)
237 treeCanvas.applyToAllViews = false;
239 treeCanvas.av = ap.av;
240 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
244 associateLeavesMenu.add(item);
247 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
249 buttonGroup.add(itemf);
250 itemf.setSelected(treeCanvas.applyToAllViews);
251 itemf.addActionListener(new ActionListener()
253 public void actionPerformed(ActionEvent evt)
255 treeCanvas.applyToAllViews = itemf.isSelected();
258 associateLeavesMenu.add(itemf);
262 class TreeLoader extends Thread
266 AlignmentView odata = null;
268 public TreeLoader(NewickFile newtree)
270 this.newtree = newtree;
273 // Must be outside run(), as Jalview2XML tries to
274 // update distance/bootstrap visibility at the same time
275 showBootstrap(newtree.HasBootstrap());
276 showDistances(newtree.HasDistances());
287 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
291 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
294 if (!tree.hasOriginalSequenceData())
296 allowOriginalSeqData(false);
303 boolean selview = av.getSelectionGroup() != null
304 && av.getSelectionGroup().getSize() > 1;
305 AlignmentView seqStrings = av.getAlignmentView(selview);
309 end = av.getAlignment().getWidth();
310 seqs = av.getAlignment().getSequencesArray();
314 start = av.getSelectionGroup().getStartRes();
315 end = av.getSelectionGroup().getEndRes() + 1;
316 seqs = av.getSelectionGroup().getSequencesInOrder(
319 ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
320 if (sm instanceof ViewBasedAnalysisI)
324 sm = sm.getClass().newInstance();
325 ((ViewBasedAnalysisI) sm)
326 .configureFromAlignmentView(treeCanvas.ap);
327 } catch (Exception q)
329 Cache.log.error("Couldn't create a scoremodel instance for "
332 tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
336 tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
342 tree.reCount(tree.getTopNode());
343 tree.findHeight(tree.getTopNode());
344 treeCanvas.setTree(tree);
345 treeCanvas.repaint();
346 av.setCurrentTree(tree);
347 if (av.getSortByTree())
349 sortByTree_actionPerformed();
354 public void showDistances(boolean b)
356 treeCanvas.setShowDistances(b);
357 distanceMenu.setSelected(b);
360 public void showBootstrap(boolean b)
362 treeCanvas.setShowBootstrap(b);
363 bootstrapMenu.setSelected(b);
366 public void showPlaceholders(boolean b)
368 placeholdersMenu.setState(b);
369 treeCanvas.setMarkPlaceholders(b);
372 private void allowOriginalSeqData(boolean b)
374 originalSeqData.setVisible(b);
380 * @return DOCUMENT ME!
382 public NJTree getTree()
393 public void textbox_actionPerformed(ActionEvent e)
395 CutAndPasteTransfer cap = new CutAndPasteTransfer();
397 StringBuffer buffer = new StringBuffer();
399 if (type.equals("AV"))
401 buffer.append("Average distance tree using ");
405 buffer.append("Neighbour joining tree using ");
408 if (pwtype.equals("BL"))
410 buffer.append("BLOSUM62");
414 buffer.append("PID");
417 NewickFile fout = new NewickFile(tree.getTopNode());
420 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
421 tree.isHasRootDistance()));
422 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
423 } catch (OutOfMemoryError oom)
425 new OOMWarning("generating newick tree file", oom);
437 public void saveAsNewick_actionPerformed(ActionEvent e)
439 JalviewFileChooser chooser = new JalviewFileChooser(
440 Cache.getProperty("LAST_DIRECTORY"));
441 chooser.setFileView(new JalviewFileView());
442 chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
443 chooser.setToolTipText(MessageManager.getString("action.save"));
445 int value = chooser.showSaveDialog(null);
447 if (value == JalviewFileChooser.APPROVE_OPTION)
449 String choice = chooser.getSelectedFile().getPath();
450 Cache.setProperty("LAST_DIRECTORY", chooser
451 .getSelectedFile().getParent());
455 NewickFile fout = new NewickFile(tree.getTopNode());
456 String output = fout.print(tree.isHasBootstrap(),
457 tree.isHasDistances(), tree.isHasRootDistance());
458 java.io.PrintWriter out = new java.io.PrintWriter(
459 new java.io.FileWriter(choice));
462 } catch (Exception ex)
464 ex.printStackTrace();
475 public void printMenu_actionPerformed(ActionEvent e)
477 // Putting in a thread avoids Swing painting problems
478 treeCanvas.startPrinting();
481 public void originalSeqData_actionPerformed(ActionEvent e)
483 if (!tree.hasOriginalSequenceData())
486 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
489 // decide if av alignment is sufficiently different to original data to
490 // warrant a new window to be created
491 // create new alignmnt window with hidden regions (unhiding hidden regions
492 // yields unaligned seqs)
493 // or create a selection box around columns in alignment view
494 // test Alignment(SeqCigar[])
498 // we try to get the associated view's gap character
499 // but this may fail if the view was closed...
