X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=084f46170f73b4c25dfddc237dd420c05873563b;hb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;hp=c22a8e715c81871533924a0b570262d2f4e2f00b;hpb=c770c52fe1c84d6b41ba1f5af352245f6b1c937c;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index c22a8e7..084f461 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,564 +1,901 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 + * 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. - * - * This program 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import jalview.analysis.*; +import jalview.analysis.AlignmentSorter; +import jalview.analysis.AverageDistanceTree; +import jalview.analysis.NJTree; +import jalview.analysis.TreeBuilder; +import jalview.analysis.TreeModel; +import jalview.analysis.scoremodels.ScoreModels; +import jalview.api.analysis.ScoreModelI; +import jalview.api.analysis.SimilarityParamsI; +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.DBRefEntry; +import jalview.datamodel.HiddenColumns; +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.util.ImageMaker; +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.beans.PropertyChangeListener; +import java.io.FileOutputStream; +import java.util.ArrayList; +import java.util.List; -import jalview.datamodel.*; +import javax.imageio.ImageIO; +import javax.swing.ButtonGroup; +import javax.swing.JMenuItem; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; -import jalview.io.*; +import org.jibble.epsgraphics.EpsGraphics2D; -import jalview.jbgui.*; +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class TreePanel extends GTreePanel +{ + String treeType; -import org.jibble.epsgraphics.*; + String scoreModelName; // if tree computed -import java.awt.*; -import java.awt.event.*; -import java.awt.image.*; + String treeTitle; // if tree loaded -import java.io.*; + SimilarityParamsI similarityParams; -import java.util.*; + private TreeCanvas treeCanvas; -import javax.imageio.*; + TreeModel tree; -import java.beans.PropertyChangeEvent; + private AlignViewport av; + /** + * Creates a new TreePanel object. + * + * @param ap + * @param type + * @param modelName + * @param options + */ + public TreePanel(AlignmentPanel ap, String type, String modelName, + SimilarityParamsI options) + { + super(); + this.similarityParams = options; + initTreePanel(ap, type, modelName, null, null); -/** - * 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); + } - // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default - // showDistances(true); - } + public TreePanel(AlignmentPanel alignPanel, NewickFile newtree, + String theTitle, AlignmentView inputData) + { + super(); + this.treeTitle = theTitle; + initTreePanel(alignPanel, null, null, newtree, inputData); + } - /** - * 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 getTreeCanvas().getViewport().getAlignment(); + } - public AlignmentI getAlignment() - { - return treeCanvas.av.getAlignment(); - } - public AlignViewport getViewPort() { - return treeCanvas.av; - } + public AlignmentViewport getViewPort() + { + return getTreeCanvas().getViewport(); + } - void initTreePanel(AlignmentPanel ap, String type, String pwtype, - NewickFile newTree, AlignmentView inputData) - { + void initTreePanel(AlignmentPanel ap, String type, String modelName, + NewickFile newTree, AlignmentView inputData) + { - av = ap.av; - this.type = type; - this.pwtype = pwtype; + setViewport(ap.av); + this.treeType = type; + this.scoreModelName = modelName; - treeCanvas = new TreeCanvas(ap, scrollPane); - scrollPane.setViewportView(treeCanvas); + treeCanvas = new TreeCanvas(this, ap, scrollPane); + scrollPane.setViewportView(getTreeCanvas()); - 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"); - if(evt.getNewValue()==null) - System.out.println("new alignment sequences vector value is null"); - - tree.UpdatePlaceHolders( (Vector) evt.getNewValue()); - treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes - repaint(); - } - } - }); + PaintRefresher.Register(this, ap.av.getSequenceSetId()); - TreeLoader tl = new TreeLoader(newTree); - if (inputData!=null) { - tl.odata=inputData; - } - tl.start(); + buildAssociatedViewMenu(); - } + final PropertyChangeListener listener = addAlignmentListener(); - class TreeLoader extends Thread + /* + * remove listener when window is closed, so that this + * panel can be garbage collected + */ + addInternalFrameListener(new InternalFrameAdapter() { - NewickFile newtree; - jalview.datamodel.AlignmentView odata=null; - public TreeLoader(NewickFile newtree) + @Override + public void internalFrameClosed(InternalFrameEvent evt) { - this.newtree = newtree; - if (newtree != null) + if (getViewport() != null) { - // Must be outside run(), as Jalview2XML tries to - // update distance/bootstrap visibility at the same time - showBootstrap(newtree.HasBootstrap()); - showDistances(newtree.HasDistances()); + getViewport().removePropertyChangeListener(listener); } } + }); - public void run() - { + TreeLoader tl = new TreeLoader(newTree, inputData); + tl.start(); - if(newtree!