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.
26 import java.util.List;
28 import javax.imageio.*;
31 import java.awt.event.*;
32 import java.awt.image.*;
35 import org.jibble.epsgraphics.*;
36 import jalview.analysis.*;
37 import jalview.commands.CommandI;
38 import jalview.commands.OrderCommand;
39 import jalview.datamodel.*;
41 import jalview.jbgui.*;
42 import jalview.util.MessageManager;
50 public class TreePanel extends GTreePanel
56 TreeCanvas treeCanvas;
63 * Creates a new TreePanel object.
78 public TreePanel(AlignmentPanel ap, String type, String pwtype)
81 initTreePanel(ap, type, pwtype, null, null);
83 // We know this tree has distances. JBPNote TODO: prolly should add this as
84 // a userdefined default
85 // showDistances(true);
89 * Creates a new TreePanel object.
102 public TreePanel(AlignmentPanel ap, String type, String pwtype,
106 initTreePanel(ap, type, pwtype, newtree, null);
109 public TreePanel(AlignmentPanel av, String type, String pwtype,
110 NewickFile newtree, AlignmentView inputData)
113 initTreePanel(av, type, pwtype, newtree, inputData);
116 public AlignmentI getAlignment()
118 return treeCanvas.av.getAlignment();
121 public AlignViewport getViewPort()
123 return treeCanvas.av;
126 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
127 NewickFile newTree, AlignmentView inputData)
132 this.pwtype = pwtype;
134 treeCanvas = new TreeCanvas(this, ap, scrollPane);
135 scrollPane.setViewportView(treeCanvas);
137 PaintRefresher.Register(this, ap.av.getSequenceSetId());
139 buildAssociatedViewMenu();
141 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
143 public void propertyChange(PropertyChangeEvent evt)
145 if (evt.getPropertyName().equals("alignment"))
149 System.out.println("tree is null");
150 // TODO: deal with case when a change event is received whilst a
151 // tree is still being calculated - should save reference for
152 // processing message later.
155 if (evt.getNewValue() == null)
158 .println("new alignment sequences vector value is null");
161 tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
162 treeCanvas.nameHash.clear(); // reset the mapping between canvas
163 // rectangles and leafnodes
169 TreeLoader tl = new TreeLoader(newTree);
170 if (inputData != null)
172 tl.odata = inputData;
178 public void viewMenu_menuSelected()
180 buildAssociatedViewMenu();
183 void buildAssociatedViewMenu()
185 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
186 .getSequenceSetId());
187 if (aps.length == 1 && treeCanvas.ap == aps[0])
189 associateLeavesMenu.setVisible(false);
193 associateLeavesMenu.setVisible(true);
195 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
197 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
200 associateLeavesMenu.removeAll();
202 JRadioButtonMenuItem item;
203 ButtonGroup buttonGroup = new ButtonGroup();
204 int i, iSize = aps.length;
205 final TreePanel thisTreePanel = this;
206 for (i = 0; i < iSize; i++)
208 final AlignmentPanel ap = aps[i];
209 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
210 buttonGroup.add(item);
211 item.addActionListener(new ActionListener()
213 public void actionPerformed(ActionEvent evt)
215 treeCanvas.applyToAllViews = false;
217 treeCanvas.av = ap.av;
218 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
222 associateLeavesMenu.add(item);
225 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
226 buttonGroup.add(itemf);
227 itemf.setSelected(treeCanvas.applyToAllViews);
228 itemf.addActionListener(new ActionListener()
230 public void actionPerformed(ActionEvent evt)
232 treeCanvas.applyToAllViews = itemf.isSelected();
235 associateLeavesMenu.add(itemf);
239 class TreeLoader extends Thread
243 jalview.datamodel.AlignmentView odata = null;
245 public TreeLoader(NewickFile newtree)
247 this.newtree = newtree;
250 // Must be outside run(), as Jalview2XML tries to
251 // update distance/bootstrap visibility at the same time
252 showBootstrap(newtree.HasBootstrap());
253 showDistances(newtree.HasDistances());
264 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
268 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
271 if (!tree.hasOriginalSequenceData())
273 allowOriginalSeqData(false);
280 boolean selview = av.getSelectionGroup() != null
281 && av.getSelectionGroup().getSize() > 1;
282 AlignmentView seqStrings = av.getAlignmentView(selview);
286 end = av.getAlignment().getWidth();
287 seqs = av.getAlignment().getSequencesArray();
291 start = av.getSelectionGroup().getStartRes();
292 end = av.getSelectionGroup().getEndRes() + 1;
293 seqs = av.getSelectionGroup().getSequencesInOrder(
297 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
301 tree.reCount(tree.getTopNode());
302 tree.findHeight(tree.getTopNode());
303 treeCanvas.setTree(tree);
304 treeCanvas.repaint();
305 av.setCurrentTree(tree);
306 if (av.getSortByTree())
308 sortByTree_actionPerformed(null);
313 public void showDistances(boolean b)
315 treeCanvas.setShowDistances(b);
316 distanceMenu.setSelected(b);
319 public void showBootstrap(boolean b)
321 treeCanvas.setShowBootstrap(b);
322 bootstrapMenu.setSelected(b);
325 public void showPlaceholders(boolean b)
327 placeholdersMenu.setState(b);
328 treeCanvas.setMarkPlaceholders(b);
331 private void allowOriginalSeqData(boolean b)
333 originalSeqData.setVisible(b);
339 * @return DOCUMENT ME!