500 gc = av.getGapCharacter();
502 } catch (Exception ex)
506 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
508 if (alAndColsel != null && alAndColsel[0] != null)
510 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
512 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
513 Alignment dataset = (av != null && av.getAlignment() != null) ? av
514 .getAlignment().getDataset() : null;
517 al.setDataset(dataset);
523 AlignFrame af = new AlignFrame(al,
524 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
525 AlignFrame.DEFAULT_HEIGHT);
527 // >>>This is a fix for the moment, until a better solution is
529 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
531 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
534 Desktop.addInternalFrame(af, MessageManager.formatMessage(
535 "label.original_data_for_params", new Object[]
536 { this.title }), AlignFrame.DEFAULT_WIDTH,
537 AlignFrame.DEFAULT_HEIGHT);
548 public void fitToWindow_actionPerformed(ActionEvent e)
550 treeCanvas.fitToWindow = fitToWindow.isSelected();
555 * sort the associated alignment view by the current tree.
560 public void sortByTree_actionPerformed()
563 if (treeCanvas.applyToAllViews)
565 final ArrayList<CommandI> commands = new ArrayList<CommandI>();
566 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
567 .getSequenceSetId()))
569 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
571 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
575 public void undoCommand(AlignmentI[] views)
577 for (CommandI tsort : commands)
579 tsort.undoCommand(views);
586 return commands.size();
590 public String getDescription()
592 return "Tree Sort (many views)";
596 public void doCommand(AlignmentI[] views)
599 for (CommandI tsort : commands)
601 tsort.doCommand(views);
605 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
606 .getSequenceSetId()))
608 // ensure all the alignFrames refresh their GI after adding an undo item
609 ap.alignFrame.updateEditMenuBar();
614 treeCanvas.ap.alignFrame
615 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
620 public CommandI sortAlignmentIn(AlignmentPanel ap)
622 AlignmentViewport av = ap.av;
623 SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
624 AlignmentSorter.sortByTree(av.getAlignment(), tree);
626 undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
628 ap.paintAlignment(true);
638 public void font_actionPerformed(ActionEvent e)
640 if (treeCanvas == null)
645 new FontChooser(this);
648 public Font getTreeFont()
650 return treeCanvas.font;
653 public void setTreeFont(Font font)
655 if (treeCanvas != null)
657 treeCanvas.setFont(font);
667 public void distanceMenu_actionPerformed(ActionEvent e)
669 treeCanvas.setShowDistances(distanceMenu.isSelected());
678 public void bootstrapMenu_actionPerformed(ActionEvent e)
680 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
689 public void placeholdersMenu_actionPerformed(ActionEvent e)
691 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
700 public void epsTree_actionPerformed(ActionEvent e)
702 boolean accurateText = true;
704 String renderStyle = Cache.getDefault("EPS_RENDERING",
707 // If we need to prompt, and if the GUI is visible then
708 // Prompt for EPS rendering style
709 if (renderStyle.equalsIgnoreCase("Prompt each time")
710 && !(System.getProperty("java.awt.headless") != null && System
711 .getProperty("java.awt.headless").equals("true")))
