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.analysis.scoremodels.ScoreModels;
26 import jalview.api.analysis.DistanceModelI;
27 import jalview.api.analysis.ViewBasedAnalysisI;
28 import jalview.bin.Cache;
29 import jalview.commands.CommandI;
30 import jalview.commands.OrderCommand;
31 import jalview.datamodel.Alignment;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.AlignmentView;
34 import jalview.datamodel.BinaryNode;
35 import jalview.datamodel.ColumnSelection;
36 import jalview.datamodel.DBRefEntry;
37 import jalview.datamodel.NodeTransformI;
38 import jalview.datamodel.SequenceFeature;
39 import jalview.datamodel.SequenceI;
40 import jalview.datamodel.SequenceNode;
41 import jalview.io.JalviewFileChooser;
42 import jalview.io.JalviewFileView;
43 import jalview.io.NewickFile;
44 import jalview.jbgui.GTreePanel;
45 import jalview.util.ImageMaker;
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);
110 public TreePanel(AlignmentPanel av, String type, String pwtype,
111 NewickFile newtree, AlignmentView inputData)
114 initTreePanel(av, type, pwtype, newtree, inputData);
117 public AlignmentI getAlignment()
119 return treeCanvas.av.getAlignment();
122 public AlignmentViewport getViewPort()
124 return treeCanvas.av;
127 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
128 NewickFile newTree, AlignmentView inputData)
133 this.pwtype = pwtype;
135 treeCanvas = new TreeCanvas(this, ap, scrollPane);
136 scrollPane.setViewportView(treeCanvas);
138 PaintRefresher.Register(this, ap.av.getSequenceSetId());
140 buildAssociatedViewMenu();
142 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
145 public void propertyChange(PropertyChangeEvent evt)
147 if (evt.getPropertyName().equals("alignment"))
151 System.out.println("tree is null");
152 // TODO: deal with case when a change event is received whilst a
153 // tree is still being calculated - should save reference for
154 // processing message later.
157 if (evt.getNewValue() == null)
160 .println("new alignment sequences vector value is null");
163 tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
164 treeCanvas.nameHash.clear(); // reset the mapping between canvas
165 // rectangles and leafnodes
171 TreeLoader tl = new TreeLoader(newTree);
172 if (inputData != null)
174 tl.odata = inputData;
181 public void viewMenu_menuSelected()
183 buildAssociatedViewMenu();
186 void buildAssociatedViewMenu()
188 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
189 .getSequenceSetId());
190 if (aps.length == 1 && treeCanvas.ap == aps[0])
192 associateLeavesMenu.setVisible(false);
196 associateLeavesMenu.setVisible(true);
198 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
200 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
203 associateLeavesMenu.removeAll();
205 JRadioButtonMenuItem item;
206 ButtonGroup buttonGroup = new ButtonGroup();
207 int i, iSize = aps.length;
208 final TreePanel thisTreePanel = this;
209 for (i = 0; i < iSize; i++)
211 final AlignmentPanel ap = aps[i];
212 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
213 buttonGroup.add(item);
214 item.addActionListener(new ActionListener()
217 public void actionPerformed(ActionEvent evt)
219 treeCanvas.applyToAllViews = false;
221 treeCanvas.av = ap.av;
222 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
226 associateLeavesMenu.add(item);
229 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
230 MessageManager.getString("label.all_views"));
231 buttonGroup.add(itemf);
232 itemf.setSelected(treeCanvas.applyToAllViews);
233 itemf.addActionListener(new ActionListener()
236 public void actionPerformed(ActionEvent evt)
238 treeCanvas.applyToAllViews = itemf.isSelected();
241 associateLeavesMenu.add(itemf);
245 class TreeLoader extends Thread
249 jalview.datamodel.AlignmentView odata = null;
251 public TreeLoader(NewickFile newtree)
253 this.newtree = newtree;
256 // Must be outside run(), as Jalview2XML tries to
257 // update distance/bootstrap visibility at the same time
258 showBootstrap(newtree.HasBootstrap());
259 showDistances(newtree.HasDistances());
271 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
275 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
278 if (!tree.hasOriginalSequenceData())
280 allowOriginalSeqData(false);
287 boolean selview = av.getSelectionGroup() != null
288 && av.getSelectionGroup().getSize() > 1;
289 AlignmentView seqStrings = av.getAlignmentView(selview);
293 end = av.getAlignment().getWidth();
294 seqs = av.getAlignment().getSequencesArray();
