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.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.MessageManager;
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
76 TreeCanvas treeCanvas;
83 * Creates a new TreePanel object.
98 public TreePanel(AlignmentPanel ap, String type, String pwtype)
101 initTreePanel(ap, type, pwtype, null, null);
103 // We know this tree has distances. JBPNote TODO: prolly should add this as
104 // a userdefined default
105 // showDistances(true);
109 * Creates a new TreePanel object.
122 public TreePanel(AlignmentPanel ap, String type, String pwtype,
126 initTreePanel(ap, type, pwtype, newtree, null);
129 public TreePanel(AlignmentPanel av, String type, String pwtype,
130 NewickFile newtree, AlignmentView inputData)
133 initTreePanel(av, type, pwtype, newtree, inputData);
136 public AlignmentI getAlignment()
138 return treeCanvas.av.getAlignment();
141 public AlignViewport getViewPort()
143 return treeCanvas.av;
146 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
147 NewickFile newTree, AlignmentView inputData)
152 this.pwtype = pwtype;
154 treeCanvas = new TreeCanvas(this, ap, scrollPane);
155 scrollPane.setViewportView(treeCanvas);
157 PaintRefresher.Register(this, ap.av.getSequenceSetId());
159 buildAssociatedViewMenu();
161 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 .println("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
189 TreeLoader tl = new TreeLoader(newTree);
190 if (inputData != null)
192 tl.odata = inputData;
198 public void viewMenu_menuSelected()
200 buildAssociatedViewMenu();
203 void buildAssociatedViewMenu()
205 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
206 .getSequenceSetId());
207 if (aps.length == 1 && treeCanvas.ap == aps[0])
209 associateLeavesMenu.setVisible(false);
213 associateLeavesMenu.setVisible(true);
215 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
217 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
220 associateLeavesMenu.removeAll();
222 JRadioButtonMenuItem item;
223 ButtonGroup buttonGroup = new ButtonGroup();
224 int i, iSize = aps.length;
225 final TreePanel thisTreePanel = this;
226 for (i = 0; i < iSize; i++)
228 final AlignmentPanel ap = aps[i];
229 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
230 buttonGroup.add(item);
231 item.addActionListener(new ActionListener()
233 public void actionPerformed(ActionEvent evt)
235 treeCanvas.applyToAllViews = false;
237 treeCanvas.av = ap.av;
238 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
242 associateLeavesMenu.add(item);
245 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
246 buttonGroup.add(itemf);
247 itemf.setSelected(treeCanvas.applyToAllViews);
248 itemf.addActionListener(new ActionListener()
250 public void actionPerformed(ActionEvent evt)
252 treeCanvas.applyToAllViews = itemf.isSelected();
255 associateLeavesMenu.add(itemf);
259 class TreeLoader extends Thread
263 jalview.datamodel.AlignmentView odata = null;
265 public TreeLoader(NewickFile newtree)
267 this.newtree = newtree;
270 // Must be outside run(), as Jalview2XML tries to
271 // update distance/bootstrap visibility at the same time
272 showBootstrap(newtree.HasBootstrap());
273 showDistances(newtree.HasDistances());
284 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
288 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
291 if (!tree.hasOriginalSequenceData())
293 allowOriginalSeqData(false);
300 boolean selview = av.getSelectionGroup() != null
301 && av.getSelectionGroup().getSize() > 1;
302 AlignmentView seqStrings = av.getAlignmentView(selview);
306 end = av.getAlignment().getWidth();
307 seqs = av.getAlignment().getSequencesArray();
311 start = av.getSelectionGroup().getStartRes();
312 end = av.getSelectionGroup().getEndRes() + 1;
313 seqs = av.getSelectionGroup().getSequencesInOrder(
316 ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
317 if (sm instanceof ViewBasedAnalysisI)
321 sm = sm.getClass().newInstance();
322 ((ViewBasedAnalysisI) sm)
323 .configureFromAlignmentView(treeCanvas.ap);
324 } catch (Exception q)
326 Cache.log.error("Couldn't create a scoremodel instance for "
329 tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
333 tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
339 tree.reCount(tree.getTopNode());
340 tree.findHeight(tree.getTopNode());
341 treeCanvas.setTree(tree);
342 treeCanvas.repaint();
343 av.setCurrentTree(tree);
344 if (av.getSortByTree())
346 sortByTree_actionPerformed(null);
351 public void showDistances(boolean b)
353 treeCanvas.setShowDistances(b);
354 distanceMenu.setSelected(b);
357 public void showBootstrap(boolean b)
359 treeCanvas.setShowBootstrap(b);
360 bootstrapMenu.setSelected(b);
363 public void showPlaceholders(boolean b)
365 placeholdersMenu.setState(b);
366 treeCanvas.setMarkPlaceholders(b);
369 private void allowOriginalSeqData(boolean b)
371 originalSeqData.setVisible(b);
377 * @return DOCUMENT ME!