713 EPSOptions eps = new EPSOptions();
714 renderStyle = eps.getValue();
716 if (renderStyle == null || eps.cancelled)
723 if (renderStyle.equalsIgnoreCase("text"))
725 accurateText = false;
728 int width = treeCanvas.getWidth();
729 int height = treeCanvas.getHeight();
733 JalviewFileChooser chooser = new JalviewFileChooser(
734 Cache.getProperty("LAST_DIRECTORY"), new String[]
735 { "eps" }, new String[]
736 { "Encapsulated Postscript" }, "Encapsulated Postscript");
737 chooser.setFileView(new jalview.io.JalviewFileView());
738 chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
739 chooser.setToolTipText(MessageManager.getString("action.save"));
741 int value = chooser.showSaveDialog(this);
743 if (value != JalviewFileChooser.APPROVE_OPTION)
748 Cache.setProperty("LAST_DIRECTORY", chooser
749 .getSelectedFile().getParent());
751 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
752 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
754 pg.setAccurateTextMode(accurateText);
756 treeCanvas.draw(pg, width, height);
760 } catch (Exception ex)
762 ex.printStackTrace();
772 public void pngTree_actionPerformed(ActionEvent e)
774 int width = treeCanvas.getWidth();
775 int height = treeCanvas.getHeight();
779 JalviewFileChooser chooser = new JalviewFileChooser(
780 Cache.getProperty("LAST_DIRECTORY"), new String[]
781 { "png" }, new String[]
782 { "Portable network graphics" }, "Portable network graphics");
784 chooser.setFileView(new JalviewFileView());
785 chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
786 chooser.setToolTipText(MessageManager.getString("action.save"));
788 int value = chooser.showSaveDialog(this);
790 if (value != JalviewFileChooser.APPROVE_OPTION)
795 Cache.setProperty("LAST_DIRECTORY", chooser
796 .getSelectedFile().getParent());
798 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
800 BufferedImage bi = new BufferedImage(width, height,
801 BufferedImage.TYPE_INT_RGB);
802 Graphics png = bi.getGraphics();
804 treeCanvas.draw(png, width, height);
806 ImageIO.write(bi, "png", out);
808 } catch (Exception ex)
810 ex.printStackTrace();
815 * change node labels to the annotation referred to by labelClass TODO:
816 * promote to a datamodel modification that can be undone TODO: make argument
817 * one case of a generic transformation function ie { undoStep = apply(Tree,
818 * TransformFunction)};
822 public void changeNames(final String labelClass)
824 tree.applyToNodes(new NodeTransformI()
827 public void transform(BinaryNode node)
829 if (node instanceof SequenceNode
830 && !((SequenceNode) node).isPlaceholder()
831 && !((SequenceNode) node).isDummy())
833 String newname = null;
834 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
837 // search dbrefs, features and annotation
838 DBRefEntry[] refs = DBRefUtils.selectRefs(
839 sq.getDBRef(), new String[]
840 { labelClass.toUpperCase() });
843 for (int i = 0; i < refs.length; i++)
847 newname = new String(refs[i].getAccessionId());
851 newname = newname + "; " + refs[i].getAccessionId();
857 SequenceFeature sf[] = sq.getSequenceFeatures();
858 for (int i = 0; sf != null && i < sf.length; i++)
860 if (sf[i].getType().equals(labelClass))
864 newname = new String(sf[i].getDescription());
868 newname = newname + "; " + sf[i].getDescription();
876 String oldname = ((SequenceNode) node).getName();
877 // TODO : save in the undo object for this modification.
878 ((SequenceNode) node).setName(newname);