341 public NJTree getTree()
352 public void textbox_actionPerformed(ActionEvent e)
354 CutAndPasteTransfer cap = new CutAndPasteTransfer();
356 StringBuffer buffer = new StringBuffer();
358 if (type.equals("AV"))
360 buffer.append("Average distance tree using ");
364 buffer.append("Neighbour joining tree using ");
367 if (pwtype.equals("BL"))
369 buffer.append("BLOSUM62");
373 buffer.append("PID");
376 jalview.io.NewickFile fout = new jalview.io.NewickFile(
380 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
381 tree.isHasRootDistance()));
382 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
383 } catch (OutOfMemoryError oom)
385 new OOMWarning("generating newick tree file", oom);
397 public void saveAsNewick_actionPerformed(ActionEvent e)
399 JalviewFileChooser chooser = new JalviewFileChooser(
400 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
401 chooser.setFileView(new JalviewFileView());
402 chooser.setDialogTitle("Save tree as newick file");
403 chooser.setToolTipText(MessageManager.getString("action.save"));
405 int value = chooser.showSaveDialog(null);
407 if (value == JalviewFileChooser.APPROVE_OPTION)
409 String choice = chooser.getSelectedFile().getPath();
410 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
411 .getSelectedFile().getParent());
415 jalview.io.NewickFile fout = new jalview.io.NewickFile(
417 String output = fout.print(tree.isHasBootstrap(),
418 tree.isHasDistances(), tree.isHasRootDistance());
419 java.io.PrintWriter out = new java.io.PrintWriter(
420 new java.io.FileWriter(choice));
423 } catch (Exception ex)
425 ex.printStackTrace();
436 public void printMenu_actionPerformed(ActionEvent e)
438 // Putting in a thread avoids Swing painting problems
439 treeCanvas.startPrinting();
442 public void originalSeqData_actionPerformed(ActionEvent e)
444 if (!tree.hasOriginalSequenceData())
446 jalview.bin.Cache.log
447 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
450 // decide if av alignment is sufficiently different to original data to
451 // warrant a new window to be created
452 // create new alignmnt window with hidden regions (unhiding hidden regions
453 // yields unaligned seqs)
454 // or create a selection box around columns in alignment view
455 // test Alignment(SeqCigar[])
459 // we try to get the associated view's gap character
460 // but this may fail if the view was closed...
461 gc = av.getGapCharacter();
463 } catch (Exception ex)
467 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
469 if (alAndColsel != null && alAndColsel[0] != null)
471 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
473 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
474 Alignment dataset = (av != null && av.getAlignment() != null) ? av
475 .getAlignment().getDataset() : null;
478 al.setDataset(dataset);
484 AlignFrame af = new AlignFrame(al,
485 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
486 AlignFrame.DEFAULT_HEIGHT);
488 // >>>This is a fix for the moment, until a better solution is
490 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
492 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
495 Desktop.addInternalFrame(af, MessageManager.formatMessage("label.original_data_for_params", new String[]{this.title}),
496 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
507 public void fitToWindow_actionPerformed(ActionEvent e)
509 treeCanvas.fitToWindow = fitToWindow.isSelected();
514 * sort the associated alignment view by the current tree.
