2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.CommandI;
33 import jalview.commands.OrderCommand;
34 import jalview.datamodel.*;
36 import jalview.jbgui.*;
44 public class TreePanel extends GTreePanel
50 TreeCanvas treeCanvas;
57 * Creates a new TreePanel object.
72 public TreePanel(AlignmentPanel ap, String type, String pwtype)
75 initTreePanel(ap, type, pwtype, null, null);
77 // We know this tree has distances. JBPNote TODO: prolly should add this as
78 // a userdefined default
79 // showDistances(true);
83 * Creates a new TreePanel object.
96 public TreePanel(AlignmentPanel ap, String type, String pwtype,
100 initTreePanel(ap, type, pwtype, newtree, null);
103 public TreePanel(AlignmentPanel av, String type, String pwtype,
104 NewickFile newtree, AlignmentView inputData)
107 initTreePanel(av, type, pwtype, newtree, inputData);
110 public AlignmentI getAlignment()
112 return treeCanvas.av.getAlignment();
115 public AlignViewport getViewPort()
117 return treeCanvas.av;
120 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
121 NewickFile newTree, AlignmentView inputData)
126 this.pwtype = pwtype;
128 treeCanvas = new TreeCanvas(this, ap, scrollPane);
129 scrollPane.setViewportView(treeCanvas);
131 PaintRefresher.Register(this, ap.av.getSequenceSetId());
133 buildAssociatedViewMenu();
135 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
137 public void propertyChange(PropertyChangeEvent evt)
139 if (evt.getPropertyName().equals("alignment"))
143 System.out.println("tree is null");
144 // TODO: deal with case when a change event is received whilst a
145 // tree is still being calculated - should save reference for
146 // processing message later.
149 if (evt.getNewValue() == null)
152 .println("new alignment sequences vector value is null");
155 tree.UpdatePlaceHolders((Vector) evt.getNewValue());
156 treeCanvas.nameHash.clear(); // reset the mapping between canvas
157 // rectangles and leafnodes
163 TreeLoader tl = new TreeLoader(newTree);
164 if (inputData != null)
166 tl.odata = inputData;
172 public void viewMenu_menuSelected()
174 buildAssociatedViewMenu();
177 void buildAssociatedViewMenu()
179 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
180 .getSequenceSetId());
181 if (aps.length == 1 && treeCanvas.ap == aps[0])
183 associateLeavesMenu.setVisible(false);
187 associateLeavesMenu.setVisible(true);
189 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
191 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
194 associateLeavesMenu.removeAll();
196 JRadioButtonMenuItem item;
197 ButtonGroup buttonGroup = new ButtonGroup();
198 int i, iSize = aps.length;
199 final TreePanel thisTreePanel = this;
200 for (i = 0; i < iSize; i++)
202 final AlignmentPanel ap = aps[i];
203 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
204 buttonGroup.add(item);
205 item.addActionListener(new ActionListener()
207 public void actionPerformed(ActionEvent evt)
209 treeCanvas.applyToAllViews = false;
211 treeCanvas.av = ap.av;
212 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
216 associateLeavesMenu.add(item);
219 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
220 buttonGroup.add(itemf);
221 itemf.setSelected(treeCanvas.applyToAllViews);
222 itemf.addActionListener(new ActionListener()
224 public void actionPerformed(ActionEvent evt)
226 treeCanvas.applyToAllViews = itemf.isSelected();
229 associateLeavesMenu.add(itemf);
233 class TreeLoader extends Thread
237 jalview.datamodel.AlignmentView odata = null;
239 public TreeLoader(NewickFile newtree)
241 this.newtree = newtree;
244 // Must be outside run(), as Jalview2XML tries to
245 // update distance/bootstrap visibility at the same time
246 showBootstrap(newtree.HasBootstrap());
247 showDistances(newtree.HasDistances());
258 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
262 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
265 if (!tree.hasOriginalSequenceData())
267 allowOriginalSeqData(false);
274 AlignmentView seqStrings = av.getAlignmentView(av
275 .getSelectionGroup() != null);
276 if (av.getSelectionGroup() == null)
279 end = av.getAlignment().getWidth();
280 seqs = av.getAlignment().getSequencesArray();
284 start = av.getSelectionGroup().getStartRes();
285 end = av.getSelectionGroup().getEndRes() + 1;
286 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
289 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
293 tree.reCount(tree.getTopNode());
294 tree.findHeight(tree.getTopNode());
295 treeCanvas.setTree(tree);
296 treeCanvas.repaint();
297 av.setCurrentTree(tree);
298 if (av.getSortByTree())
300 sortByTree_actionPerformed(null);
305 public void showDistances(boolean b)
307 treeCanvas.setShowDistances(b);
308 distanceMenu.setSelected(b);
311 public void showBootstrap(boolean b)
313 treeCanvas.setShowBootstrap(b);
314 bootstrapMenu.setSelected(b);
317 public void showPlaceholders(boolean b)
319 placeholdersMenu.setState(b);
320 treeCanvas.setMarkPlaceholders(b);
323 private void allowOriginalSeqData(boolean b)
325 originalSeqData.setVisible(b);
331 * @return DOCUMENT ME!