298 start = av.getSelectionGroup().getStartRes();
299 end = av.getSelectionGroup().getEndRes() + 1;
300 seqs = av.getSelectionGroup().getSequencesInOrder(
303 DistanceModelI sm = ScoreModels.getInstance().forName(pwtype);
304 if (sm instanceof ViewBasedAnalysisI)
308 sm = sm.getClass().newInstance();
309 ((ViewBasedAnalysisI) sm)
310 .configureFromAlignmentView(treeCanvas.ap);
311 } catch (Exception q)
313 Cache.log.error("Couldn't create a scoremodel instance for "
316 tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
320 tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
326 tree.reCount(tree.getTopNode());
327 tree.findHeight(tree.getTopNode());
328 treeCanvas.setTree(tree);
329 treeCanvas.repaint();
330 av.setCurrentTree(tree);
331 if (av.getSortByTree())
333 sortByTree_actionPerformed();
338 public void showDistances(boolean b)
340 treeCanvas.setShowDistances(b);
341 distanceMenu.setSelected(b);
344 public void showBootstrap(boolean b)
346 treeCanvas.setShowBootstrap(b);
347 bootstrapMenu.setSelected(b);
350 public void showPlaceholders(boolean b)
352 placeholdersMenu.setState(b);
353 treeCanvas.setMarkPlaceholders(b);
356 private void allowOriginalSeqData(boolean b)
358 originalSeqData.setVisible(b);
364 * @return DOCUMENT ME!
366 public NJTree getTree()
378 public void textbox_actionPerformed(ActionEvent e)
380 CutAndPasteTransfer cap = new CutAndPasteTransfer();
382 String newTitle = getPanelTitle(type, pwtype);
384 NewickFile fout = new NewickFile(tree.getTopNode());
387 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
388 tree.isHasRootDistance()));
389 Desktop.addInternalFrame(cap, newTitle, 500, 100);
390 } catch (OutOfMemoryError oom)
392 new OOMWarning("generating newick tree file", oom);
405 public void saveAsNewick_actionPerformed(ActionEvent e)
407 JalviewFileChooser chooser = new JalviewFileChooser(
408 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
409 chooser.setFileView(new JalviewFileView());
410 chooser.setDialogTitle(MessageManager
411 .getString("label.save_tree_as_newick"));
412 chooser.setToolTipText(MessageManager.getString("action.save"));
414 int value = chooser.showSaveDialog(null);
416 if (value == JalviewFileChooser.APPROVE_OPTION)
418 String choice = chooser.getSelectedFile().getPath();
419 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
420 .getSelectedFile().getParent());
424 jalview.io.NewickFile fout = new jalview.io.NewickFile(
426 String output = fout.print(tree.isHasBootstrap(),
427 tree.isHasDistances(), tree.isHasRootDistance());
428 java.io.PrintWriter out = new java.io.PrintWriter(
429 new java.io.FileWriter(choice));
432 } catch (Exception ex)
434 ex.printStackTrace();
446 public void printMenu_actionPerformed(ActionEvent e)
448 // Putting in a thread avoids Swing painting problems
449 treeCanvas.startPrinting();
453 public void originalSeqData_actionPerformed(ActionEvent e)
455 if (!tree.hasOriginalSequenceData())
457 jalview.bin.Cache.log
458 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
461 // decide if av alignment is sufficiently different to original data to
462 // warrant a new window to be created
463 // create new alignmnt window with hidden regions (unhiding hidden regions
464 // yields unaligned seqs)
465 // or create a selection box around columns in alignment view
466 // test Alignment(SeqCigar[])
470 // we try to get the associated view's gap character
471 // but this may fail if the view was closed...
472 gc = av.getGapCharacter();
474 } catch (Exception ex)
478 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
480 if (alAndColsel != null && alAndColsel[0] != null)
482 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
484 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
485 AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
486 .getAlignment().getDataset() : null;
489 al.setDataset(dataset);
495 AlignFrame af = new AlignFrame(al,
496 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
497 AlignFrame.DEFAULT_HEIGHT);
499 // >>>This is a fix for the moment, until a better solution is
501 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
503 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
506 Desktop.addInternalFrame(af, MessageManager.formatMessage(
507 "label.original_data_for_params",
508 new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
509 AlignFrame.DEFAULT_HEIGHT);
521 public void fitToWindow_actionPerformed(ActionEvent e)
523 treeCanvas.fitToWindow = fitToWindow.isSelected();
528 * sort the associated alignment view by the current tree.