379 public NJTree getTree()
390 public void textbox_actionPerformed(ActionEvent e)
392 CutAndPasteTransfer cap = new CutAndPasteTransfer();
394 StringBuffer buffer = new StringBuffer();
396 if (type.equals("AV"))
398 buffer.append("Average distance tree using ");
402 buffer.append("Neighbour joining tree using ");
405 if (pwtype.equals("BL"))
407 buffer.append("BLOSUM62");
411 buffer.append("PID");
414 jalview.io.NewickFile fout = new jalview.io.NewickFile(
418 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
419 tree.isHasRootDistance()));
420 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
421 } catch (OutOfMemoryError oom)
423 new OOMWarning("generating newick tree file", oom);
435 public void saveAsNewick_actionPerformed(ActionEvent e)
437 JalviewFileChooser chooser = new JalviewFileChooser(
438 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
439 chooser.setFileView(new JalviewFileView());
440 chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
441 chooser.setToolTipText(MessageManager.getString("action.save"));
443 int value = chooser.showSaveDialog(null);
445 if (value == JalviewFileChooser.APPROVE_OPTION)
447 String choice = chooser.getSelectedFile().getPath();
448 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
449 .getSelectedFile().getParent());
453 jalview.io.NewickFile fout = new jalview.io.NewickFile(
455 String output = fout.print(tree.isHasBootstrap(),
456 tree.isHasDistances(), tree.isHasRootDistance());
457 java.io.PrintWriter out = new java.io.PrintWriter(
458 new java.io.FileWriter(choice));
461 } catch (Exception ex)
463 ex.printStackTrace();
474 public void printMenu_actionPerformed(ActionEvent e)
476 // Putting in a thread avoids Swing painting problems
477 treeCanvas.startPrinting();
480 public void originalSeqData_actionPerformed(ActionEvent e)
482 if (!tree.hasOriginalSequenceData())
484 jalview.bin.Cache.log
485 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
488 // decide if av alignment is sufficiently different to original data to
489 // warrant a new window to be created
490 // create new alignmnt window with hidden regions (unhiding hidden regions
491 // yields unaligned seqs)
492 // or create a selection box around columns in alignment view
493 // test Alignment(SeqCigar[])
497 // we try to get the associated view's gap character
498 // but this may fail if the view was closed...
499 gc = av.getGapCharacter();
501 } catch (Exception ex)
505 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
507 if (alAndColsel != null && alAndColsel[0] != null)
509 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
511 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
512 Alignment dataset = (av != null && av.getAlignment() != null) ? av
513 .getAlignment().getDataset() : null;
516 al.setDataset(dataset);
522 AlignFrame af = new AlignFrame(al,
523 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
524 AlignFrame.DEFAULT_HEIGHT);
526 // >>>This is a fix for the moment, until a better solution is
528 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
530 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
533 Desktop.addInternalFrame(af, MessageManager.formatMessage(
534 "label.original_data_for_params", new String[]
535 { this.title }), AlignFrame.DEFAULT_WIDTH,
536 AlignFrame.DEFAULT_HEIGHT);
547 public void fitToWindow_actionPerformed(ActionEvent e)
549 treeCanvas.fitToWindow = fitToWindow.isSelected();
554 * sort the associated alignment view by the current tree.