333 public NJTree getTree()
344 public void textbox_actionPerformed(ActionEvent e)
346 CutAndPasteTransfer cap = new CutAndPasteTransfer();
348 StringBuffer buffer = new StringBuffer();
350 if (type.equals("AV"))
352 buffer.append("Average distance tree using ");
356 buffer.append("Neighbour joining tree using ");
359 if (pwtype.equals("BL"))
361 buffer.append("BLOSUM62");
365 buffer.append("PID");
368 jalview.io.NewickFile fout = new jalview.io.NewickFile(
372 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
373 tree.isHasRootDistance()));
374 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
375 } catch (OutOfMemoryError oom)
377 new OOMWarning("generating newick tree file", oom);
389 public void saveAsNewick_actionPerformed(ActionEvent e)
391 JalviewFileChooser chooser = new JalviewFileChooser(
392 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
393 chooser.setFileView(new JalviewFileView());
394 chooser.setDialogTitle("Save tree as newick file");
395 chooser.setToolTipText("Save");
397 int value = chooser.showSaveDialog(null);
399 if (value == JalviewFileChooser.APPROVE_OPTION)
401 String choice = chooser.getSelectedFile().getPath();
402 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
403 .getSelectedFile().getParent());
407 jalview.io.NewickFile fout = new jalview.io.NewickFile(
409 String output = fout.print(tree.isHasBootstrap(),
410 tree.isHasDistances(), tree.isHasRootDistance());
411 java.io.PrintWriter out = new java.io.PrintWriter(
412 new java.io.FileWriter(choice));
415 } catch (Exception ex)
417 ex.printStackTrace();
428 public void printMenu_actionPerformed(ActionEvent e)
430 // Putting in a thread avoids Swing painting problems
431 treeCanvas.startPrinting();
434 public void originalSeqData_actionPerformed(ActionEvent e)
436 if (!tree.hasOriginalSequenceData())
438 jalview.bin.Cache.log
439 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
442 // decide if av alignment is sufficiently different to original data to
443 // warrant a new window to be created
444 // create new alignmnt window with hidden regions (unhiding hidden regions
445 // yields unaligned seqs)
446 // or create a selection box around columns in alignment view
447 // test Alignment(SeqCigar[])
451 // we try to get the associated view's gap character
452 // but this may fail if the view was closed...
453 gc = av.getGapCharacter();
455 } catch (Exception ex)
459 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
461 if (alAndColsel != null && alAndColsel[0] != null)
463 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
465 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
466 Alignment dataset = (av != null && av.getAlignment() != null) ? av
467 .getAlignment().getDataset() : null;
470 al.setDataset(dataset);
476 AlignFrame af = new AlignFrame(al,
477 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
478 AlignFrame.DEFAULT_HEIGHT);
480 // >>>This is a fix for the moment, until a better solution is
482 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
484 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
487 Desktop.addInternalFrame(af, "Original Data for " + this.title,
488 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
499 public void fitToWindow_actionPerformed(ActionEvent e)
501 treeCanvas.fitToWindow = fitToWindow.isSelected();
506 * sort the associated alignment view by the current tree.