=null) - { - if (odata==null) { - tree = new NJTree(av.alignment.getSequencesArray(), - newtree); - } else { - tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree); - } - if (!tree.hasOriginalSequenceData()) - allowOriginalSeqData(false); - } - else + } + + /** + * @return + */ + protected PropertyChangeListener addAlignmentListener() + { + final PropertyChangeListener listener = new PropertyChangeListener() + { + @Override + public void propertyChange(PropertyChangeEvent evt) + { + if (evt.getPropertyName().equals("alignment")) { - int start, end; - SequenceI [] seqs; - AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null); - if(av.getSelectionGroup()==null) + if (tree == null) { - start = 0; - end = av.alignment.getWidth(); - seqs = av.alignment.getSequencesArray(); + 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; } - else + if (evt.getNewValue() == null) { - start = av.getSelectionGroup().getStartRes(); - end = av.getSelectionGroup().getEndRes()+1; - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); + System.out.println( + "new alignment sequences vector value is null"); } - tree = new NJTree(seqs, seqStrings, type, pwtype, start, end); - showDistances(true); + tree.updatePlaceHolders((List) evt.getNewValue()); + getTreeCanvas().nameHash.clear(); // reset the mapping between canvas + // rectangles and leafnodes + repaint(); } - - - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - treeCanvas.setTree(tree); - treeCanvas.repaint(); - av.setCurrentTree(tree); - } - } - - public void showDistances(boolean b) + }; + getViewport().addPropertyChangeListener(listener); + return listener; + } + + @Override + public void viewMenu_menuSelected() + { + buildAssociatedViewMenu(); + } + + void buildAssociatedViewMenu() + { + AlignmentPanel[] aps = PaintRefresher + .getAssociatedPanels(getViewport().getSequenceSetId()); + if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0]) { - treeCanvas.setShowDistances(b); - distanceMenu.setSelected(b); + associateLeavesMenu.setVisible(false); + return; } - public void showBootstrap(boolean b) + associateLeavesMenu.setVisible(true); + + if ((viewMenu + .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) { - treeCanvas.setShowBootstrap(b); - bootstrapMenu.setSelected(b); + viewMenu.insertSeparator(viewMenu.getItemCount() - 1); } - public void showPlaceholders(boolean b) + associateLeavesMenu.removeAll(); + + JRadioButtonMenuItem item; + ButtonGroup buttonGroup = new ButtonGroup(); + int i, iSize = aps.length; + final TreePanel thisTreePanel = this; + for (i = 0; i < iSize; i++) { - placeholdersMenu.setState(b); - treeCanvas.setMarkPlaceholders(b); - } + final AlignmentPanel ap = aps[i]; + item = new JRadioButtonMenuItem(ap.av.getViewName(), ap == getTreeCanvas().getAssociatedPanel()); + buttonGroup.add(item); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent evt) + { + getTreeCanvas().applyToAllViews = false; + getTreeCanvas().setAssociatedPanel(ap); + getTreeCanvas().setViewport(ap.av); + PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId()); + } + }); - private void allowOriginalSeqData(boolean b) { - originalSeqData.setVisible(b); + associateLeavesMenu.add(item); } + final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem( + MessageManager.getString("label.all_views")); + buttonGroup.add(itemf); + itemf.setSelected(getTreeCanvas().applyToAllViews); + itemf.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent evt) + { + getTreeCanvas().applyToAllViews = itemf.isSelected(); + } + }); + associateLeavesMenu.add(itemf); + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public NJTree getTree() - { - return tree; - } + class TreeLoader extends Thread + { + private NewickFile newtree; + private AlignmentView odata = null; - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void textbox_actionPerformed(ActionEvent e) + public TreeLoader(NewickFile newickFile, AlignmentView inputData) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); + this.newtree = newickFile; + this.odata = inputData; - StringBuffer buffer = new StringBuffer(); + if (newickFile != null) + { + // Must be outside run(), as Jalview2XML tries to + // update distance/bootstrap visibility at the same time + showBootstrap(newickFile.HasBootstrap()); + showDistances(newickFile.HasDistances()); + } + } - if (type.equals("AV")) - { - buffer.append("Average distance tree using "); - } - else - { - buffer.append("Neighbour joining tree using "); - } + @Override + public void run() + { - if (pwtype.equals("BL")) - { - buffer.append("BLOSUM62"); - } - else + if (newtree != null) + { + tree = new TreeModel(getViewport().getAlignment().getSequencesArray(), odata, + newtree); + if (tree.getOriginalData() == null) { - buffer.append("PID"); + originalSeqData.setVisible(false); } + } + else + { + ScoreModelI sm = ScoreModels.getInstance() + .getScoreModel(scoreModelName, getTreeCanvas().getAssociatedPanel()); + TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) + ? new NJTree(getViewport(), sm, similarityParams) + : new AverageDistanceTree(getViewport(), sm, similarityParams); + tree = new TreeModel(njtree); + showDistances(true); + } - Desktop.addInternalFrame(cap, buffer.toString(), 500, 100); - - jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode()); - cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance())); + tree.reCount(tree.getTopNode()); + tree.findHeight(tree.getTopNode()); + getTreeCanvas().setTree(tree); + getTreeCanvas().repaint(); + getViewport().setCurrentTree(tree); + if (getViewport().getSortByTree()) + { + sortByTree_actionPerformed(); + } } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void saveAsNewick_actionPerformed(ActionEvent e) + } + + public void showDistances(boolean b) + { + getTreeCanvas().setShowDistances(b); + distanceMenu.setSelected(b); + } + + public void showBootstrap(boolean b) + { + getTreeCanvas().setShowBootstrap(b); + bootstrapMenu.setSelected(b); + } + + public void showPlaceholders(boolean b) + { + placeholdersMenu.setState(b); + getTreeCanvas().setMarkPlaceholders(b); + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public TreeModel getTree() + { + return tree; + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void textbox_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + + String newTitle = getPanelTitle(); + + NewickFile fout = new NewickFile(tree.getTopNode()); + try { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( - "LAST_DIRECTORY")); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save tree as newick file"); - chooser.setToolTipText("Save"); - - int value = chooser.showSaveDialog(null); + cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(), + tree.hasRootDistance())); + Desktop.addInternalFrame(cap, newTitle, 500, 100); + } catch (OutOfMemoryError oom) + { + new OOMWarning("generating newick tree file", oom); + cap.dispose(); + } - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void saveAsNewick_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.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(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); - try - { - jalview.io.NewickFile fout = new jalview.io.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(); - } - } + try + { + jalview.io.NewickFile fout = new jalview.io.NewickFile( + tree.getTopNode()); + String output = fout.print(tree.hasBootstrap(), tree.hasDistances(), + tree.hasRootDistance()); + 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! + */ + @Override + public void printMenu_actionPerformed(ActionEvent e) + { + // Putting in a thread avoids Swing painting problems + getTreeCanvas().startPrinting(); + } + + @Override + public void originalSeqData_actionPerformed(ActionEvent e) + { + AlignmentView originalData = tree.getOriginalData(); + if (originalData == null) + { + jalview.bin.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 = getViewport().getGapCharacter(); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void printMenu_actionPerformed(ActionEvent e) + } catch (Exception ex) { - //Putting in a thread avoids Swing painting problems - treeCanvas.startPrinting(); } + Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc); - public void originalSeqData_actionPerformed(ActionEvent e) + if (alAndColsel != null && alAndColsel[0] != null) { - if (!tree.hasOriginalSequenceData()) + // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); + + AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); + AlignmentI dataset = (getViewport() != null && getViewport().getAlignment() != null) + ? getViewport().getAlignment().getDataset() + : null; + if (dataset != null) { - jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); - return; + al.setDataset(dataset); } - // 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[]) - Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av. - getGapCharacter()); - - - if (alAndColsel != null && alAndColsel[0]!=null) - { - // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); - - Alignment al = new Alignment((SequenceI[]) alAndColsel[0]); - Alignment dataset = av.getAlignment().getDataset(); - 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, "Original Data for " + this.title, - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); - } - } - } + if (true) + { + // make a new frame! + AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1], + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void fitToWindow_actionPerformed(ActionEvent e) - { - treeCanvas.fitToWindow = fitToWindow.isSelected(); - repaint(); - } + // >>>This is a fix for the moment, until a better solution is + // found!!