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.TreeModel;
25 import jalview.bin.Cache;
26 import jalview.commands.CommandI;
27 import jalview.commands.OrderCommand;
28 import jalview.datamodel.Alignment;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.AlignmentView;
31 import jalview.datamodel.BinaryNode;
32 import jalview.datamodel.DBRefEntry;
33 import jalview.datamodel.HiddenColumns;
34 import jalview.datamodel.NodeTransformI;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceI;
37 import jalview.datamodel.SequenceNode;
38 import jalview.ext.archaeopteryx.ArchaeopteryxNewickInit;
39 import jalview.io.JalviewFileChooser;
40 import jalview.io.JalviewFileView;
41 import jalview.io.NewickFile;
42 import jalview.jbgui.GTreePanel;
43 import jalview.util.ImageMaker;
44 import jalview.util.MessageManager;
45 import jalview.viewmodel.AlignmentViewport;
48 import java.awt.Graphics;
49 import java.awt.event.ActionEvent;
50 import java.awt.event.ActionListener;
51 import java.awt.image.BufferedImage;
52 import java.beans.PropertyChangeEvent;
53 import java.io.FileOutputStream;
54 import java.util.ArrayList;
55 import java.util.List;
57 import javax.imageio.ImageIO;
58 import javax.swing.ButtonGroup;
59 import javax.swing.JMenuItem;
60 import javax.swing.JRadioButtonMenuItem;
62 import org.jibble.epsgraphics.EpsGraphics2D;
70 public class TreePanel extends GTreePanel
72 String substitutionMatrix;
76 String treeTitle; // if tree loaded
78 TreeCanvas treeCanvas;
85 * Creates a new TreePanel object.
90 * @param substitutionMatrix
92 public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType,
93 String substitutionMatrix)
96 this.treeType = treeType;
97 this.substitutionMatrix = substitutionMatrix;
99 initNewTreePanel(ap, tree);
101 // We know this tree has distances. JBPNote TODO: prolly should add this as
102 // a userdefined default
103 // showDistances(true);
107 * Creates a new TreePanel object.
114 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
115 String theTitle, AlignmentView inputData)
118 this.treeTitle = theTitle;
119 initLoadedTreePanel(alignPanel, newtree, inputData);
122 public AlignmentI getAlignment()
124 return treeCanvas.av.getAlignment();
127 public AlignmentViewport getViewPort()
129 return treeCanvas.av;
132 void initNewTreePanel(AlignmentPanel ap, TreeModel tree)
136 TreeLoader tl = new TreeLoader(null, null);
140 void initLoadedTreePanel(AlignmentPanel ap,
141 NewickFile newTree, AlignmentView inputData)
145 TreeLoader tl = new TreeLoader(newTree, inputData);
149 public void buildTreeCanvas(AlignmentPanel ap) {
152 treeCanvas = new TreeCanvas(this, ap, scrollPane);
153 scrollPane.setViewportView(treeCanvas);
156 PaintRefresher.Register(this, ap.av.getSequenceSetId());
158 buildAssociatedViewMenu();
160 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
163 public void propertyChange(PropertyChangeEvent evt)
165 if (evt.getPropertyName().equals("alignment"))
169 System.out.println("tree is null");
170 // TODO: deal with case when a change event is received whilst a
171 // tree is still being calculated - should save reference for
172 // processing message later.
175 if (evt.getNewValue() == null)
178 "new alignment sequences vector value is null");
181 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
182 treeCanvas.nameHash.clear(); // reset the mapping between canvas
183 // rectangles and leafnodes
195 public void viewMenu_menuSelected()
197 buildAssociatedViewMenu();
200 void buildAssociatedViewMenu()
202 AlignmentPanel[] aps = PaintRefresher
203 .getAssociatedPanels(av.getSequenceSetId());
204 if (aps.length == 1 && treeCanvas.ap == aps[0])
206 associateLeavesMenu.setVisible(false);
210 associateLeavesMenu.setVisible(true);
213 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
215 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
218 associateLeavesMenu.removeAll();
220 JRadioButtonMenuItem item;
221 ButtonGroup buttonGroup = new ButtonGroup();
222 int i, iSize = aps.length;
223 final TreePanel thisTreePanel = this;
224 for (i = 0; i < iSize; i++)
226 final AlignmentPanel ap = aps[i];
227 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
228 buttonGroup.add(item);
229 item.addActionListener(new ActionListener()
232 public void actionPerformed(ActionEvent evt)
234 treeCanvas.applyToAllViews = false;
236 treeCanvas.av = ap.av;
237 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
241 associateLeavesMenu.add(item);
244 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
245 MessageManager.getString("label.all_views"));
246 buttonGroup.add(itemf);
247 itemf.setSelected(treeCanvas.applyToAllViews);
248 itemf.addActionListener(new ActionListener()
251 public void actionPerformed(ActionEvent evt)
253 treeCanvas.applyToAllViews = itemf.isSelected();
256 associateLeavesMenu.add(itemf);
260 class TreeLoader extends Thread
262 private NewickFile newTree;
264 private AlignmentView odata = null;
266 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
268 this.newTree = newickFile;
269 this.odata = inputData;
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());
288 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
290 if (tree.getOriginalData() == null)
292 originalSeqData.setVisible(false);
302 public void showTree(TreeModel tree)
304 tree.reCount(tree.getTopNode());
305 tree.findHeight(tree.getTopNode());
306 treeCanvas.setTree(tree);
307 treeCanvas.repaint();
309 av.setCurrentTree(tree);
310 if (av.getSortByTree())
312 sortByTree_actionPerformed();
315 ArchaeopteryxNewickInit archae = new ArchaeopteryxNewickInit(tree);
316 archae.startArchaeopteryx();
320 public void showDistances(boolean b)
322 treeCanvas.setShowDistances(b);
323 distanceMenu.setSelected(b);
326 public void showBootstrap(boolean b)
328 treeCanvas.setShowBootstrap(b);
329 bootstrapMenu.setSelected(b);
332 public void showPlaceholders(boolean b)
334 placeholdersMenu.setState(b);
335 treeCanvas.setMarkPlaceholders(b);
341 * @return DOCUMENT ME!