510 public void sortByTree_actionPerformed(ActionEvent e)
513 if (treeCanvas.applyToAllViews)
515 final ArrayList<CommandI> commands = new ArrayList<CommandI>();
516 for (AlignmentPanel ap: PaintRefresher.getAssociatedPanels(av
517 .getSequenceSetId()))
519 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
521 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
525 public void undoCommand(AlignmentI[] views)
527 for (CommandI tsort:commands)
529 tsort.undoCommand(views);
536 return commands.size();
540 public String getDescription()
542 return "Tree Sort (many views)";
546 public void doCommand(AlignmentI[] views)
549 for (CommandI tsort:commands)
551 tsort.doCommand(views);
555 for (AlignmentPanel ap: PaintRefresher.getAssociatedPanels(av
556 .getSequenceSetId()))
558 // ensure all the alignFrames refresh their GI after adding an undo item
559 ap.alignFrame.updateEditMenuBar();
562 treeCanvas.ap.alignFrame.addHistoryItem(sortAlignmentIn(treeCanvas.ap));
566 public CommandI sortAlignmentIn(AlignmentPanel ap)
568 AlignViewport av = ap.av;
569 SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
570 AlignmentSorter.sortByTree(av.getAlignment(), tree);
572 undo=new OrderCommand("Tree Sort", oldOrder,
575 ap.paintAlignment(true);
584 public void font_actionPerformed(ActionEvent e)
586 if (treeCanvas == null)
591 new FontChooser(this);
594 public Font getTreeFont()
596 return treeCanvas.font;
599 public void setTreeFont(Font font)
601 if (treeCanvas != null)
603 treeCanvas.setFont(font);
613 public void distanceMenu_actionPerformed(ActionEvent e)
615 treeCanvas.setShowDistances(distanceMenu.isSelected());
624 public void bootstrapMenu_actionPerformed(ActionEvent e)
626 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
635 public void placeholdersMenu_actionPerformed(ActionEvent e)
637 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
646 public void epsTree_actionPerformed(ActionEvent e)
648 boolean accurateText = true;
650 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
653 // If we need to prompt, and if the GUI is visible then
654 // Prompt for EPS rendering style
655 if (renderStyle.equalsIgnoreCase("Prompt each time")
656 && !(System.getProperty("java.awt.headless") != null && System
657 .getProperty("java.awt.headless").equals("true")))
659 EPSOptions eps = new EPSOptions();
660 renderStyle = eps.getValue();
662 if (renderStyle == null || eps.cancelled)
669 if (renderStyle.equalsIgnoreCase("text"))
671 accurateText = false;
674 int width = treeCanvas.getWidth();
675 int height = treeCanvas.getHeight();
679 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
680 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
681 { "eps" }, new String[]
682 { "Encapsulated Postscript" }, "Encapsulated Postscript");
683 chooser.setFileView(new jalview.io.JalviewFileView());
684 chooser.setDialogTitle("Create EPS file from tree");
685 chooser.setToolTipText("Save");
687 int value = chooser.showSaveDialog(this);
689 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
694 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
695 .getSelectedFile().getParent());
697 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
698 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
700 pg.setAccurateTextMode(accurateText);
702 treeCanvas.draw(pg, width, height);
706 } catch (Exception ex)
708 ex.printStackTrace();
718 public void pngTree_actionPerformed(ActionEvent e)
720 int width = treeCanvas.getWidth();
721 int height = treeCanvas.getHeight();
725 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
726 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
727 { "png" }, new String[]
728 { "Portable network graphics" }, "Portable network graphics");
730 chooser.setFileView(new jalview.io.JalviewFileView());
731 chooser.setDialogTitle("Create PNG image from tree");
732 chooser.setToolTipText("Save");
734 int value = chooser.showSaveDialog(this);
736 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
741 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
742 .getSelectedFile().getParent());
744 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
746 BufferedImage bi = new BufferedImage(width, height,
747 BufferedImage.TYPE_INT_RGB);
748 Graphics png = bi.getGraphics();
750 treeCanvas.draw(png, width, height);
752 ImageIO.write(bi, "png", out);
754 } catch (Exception ex)
756 ex.printStackTrace();
761 * change node labels to the annotation referred to by labelClass TODO:
762 * promote to a datamodel modification that can be undone TODO: make argument
763 * one case of a generic transformation function ie { undoStep = apply(Tree,
764 * TransformFunction)};
768 public void changeNames(final String labelClass)
770 tree.applyToNodes(new NodeTransformI()
773 public void transform(BinaryNode node)
775 if (node instanceof SequenceNode
776 && !((SequenceNode) node).isPlaceholder()
777 && !((SequenceNode) node).isDummy())
779 String newname = null;
780 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
783 // search dbrefs, features and annotation
784 DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
785 sq.getDBRef(), new String[]
786 { labelClass.toUpperCase() });
789 for (int i = 0; i < refs.length; i++)
793 newname = new String(refs[i].getAccessionId());
797 newname = newname + "; " + refs[i].getAccessionId();
803 SequenceFeature sf[] = sq.getSequenceFeatures();
804 for (int i = 0; sf != null && i < sf.length; i++)
806 if (sf[i].getType().equals(labelClass))
810 newname = new String(sf[i].getDescription());
814 newname = newname + "; " + sf[i].getDescription();
822 String oldname = ((SequenceNode) node).getName();
823 // TODO : save in the undo object for this modification.
824 ((SequenceNode) node).setName(newname);