533 public void sortByTree_actionPerformed()
536 if (treeCanvas.applyToAllViews)
538 final ArrayList<CommandI> commands = new ArrayList<CommandI>();
539 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
540 .getSequenceSetId()))
542 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
544 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
548 public void undoCommand(AlignmentI[] views)
550 for (CommandI tsort : commands)
552 tsort.undoCommand(views);
559 return commands.size();
563 public String getDescription()
565 return "Tree Sort (many views)";
569 public void doCommand(AlignmentI[] views)
572 for (CommandI tsort : commands)
574 tsort.doCommand(views);
578 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
579 .getSequenceSetId()))
581 // ensure all the alignFrames refresh their GI after adding an undo item
582 ap.alignFrame.updateEditMenuBar();
587 treeCanvas.ap.alignFrame
588 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
593 public CommandI sortAlignmentIn(AlignmentPanel ap)
595 AlignmentViewport av = ap.av;
596 SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
597 AlignmentSorter.sortByTree(av.getAlignment(), tree);
599 undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
601 ap.paintAlignment(true);
612 public void font_actionPerformed(ActionEvent e)
614 if (treeCanvas == null)
619 new FontChooser(this);
622 public Font getTreeFont()
624 return treeCanvas.font;
627 public void setTreeFont(Font font)
629 if (treeCanvas != null)
631 treeCanvas.setFont(font);
642 public void distanceMenu_actionPerformed(ActionEvent e)
644 treeCanvas.setShowDistances(distanceMenu.isSelected());
654 public void bootstrapMenu_actionPerformed(ActionEvent e)
656 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
666 public void placeholdersMenu_actionPerformed(ActionEvent e)
668 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 JalviewFileChooser chooser = new JalviewFileChooser(
712 ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
713 chooser.setFileView(new JalviewFileView());
714 chooser.setDialogTitle(MessageManager
715 .getString("label.create_eps_from_tree"));
716 chooser.setToolTipText(MessageManager.getString("action.save"));
718 int value = chooser.showSaveDialog(this);
720 if (value != JalviewFileChooser.APPROVE_OPTION)
725 Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile()
728 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
729 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
731 pg.setAccurateTextMode(accurateText);
733 treeCanvas.draw(pg, width, height);
737 } catch (Exception ex)
739 ex.printStackTrace();
750 public void pngTree_actionPerformed(ActionEvent e)
752 int width = treeCanvas.getWidth();
753 int height = treeCanvas.getHeight();
757 JalviewFileChooser chooser = new JalviewFileChooser(
758 ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
760 chooser.setFileView(new jalview.io.JalviewFileView());
761 chooser.setDialogTitle(MessageManager
762 .getString("label.create_png_from_tree"));
763 chooser.setToolTipText(MessageManager.getString("action.save"));
765 int value = chooser.showSaveDialog(this);
767 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
772 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
773 .getSelectedFile().getParent());
775 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
777 BufferedImage bi = new BufferedImage(width, height,
778 BufferedImage.TYPE_INT_RGB);
779 Graphics png = bi.getGraphics();
781 treeCanvas.draw(png, width, height);
783 ImageIO.write(bi, "png", out);
785 } catch (Exception ex)
787 ex.printStackTrace();
792 * change node labels to the annotation referred to by labelClass TODO:
793 * promote to a datamodel modification that can be undone TODO: make argument
794 * one case of a generic transformation function ie { undoStep = apply(Tree,
795 * TransformFunction)};
799 public void changeNames(final String labelClass)
801 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(
818 new String[] { 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);
864 * Formats a localised title for the tree panel, like
866 * Neighbour Joining Using BLOSUM62
868 * For a tree loaded from file, just uses the file name
871 * NJ or AV or FromFile
872 * @param modelOrFileName
875 public static String getPanelTitle(String treeType, String modelOrFileName)
877 if (NJTree.FROM_FILE.equals(treeType))
879 return modelOrFileName;
883 * i18n description of Neighbour Joining or Average Distance method
885 String treecalcnm = MessageManager.getString("label.tree_calc_"
886 + treeType.toLowerCase());
889 * i18n description (if any) of score model used
891 String smn = MessageManager.getStringOrReturn("label.score_model_",
895 * put them together as <method> Using <model>
897 final String ttl = MessageManager.formatMessage("label.treecalc_title",