/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import jalview.analysis.AlignmentSorter; import jalview.analysis.NJTree; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.ViewBasedAnalysisI; import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.OrderCommand; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.BinaryNode; import jalview.datamodel.ColumnSelection; import jalview.datamodel.DBRefEntry; import jalview.datamodel.NodeTransformI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.datamodel.SequenceNode; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.NewickFile; import jalview.jbgui.GTreePanel; import jalview.schemes.ResidueProperties; import jalview.util.DBRefUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import java.awt.Font; import java.awt.Graphics; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.image.BufferedImage; import java.beans.PropertyChangeEvent; import java.io.FileOutputStream; import java.util.ArrayList; import java.util.List; import javax.imageio.ImageIO; import javax.swing.ButtonGroup; import javax.swing.JMenuItem; import javax.swing.JRadioButtonMenuItem; import org.jibble.epsgraphics.EpsGraphics2D; /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ public class TreePanel extends GTreePanel { String type; String pwtype; TreeCanvas treeCanvas; NJTree tree; AlignViewport av; /** * Creates a new TreePanel object. * * @param av * DOCUMENT ME! * @param seqVector * DOCUMENT ME! * @param type * DOCUMENT ME! * @param pwtype * DOCUMENT ME! * @param s * DOCUMENT ME! * @param e * DOCUMENT ME! */ public TreePanel(AlignmentPanel ap, String type, String pwtype) { super(); initTreePanel(ap, type, pwtype, null, null); // We know this tree has distances. JBPNote TODO: prolly should add this as // a userdefined default // showDistances(true); } /** * Creates a new TreePanel object. * * @param av * DOCUMENT ME! * @param seqVector * DOCUMENT ME! * @param newtree * DOCUMENT ME! * @param type * DOCUMENT ME! * @param pwtype * DOCUMENT ME! */ public TreePanel(AlignmentPanel ap, String type, String pwtype, NewickFile newtree) { super(); initTreePanel(ap, type, pwtype, newtree, null); } public TreePanel(AlignmentPanel av, String type, String pwtype, NewickFile newtree, AlignmentView inputData) { super(); initTreePanel(av, type, pwtype, newtree, inputData); } public AlignmentI getAlignment() { return treeCanvas.av.getAlignment(); } public AlignmentViewport getViewPort() { return treeCanvas.av; } void initTreePanel(AlignmentPanel ap, String type, String pwtype, NewickFile newTree, AlignmentView inputData) { av = ap.av; this.type = type; this.pwtype = pwtype; treeCanvas = new TreeCanvas(this, ap, scrollPane); scrollPane.setViewportView(treeCanvas); PaintRefresher.Register(this, ap.av.getSequenceSetId()); buildAssociatedViewMenu(); av.addPropertyChangeListener(new java.beans.PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) { if (tree == null) { System.out.println("tree is null"); // TODO: deal with case when a change event is received whilst a // tree is still being calculated - should save reference for // processing message later. return; } if (evt.getNewValue() == null) { System.out .println("new alignment sequences vector value is null"); } tree.UpdatePlaceHolders((List) evt.getNewValue()); treeCanvas.nameHash.clear(); // reset the mapping between canvas // rectangles and leafnodes repaint(); } } }); TreeLoader tl = new TreeLoader(newTree); if (inputData != null) { tl.odata = inputData; } tl.start(); } public void viewMenu_menuSelected() { buildAssociatedViewMenu(); } void buildAssociatedViewMenu() { AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av .getSequenceSetId()); if (aps.length == 1 && treeCanvas.ap == aps[0]) { associateLeavesMenu.setVisible(false); return; } associateLeavesMenu.setVisible(true); if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) { viewMenu.insertSeparator(viewMenu.getItemCount() - 1); } associateLeavesMenu.removeAll(); JRadioButtonMenuItem item; ButtonGroup buttonGroup = new ButtonGroup(); int i, iSize = aps.length; final TreePanel thisTreePanel = this; for (i = 0; i < iSize; i++) { final AlignmentPanel ap = aps[i]; item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap); buttonGroup.add(item); item.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = false; treeCanvas.ap = ap; treeCanvas.av = ap.av; PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId()); } }); associateLeavesMenu.add(item); } final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem( "label.all_views"); buttonGroup.add(itemf); itemf.setSelected(treeCanvas.applyToAllViews); itemf.