343 public TreeModel getTree()
355 public void textbox_actionPerformed(ActionEvent e)
357 CutAndPasteTransfer cap = new CutAndPasteTransfer();
359 String newTitle = getPanelTitle();
361 NewickFile fout = new NewickFile(tree.getTopNode());
364 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
365 tree.hasRootDistance()));
366 Desktop.addInternalFrame(cap, newTitle, 500, 100);
367 } catch (OutOfMemoryError oom)
369 new OOMWarning("generating newick tree file", oom);
382 public void saveAsNewick_actionPerformed(ActionEvent e)
384 JalviewFileChooser chooser = new JalviewFileChooser(
385 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
386 chooser.setFileView(new JalviewFileView());
387 chooser.setDialogTitle(
388 MessageManager.getString("label.save_tree_as_newick"));
389 chooser.setToolTipText(MessageManager.getString("action.save"));
391 int value = chooser.showSaveDialog(null);
393 if (value == JalviewFileChooser.APPROVE_OPTION)
395 String choice = chooser.getSelectedFile().getPath();
396 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
397 chooser.getSelectedFile().getParent());
401 jalview.io.NewickFile fout = new jalview.io.NewickFile(
403 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
404 tree.hasRootDistance());
405 java.io.PrintWriter out = new java.io.PrintWriter(
406 new java.io.FileWriter(choice));
409 } catch (Exception ex)
411 ex.printStackTrace();
423 public void printMenu_actionPerformed(ActionEvent e)
425 // Putting in a thread avoids Swing painting problems
426 treeCanvas.startPrinting();
430 public void originalSeqData_actionPerformed(ActionEvent e)
432 AlignmentView originalData = tree.getOriginalData();
433 if (originalData == null)
435 jalview.bin.Cache.log.info(
436 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
439 // decide if av alignment is sufficiently different to original data to
440 // warrant a new window to be created
441 // create new alignmnt window with hidden regions (unhiding hidden regions
442 // yields unaligned seqs)
443 // or create a selection box around columns in alignment view
444 // test Alignment(SeqCigar[])
448 // we try to get the associated view's gap character
449 // but this may fail if the view was closed...
450 gc = av.getGapCharacter();
452 } catch (Exception ex)
456 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
458 if (alAndColsel != null && alAndColsel[0] != null)
460 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
462 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
463 AlignmentI dataset = (av != null && av.getAlignment() != null)
464 ? av.getAlignment().getDataset()
468 al.setDataset(dataset);
474 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
475 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
477 // >>>This is a fix for the moment, until a better solution is
479 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
481 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
484 Desktop.addInternalFrame(af, MessageManager.formatMessage(
485 "label.original_data_for_params", new Object[]
486 { this.title }), AlignFrame.DEFAULT_WIDTH,
487 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.