518 public void sortByTree_actionPerformed(ActionEvent e)
521 if (treeCanvas.applyToAllViews)
523 final ArrayList<CommandI> commands = new ArrayList<CommandI>();
524 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
525 .getSequenceSetId()))
527 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
529 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
533 public void undoCommand(AlignmentI[] views)
535 for (CommandI tsort : commands)
537 tsort.undoCommand(views);
544 return commands.size();
548 public String getDescription()
550 return "Tree Sort (many views)";
554 public void doCommand(AlignmentI[] views)
557 for (CommandI tsort : commands)
559 tsort.doCommand(views);
563 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
564 .getSequenceSetId()))
566 // ensure all the alignFrames refresh their GI after adding an undo item
567 ap.alignFrame.updateEditMenuBar();
572 treeCanvas.ap.alignFrame
573 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
578 public CommandI sortAlignmentIn(AlignmentPanel ap)
580 AlignViewport av = ap.av;
581 SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
582 AlignmentSorter.sortByTree(av.getAlignment(), tree);
584 undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
586 ap.paintAlignment(true);
596 public void font_actionPerformed(ActionEvent e)
598 if (treeCanvas == null)
603 new FontChooser(this);
606 public Font getTreeFont()
608 return treeCanvas.font;
611 public void setTreeFont(Font font)
613 if (treeCanvas != null)
615 treeCanvas.setFont(font);
625 public void distanceMenu_actionPerformed(ActionEvent e)
627 treeCanvas.setShowDistances(distanceMenu.isSelected());
636 public void bootstrapMenu_actionPerformed(ActionEvent e)
638 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
647 public void placeholdersMenu_actionPerformed(ActionEvent e)
649 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
658 public void epsTree_actionPerformed(ActionEvent e)
660 boolean accurateText = true;
662 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
665 // If we need to prompt, and if the GUI is visible then
666 // Prompt for EPS rendering style
667 if (renderStyle.equalsIgnoreCase("Prompt each time")
668 && !(System.getProperty("java.awt.headless") != null && System
669 .getProperty("java.awt.headless").equals("true")))
671 EPSOptions eps = new EPSOptions();
672 renderStyle = eps.getValue();
674 if (renderStyle == null || eps.cancelled)
681 if (renderStyle.equalsIgnoreCase("text"))
683 accurateText = false;
686 int width = treeCanvas.getWidth();
687 int height = treeCanvas.getHeight();
691 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
692 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
693 { "eps" }, new String[]
694 { "Encapsulated Postscript" }, "Encapsulated Postscript");
695 chooser.setFileView(new jalview.io.JalviewFileView());
696 chooser.setDialogTitle("Create EPS file from tree");
697 chooser.setToolTipText(MessageManager.getString("action.save"));
699 int value = chooser.showSaveDialog(this);
701 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
706 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
707 .getSelectedFile().getParent());
709 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
710 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
712 pg.setAccurateTextMode(accurateText);
714 treeCanvas.draw(pg, width, height);
718 } catch (Exception ex)
720 ex.printStackTrace();
730 public void pngTree_actionPerformed(ActionEvent e)
732 int width = treeCanvas.getWidth();
733 int height = treeCanvas.getHeight();
737 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
738 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
739 { "png" }, new String[]
740 { "Portable network graphics" }, "Portable network graphics");
742 chooser.setFileView(new jalview.io.JalviewFileView());
743 chooser.setDialogTitle("Create PNG image from tree");
744 chooser.setToolTipText(MessageManager.getString("action.save"));
746 int value = chooser.showSaveDialog(this);
748 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
753 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
754 .getSelectedFile().getParent());
756 FileOutputStream out = new FileOutputStream(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()
785 public void transform(BinaryNode node)
787 if (node instanceof SequenceNode
788 && !((SequenceNode) node).isPlaceholder()
789 && !((SequenceNode) node).isDummy())
791 String newname = null;
792 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
795 // search dbrefs, features and annotation
796 DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
797 sq.getDBRef(), new String[]
798 { labelClass.toUpperCase() });
801 for (int i = 0; i < refs.length; i++)
805 newname = new String(refs[i].getAccessionId());
809 newname = newname + "; " + refs[i].getAccessionId();
815 SequenceFeature sf[] = sq.getSequenceFeatures();
816 for (int i = 0; sf != null && i < sf.length; i++)
818 if (sf[i].getType().equals(labelClass))
822 newname = new String(sf[i].getDescription());
826 newname = newname + "; " + sf[i].getDescription();
834 String oldname = ((SequenceNode) node).getName();
835 // TODO : save in the undo object for this modification.
836 ((SequenceNode) node).setName(newname);