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = itemf.isSelected(); } }); associateLeavesMenu.add(itemf); } class TreeLoader extends Thread { NewickFile newtree; AlignmentView odata = null; public TreeLoader(NewickFile newtree) { this.newtree = newtree; if (newtree != null) { // Must be outside run(), as Jalview2XML tries to // update distance/bootstrap visibility at the same time showBootstrap(newtree.HasBootstrap()); showDistances(newtree.HasDistances()); } } public void run() { if (newtree != null) { if (odata == null) { tree = new NJTree(av.getAlignment().getSequencesArray(), newtree); } else { tree = new NJTree(av.getAlignment().getSequencesArray(), odata, newtree); } if (!tree.hasOriginalSequenceData()) { allowOriginalSeqData(false); } } else { int start, end; SequenceI[] seqs; boolean selview = av.getSelectionGroup() != null && av.getSelectionGroup().getSize() > 1; AlignmentView seqStrings = av.getAlignmentView(selview); if (!selview) { start = 0; end = av.getAlignment().getWidth(); seqs = av.getAlignment().getSequencesArray(); } else { start = av.getSelectionGroup().getStartRes(); end = av.getSelectionGroup().getEndRes() + 1; seqs = av.getSelectionGroup().getSequencesInOrder( av.getAlignment()); } ScoreModelI sm = ResidueProperties.getScoreModel(pwtype); if (sm instanceof ViewBasedAnalysisI) { try { sm = sm.getClass().newInstance(); ((ViewBasedAnalysisI) sm) .configureFromAlignmentView(treeCanvas.ap); } catch (Exception q) { Cache.log.error("Couldn't create a scoremodel instance for " + sm.getName()); } tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end); } else { tree = new NJTree(seqs, seqStrings, type, pwtype, null, start, end); } showDistances(true); } tree.reCount(tree.getTopNode()); tree.findHeight(tree.getTopNode()); treeCanvas.setTree(tree); treeCanvas.repaint(); av.setCurrentTree(tree); if (av.getSortByTree()) { sortByTree_actionPerformed(); } } } public void showDistances(boolean b) { treeCanvas.setShowDistances(b); distanceMenu.setSelected(b); } public void showBootstrap(boolean b) { treeCanvas.setShowBootstrap(b); bootstrapMenu.setSelected(b); } public void showPlaceholders(boolean b) { placeholdersMenu.setState(b); treeCanvas.setMarkPlaceholders(b); } private void allowOriginalSeqData(boolean b) { originalSeqData.setVisible(b); } /** * DOCUMENT ME! * * @return DOCUMENT ME! */ public NJTree getTree() { return tree; } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void textbox_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); StringBuffer buffer = new StringBuffer(); if (type.equals("AV")) { buffer.append("Average distance tree using "); } else { buffer.append("Neighbour joining tree using "); } if (pwtype.equals("BL")) { buffer.append("BLOSUM62"); } else { buffer.append("PID"); } NewickFile fout = new NewickFile(tree.getTopNode()); try { cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance())); Desktop.addInternalFrame(cap, buffer.toString(), 500, 100); } catch (OutOfMemoryError oom) { new OOMWarning("generating newick tree file", oom); cap.dispose(); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void saveAsNewick_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(null); if (value == JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); Cache.setProperty("LAST_DIRECTORY", chooser .getSelectedFile().getParent()); try { NewickFile fout = new NewickFile(tree.getTopNode()); String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()); java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter(choice)); out.println(output); out.close(); } catch (Exception ex) { ex.printStackTrace(); } } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void printMenu_actionPerformed(ActionEvent e) { // Putting in a thread avoids Swing painting problems treeCanvas.startPrinting(); } public void originalSeqData_actionPerformed(ActionEvent e) { if (!tree.hasOriginalSequenceData()) { Cache.log .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); return; } // decide if av alignment is sufficiently different to original data to // warrant a new window to be created // create new alignmnt window with hidden regions (unhiding hidden regions // yields unaligned seqs) // or create a selection box around columns in alignment view // test Alignment(SeqCigar[]) char gc = '-'; try { // we try to get the associated view's gap character // but this may fail if the view was closed... gc = av.getGapCharacter(); } catch (Exception ex) { } ; Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc); if (alAndColsel != null && alAndColsel[0] != null) { // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); Alignment al = new Alignment((SequenceI[]) alAndColsel[0]); Alignment dataset = (av != null && av.getAlignment() != null) ? av .getAlignment().getDataset() : null; if (dataset != null) { al.setDataset(dataset); } if (true) { // make a new frame! AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); // >>>This is a fix for the moment, until a better solution is // found!!