511 public void sortByTree_actionPerformed()
514 if (treeCanvas.applyToAllViews)
516 final ArrayList<CommandI> commands = new ArrayList<>();
517 for (AlignmentPanel ap : PaintRefresher
518 .getAssociatedPanels(av.getSequenceSetId()))
520 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
522 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
526 public void undoCommand(AlignmentI[] views)
528 for (CommandI tsort : commands)
530 tsort.undoCommand(views);
537 return commands.size();
541 public String getDescription()
543 return "Tree Sort (many views)";
547 public void doCommand(AlignmentI[] views)
550 for (CommandI tsort : commands)
552 tsort.doCommand(views);
556 for (AlignmentPanel ap : PaintRefresher
557 .getAssociatedPanels(av.getSequenceSetId()))
559 // ensure all the alignFrames refresh their GI after adding an undo item
560 ap.alignFrame.updateEditMenuBar();
565 treeCanvas.ap.alignFrame
566 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
571 public CommandI sortAlignmentIn(AlignmentPanel ap)
573 AlignmentViewport viewport = ap.av;
574 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
575 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
577 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
579 ap.paintAlignment(true);
590 public void font_actionPerformed(ActionEvent e)
592 if (treeCanvas == null)
597 new FontChooser(this);
600 public Font getTreeFont()
602 return treeCanvas.font;
605 public void setTreeFont(Font f)
607 if (treeCanvas != null)
609 treeCanvas.setFont(f);
620 public void distanceMenu_actionPerformed(ActionEvent e)
622 treeCanvas.setShowDistances(distanceMenu.isSelected());
632 public void bootstrapMenu_actionPerformed(ActionEvent e)
634 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
644 public void placeholdersMenu_actionPerformed(ActionEvent e)
646 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
656 public void epsTree_actionPerformed(ActionEvent e)
658 boolean accurateText = true;
660 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
663 // If we need to prompt, and if the GUI is visible then
664 // Prompt for EPS rendering style
665 if (renderStyle.equalsIgnoreCase("Prompt each time")
666 && !(System.getProperty("java.awt.headless") != null && System
667 .getProperty("java.awt.headless").equals("true")))
669 EPSOptions eps = new EPSOptions();
670 renderStyle = eps.getValue();
672 if (renderStyle == null || eps.cancelled)
679 if (renderStyle.equalsIgnoreCase("text"))
681 accurateText = false;
684 int width = treeCanvas.getWidth();
685 int height = treeCanvas.getHeight();
689 JalviewFileChooser chooser = new JalviewFileChooser(
690 ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
691 chooser.setFileView(new JalviewFileView());
692 chooser.setDialogTitle(
693 MessageManager.getString("label.create_eps_from_tree"));
694 chooser.setToolTipText(MessageManager.getString("action.save"));
696 int value = chooser.showSaveDialog(this);
698 if (value != JalviewFileChooser.APPROVE_OPTION)
703 Cache.setProperty("LAST_DIRECTORY",
704 chooser.getSelectedFile().getParent());
706 FileOutputStream out = new FileOutputStream(
707 chooser.getSelectedFile());
708 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
711 pg.setAccurateTextMode(accurateText);
713 treeCanvas.draw(pg, width, height);
717 } catch (Exception ex)
719 ex.printStackTrace();
730 public void pngTree_actionPerformed(ActionEvent e)
732 int width = treeCanvas.getWidth();
733 int height = treeCanvas.getHeight();
737 JalviewFileChooser chooser = new JalviewFileChooser(
738 ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
740 chooser.setFileView(new jalview.io.JalviewFileView());
741 chooser.setDialogTitle(
742 MessageManager.getString("label.create_png_from_tree"));
743 chooser.setToolTipText(MessageManager.getString("action.save"));
745 int value = chooser.showSaveDialog(this);
747 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
752 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
753 chooser.getSelectedFile().getParent());
755 FileOutputStream out = new FileOutputStream(
756 chooser.getSelectedFile());
758 BufferedImage bi = new BufferedImage(width, height,
759 BufferedImage.TYPE_INT_RGB);
760 Graphics png = bi.getGraphics();
762 treeCanvas.draw(png, width, height);
764 ImageIO.write(bi, "png", out);
766 } catch (Exception ex)
768 ex.printStackTrace();
773 * change node labels to the annotation referred to by labelClass TODO:
774 * promote to a datamodel modification that can be undone TODO: make argument
775 * one case of a generic transformation function ie { undoStep = apply(Tree,
776 * TransformFunction)};
780 public void changeNames(final String labelClass)
782 tree.applyToNodes(new NodeTransformI()
786 public void transform(BinaryNode node)
788 if (node instanceof SequenceNode
789 && !((SequenceNode) node).isPlaceholder()
790 && !((SequenceNode) node).isDummy())
792 String newname = null;
793 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
796 // search dbrefs, features and annotation
797 DBRefEntry[] refs = jalview.util.DBRefUtils
798 .selectRefs(sq.getDBRefs(), new String[]
799 { labelClass.toUpperCase() });
802 for (int i = 0; i < refs.length; i++)
806 newname = new String(refs[i].getAccessionId());
810 newname = newname + "; " + refs[i].getAccessionId();
816 List<SequenceFeature> features = sq.getFeatures()
817 .getPositionalFeatures(labelClass);
818 for (SequenceFeature feature : features)
822 newname = feature.getDescription();
826 newname = newname + "; " + feature.getDescription();
833 // String oldname = ((SequenceNode) node).getName();
834 // TODO : save oldname in the undo object for this modification.
835 ((SequenceNode) node).setName(newname);
843 * Formats a localised title for the tree panel, like
845 * Neighbour Joining Using BLOSUM62
847 * For a tree loaded from file, just uses the file name
851 public String getPanelTitle() // to be moved/fixed
853 if (treeTitle != null)
860 * i18n description of Neighbour Joining or Average Distance method
862 String treecalcnm = MessageManager
863 .getString("label.tree_calc_" + treeType.toLowerCase());
866 * short score model name (long description can be too long)
868 String smn = substitutionMatrix;
871 * put them together as <method> Using <model>
873 final String ttl = MessageManager
874 .formatMessage("label.treecalc_title", treecalcnm, smn);