558 public void sortByTree_actionPerformed(ActionEvent e)
561 if (treeCanvas.applyToAllViews)
563 final ArrayList<CommandI> commands = new ArrayList<CommandI>();
564 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
565 .getSequenceSetId()))
567 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
569 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
573 public void undoCommand(AlignmentI[] views)
575 for (CommandI tsort : commands)
577 tsort.undoCommand(views);
584 return commands.size();
588 public String getDescription()
590 return "Tree Sort (many views)";
594 public void doCommand(AlignmentI[] views)
597 for (CommandI tsort : commands)
599 tsort.doCommand(views);
603 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
604 .getSequenceSetId()))
606 // ensure all the alignFrames refresh their GI after adding an undo item
607 ap.alignFrame.updateEditMenuBar();
612 treeCanvas.ap.alignFrame
613 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
618 public CommandI sortAlignmentIn(AlignmentPanel ap)
620 AlignViewport av = ap.av;
621 SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
622 AlignmentSorter.sortByTree(av.getAlignment(), tree);
624 undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
626 ap.paintAlignment(true);
636 public void font_actionPerformed(ActionEvent e)
638 if (treeCanvas == null)
643 new FontChooser(this);
646 public Font getTreeFont()
648 return treeCanvas.font;
651 public void setTreeFont(Font font)
653 if (treeCanvas != null)
655 treeCanvas.setFont(font);
665 public void distanceMenu_actionPerformed(ActionEvent e)
667 treeCanvas.setShowDistances(distanceMenu.isSelected());
676 public void bootstrapMenu_actionPerformed(ActionEvent e)
678 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
687 public void placeholdersMenu_actionPerformed(ActionEvent e)
689 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
698 public void epsTree_actionPerformed(ActionEvent e)
700 boolean accurateText = true;
702 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
705 // If we need to prompt, and if the GUI is visible then
706 // Prompt for EPS rendering style
707 if (renderStyle.equalsIgnoreCase("Prompt each time")
708 && !(System.getProperty("java.awt.headless") != null && System
709 .getProperty("java.awt.headless").equals("true")))
711 EPSOptions eps = new EPSOptions();
712 renderStyle = eps.getValue();
714 if (renderStyle == null || eps.cancelled)
721 if (renderStyle.equalsIgnoreCase("text"))
723 accurateText = false;
726 int width = treeCanvas.getWidth();
727 int height = treeCanvas.getHeight();
731 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
732 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
733 { "eps" }, new String[]
734 { "Encapsulated Postscript" }, "Encapsulated Postscript");
735 chooser.setFileView(new jalview.io.JalviewFileView());
736 chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
737 chooser.setToolTipText(MessageManager.getString("action.save"));
739 int value = chooser.showSaveDialog(this);
741 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
746 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
747 .getSelectedFile().getParent());
749 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
750 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
752 pg.setAccurateTextMode(accurateText);
754 treeCanvas.draw(pg, width, height);
758 } catch (Exception ex)
760 ex.printStackTrace();
770 public void pngTree_actionPerformed(ActionEvent e)
772 int width = treeCanvas.getWidth();
773 int height = treeCanvas.getHeight();
777 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
778 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
779 { "png" }, new String[]
780 { "Portable network graphics" }, "Portable network graphics");
782 chooser.setFileView(new jalview.io.JalviewFileView());
783 chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
784 chooser.setToolTipText(MessageManager.getString("action.save"));
786 int value = chooser.showSaveDialog(this);
788 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
793 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
794 .getSelectedFile().getParent());
796 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
798 BufferedImage bi = new BufferedImage(width, height,
799 BufferedImage.TYPE_INT_RGB);
800 Graphics png = bi.getGraphics();
802 treeCanvas.draw(png, width, height);
804 ImageIO.write(bi, "png", out);
806 } catch (Exception ex)
808 ex.printStackTrace();
813 * change node labels to the annotation referred to by labelClass TODO:
814 * promote to a datamodel modification that can be undone TODO: make argument
815 * one case of a generic transformation function ie { undoStep = apply(Tree,
816 * TransformFunction)};
820 public void changeNames(final String labelClass)
822 tree.applyToNodes(new NodeTransformI()
825 public void transform(BinaryNode node)
827 if (node instanceof SequenceNode
828 && !((SequenceNode) node).isPlaceholder()
829 && !((SequenceNode) node).isDummy())
831 String newname = null;
832 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
835 // search dbrefs, features and annotation
836 DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
837 sq.getDBRef(), new String[]
838 { labelClass.toUpperCase() });
841 for (int i = 0; i < refs.length; i++)
845 newname = new String(refs[i].getAccessionId());
849 newname = newname + "; " + refs[i].getAccessionId();
855 SequenceFeature sf[] = sq.getSequenceFeatures();
856 for (int i = 0; sf != null && i < sf.length; i++)
858 if (sf[i].getType().equals(labelClass))
862 newname = new String(sf[i].getDescription());
866 newname = newname + "; " + sf[i].getDescription();
874 String oldname = ((SequenceNode) node).getName();
875 // TODO : save in the undo object for this modification.
876 ((SequenceNode) node).setName(newname);