<<< // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer()); // af.addSortByOrderMenuItem(ServiceName + " Ordering", // msaorder); Desktop.addInternalFrame(af, MessageManager.formatMessage( "label.original_data_for_params", new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void fitToWindow_actionPerformed(ActionEvent e) { treeCanvas.fitToWindow = fitToWindow.isSelected(); repaint(); } /** * sort the associated alignment view by the current tree. * * @param e */ @Override public void sortByTree_actionPerformed() { if (treeCanvas.applyToAllViews) { final ArrayList commands = new ArrayList(); for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av .getSequenceSetId())) { commands.add(sortAlignmentIn(ap.av.getAlignPanel())); } av.getAlignPanel().alignFrame.addHistoryItem(new CommandI() { @Override public void undoCommand(AlignmentI[] views) { for (CommandI tsort : commands) { tsort.undoCommand(views); } } @Override public int getSize() { return commands.size(); } @Override public String getDescription() { return "Tree Sort (many views)"; } @Override public void doCommand(AlignmentI[] views) { for (CommandI tsort : commands) { tsort.doCommand(views); } } }); for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av .getSequenceSetId())) { // ensure all the alignFrames refresh their GI after adding an undo item ap.alignFrame.updateEditMenuBar(); } } else { treeCanvas.ap.alignFrame .addHistoryItem(sortAlignmentIn(treeCanvas.ap)); } } public CommandI sortAlignmentIn(AlignmentPanel ap) { AlignmentViewport av = ap.av; SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); AlignmentSorter.sortByTree(av.getAlignment(), tree); CommandI undo; undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment()); ap.paintAlignment(true); return undo; } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void font_actionPerformed(ActionEvent e) { if (treeCanvas == null) { return; } new FontChooser(this); } public Font getTreeFont() { return treeCanvas.font; } public void setTreeFont(Font font) { if (treeCanvas != null) { treeCanvas.setFont(font); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void distanceMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowDistances(distanceMenu.isSelected()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void bootstrapMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void placeholdersMenu_actionPerformed(ActionEvent e) { treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void epsTree_actionPerformed(ActionEvent e) { boolean accurateText = true; String renderStyle = Cache.getDefault("EPS_RENDERING", "Prompt each time"); // If we need to prompt, and if the GUI is visible then // Prompt for EPS rendering style if (renderStyle.equalsIgnoreCase("Prompt each time") && !(System.getProperty("java.awt.headless") != null && System .getProperty("java.awt.headless").equals("true"))) { EPSOptions eps = new EPSOptions(); renderStyle = eps.getValue(); if (renderStyle == null || eps.cancelled) { return; } } if (renderStyle.equalsIgnoreCase("text")) { accurateText = false; } int width = treeCanvas.getWidth(); int height = treeCanvas.getHeight(); try { JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY"), new String[] { "eps" }, new String[] { "Encapsulated Postscript" }, "Encapsulated Postscript"); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); if (value != JalviewFileChooser.APPROVE_OPTION) { return; } Cache.setProperty("LAST_DIRECTORY", chooser .getSelectedFile().getParent()); FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height); pg.setAccurateTextMode(accurateText); treeCanvas.draw(pg, width, height); pg.flush(); pg.close(); } catch (Exception ex) { ex.printStackTrace(); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void pngTree_actionPerformed(ActionEvent e) { int width = treeCanvas.getWidth(); int height = treeCanvas.getHeight(); try { JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY"), new String[] { "png" }, new String[] { "Portable network graphics" }, "Portable network graphics"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); if (value != JalviewFileChooser.APPROVE_OPTION) { return; } Cache.setProperty("LAST_DIRECTORY", chooser .getSelectedFile().getParent()); FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); Graphics png = bi.getGraphics(); treeCanvas.draw(png, width, height); ImageIO.write(bi, "png", out); out.close(); } catch (Exception ex) { ex.printStackTrace(); } } /** * change node labels to the annotation referred to by labelClass TODO: * promote to a datamodel modification that can be undone TODO: make argument * one case of a generic transformation function ie { undoStep = apply(Tree, * TransformFunction)}; * * @param labelClass */ public void changeNames(final String labelClass) { tree.applyToNodes(new NodeTransformI() { public void transform(BinaryNode node) { if (node instanceof SequenceNode && !((SequenceNode) node).isPlaceholder() && !((SequenceNode) node).isDummy()) { String newname = null; SequenceI sq = (SequenceI) ((SequenceNode) node).element(); if (sq != null) { // search dbrefs, features and annotation DBRefEntry[] refs = DBRefUtils.selectRefs( sq.getDBRef(), new String[] { labelClass.toUpperCase() }); if (refs != null) { for (int i = 0; i < refs.length; i++) { if (newname == null) { newname = new String(refs[i].getAccessionId()); } else { newname = newname + "; " + refs[i].getAccessionId(); } } } if (newname == null) { SequenceFeature sf[] = sq.getSequenceFeatures(); for (int i = 0; sf != null && i < sf.length; i++) { if (sf[i].getType().equals(labelClass)) { if (newname == null) { newname = new String(sf[i].getDescription()); } else { newname = newname + "; " + sf[i].getDescription(); } } } } } if (newname != null) { String oldname = ((SequenceNode) node).getName(); // TODO : save in the undo object for this modification. ((SequenceNode) node).setName(newname); } } } }); } }