<<< + // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer()); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void font_actionPerformed(ActionEvent e) + // 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! + */ + @Override + public void fitToWindow_actionPerformed(ActionEvent e) + { + getTreeCanvas().fitToWindow = fitToWindow.isSelected(); + repaint(); + } + + /** + * sort the associated alignment view by the current tree. + * + * @param e + */ + @Override + public void sortByTree_actionPerformed() + { + + if (getTreeCanvas().applyToAllViews) { - if (treeCanvas == null) + final ArrayList commands = new ArrayList<>(); + for (AlignmentPanel ap : PaintRefresher + .getAssociatedPanels(getViewport().getSequenceSetId())) + { + commands.add(sortAlignmentIn(ap.av.getAlignPanel())); + } + getViewport().getAlignPanel().alignFrame.addHistoryItem(new CommandI() + { + + @Override + public void undoCommand(AlignmentI[] views) { - return; + for (CommandI tsort : commands) + { + tsort.undoCommand(views); + } } - new FontChooser(this); - } + @Override + public int getSize() + { + return commands.size(); + } - public Font getTreeFont() + @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(getViewport().getSequenceSetId())) + { + // ensure all the alignFrames refresh their GI after adding an undo item + ap.alignFrame.updateEditMenuBar(); + } + } + else { - return treeCanvas.font; + getTreeCanvas().getAssociatedPanel().alignFrame + .addHistoryItem(sortAlignmentIn(getTreeCanvas().getAssociatedPanel())); } - public void setTreeFont(Font font) + } + + public CommandI sortAlignmentIn(AlignmentPanel ap) + { + // TODO: move to alignment view controller + AlignmentViewport viewport = ap.av; + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByTree(viewport.getAlignment(), tree); + CommandI undo; + undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment()); + + ap.paintAlignment(true, false); + return undo; + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void font_actionPerformed(ActionEvent e) + { + if (getTreeCanvas() == null) { - if(treeCanvas!=null) - treeCanvas.setFont(font); + return; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void distanceMenu_actionPerformed(ActionEvent e) + new FontChooser(this); + } + + public Font getTreeFont() + { + return getTreeCanvas().font; + } + + public void setTreeFont(Font f) + { + if (getTreeCanvas() != null) { - treeCanvas.setShowDistances(distanceMenu.isSelected()); + getTreeCanvas().setFont(f); } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void distanceMenu_actionPerformed(ActionEvent e) + { + getTreeCanvas().setShowDistances(distanceMenu.isSelected()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void bootstrapMenu_actionPerformed(ActionEvent e) + { + getTreeCanvas().setShowBootstrap(bootstrapMenu.isSelected()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void placeholdersMenu_actionPerformed(ActionEvent e) + { + getTreeCanvas().setMarkPlaceholders(placeholdersMenu.isSelected()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void epsTree_actionPerformed(ActionEvent e) + { + boolean accurateText = true; + + String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING", + "Prompt each time"); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void bootstrapMenu_actionPerformed(ActionEvent e) + // 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"))) { - treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); + EPSOptions eps = new EPSOptions(); + renderStyle = eps.getValue(); + + if (renderStyle == null || eps.cancelled) + { + return; + } + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void placeholdersMenu_actionPerformed(ActionEvent e) + if (renderStyle.equalsIgnoreCase("text")) { - treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); + accurateText = false; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void epsTree_actionPerformed(ActionEvent e) + int width = getTreeCanvas().getWidth(); + int height = getTreeCanvas().getHeight(); + + try { - boolean accurateText = true; + JalviewFileChooser chooser = new JalviewFileChooser( + ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle( + MessageManager.getString("label.create_eps_from_tree")); + chooser.setToolTipText(MessageManager.getString("action.save")); - String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING", - "Prompt each time"); + int value = chooser.showSaveDialog(this); - // 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"))) + if (value != JalviewFileChooser.APPROVE_OPTION) { - EPSOptions eps = new EPSOptions(); - renderStyle = eps.getValue(); + return; + } - if (renderStyle==null || eps.cancelled) - 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); - if (renderStyle.equalsIgnoreCase("text")) - { - accurateText = false; - } + getTreeCanvas().draw(pg, width, height); - int width = treeCanvas.getWidth(); - int height = treeCanvas.getHeight(); + pg.flush(); + pg.close(); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void pngTree_actionPerformed(ActionEvent e) + { + int width = getTreeCanvas().getWidth(); + int height = getTreeCanvas().getHeight(); + + try + { + JalviewFileChooser chooser = new JalviewFileChooser( + ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION); - try - { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), new String[] { "eps" }, - new String[] { "Encapsulated Postscript" }, - "Encapsulated Postscript"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Create EPS file from tree"); - chooser.setToolTipText("Save"); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle( + MessageManager.getString("label.create_png_from_tree")); + chooser.setToolTipText(MessageManager.getString("action.save")); - int value = chooser.showSaveDialog(this); + int value = chooser.showSaveDialog(this); - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) - { - return; - } + if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + { + return; + } - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); - FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); - EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, - height); + FileOutputStream out = new FileOutputStream( + chooser.getSelectedFile()); - pg.setAccurateTextMode(accurateText); + BufferedImage bi = new BufferedImage(width, height, + BufferedImage.TYPE_INT_RGB); + Graphics png = bi.getGraphics(); - treeCanvas.draw(pg, width, height); + getTreeCanvas().draw(png, width, height); - pg.flush(); - pg.close(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } + ImageIO.write(bi, "png", out); + out.close(); + } catch (Exception ex) + { + ex.printStackTrace(); } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void pngTree_actionPerformed(ActionEvent e) + } + + /** + * 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() { - int width = treeCanvas.getWidth(); - int height = treeCanvas.getHeight(); - try + @Override + public void transform(BinaryNode node) + { + if (node instanceof SequenceNode + && !((SequenceNode) node).isPlaceholder() + && !((SequenceNode) node).isDummy()) { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), new String[] { "png" }, - new String[] { "Portable network graphics" }, - "Portable network graphics"); - - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Create PNG image from tree"); - chooser.setToolTipText("Save"); - - int value = chooser.showSaveDialog(this); - - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + String newname = null; + SequenceI sq = (SequenceI) ((SequenceNode) node).element(); + if (sq != null) + { + // search dbrefs, features and annotation + DBRefEntry[] refs = jalview.util.DBRefUtils + .selectRefs(sq.getDBRefs(), new String[] + { labelClass.toUpperCase() }); + if (refs != null) { - return; + 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) + { + List features = sq.getFeatures() + .getPositionalFeatures(labelClass); + for (SequenceFeature feature : features) + { + if (newname == null) + { + newname = feature.getDescription(); + } + else + { + newname = newname + "; " + feature.getDescription(); + } + } + } + } + if (newname != null) + { + // String oldname = ((SequenceNode) node).getName(); + // TODO : save oldname in the undo object for this modification. + ((SequenceNode) node).setName(newname); + } + } + } + }); + } + + /** + * Formats a localised title for the tree panel, like + *

+ * Neighbour Joining Using BLOSUM62 + *

+ * For a tree loaded from file, just uses the file name + * + * @return + */ + public String getPanelTitle() + { + if (treeTitle != null) + { + return treeTitle; + } - jalview.bin.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(); + /* + * i18n description of Neighbour Joining or Average Distance method + */ + String treecalcnm = MessageManager + .getString("label.tree_calc_" + treeType.toLowerCase()); - treeCanvas.draw(png, width, height); + /* + * short score model name (long description can be too long) + */ + String smn = scoreModelName; - ImageIO.write(bi, "png", out); - out.close(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } + /* + * put them together as Using + */ + final String ttl = MessageManager.formatMessage("label.treecalc_title", + treecalcnm, smn); + return ttl; + } + + public AlignViewport getViewport() + { + return av; + } + + public void setViewport(AlignViewport av) + { + this.av = av; + } + + public TreeCanvas getTreeCanvas() + { + return treeCanvas; + } }