X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=ca4f84e53a4e4da494d3334a3b4d349b590cf7cc;hb=09d3b755d9b00f5c3acb44049aedd49361dc0690;hp=72bdbf113fde5343559919ac6be2b3f82aedfab8;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 72bdbf1..ca4f84e 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,127 +1,180 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 java.beans.*; -import java.io.*; -import java.util.*; -import javax.imageio.*; - -import java.awt.*; -import java.awt.event.*; -import java.awt.image.*; -import javax.swing.*; - -import org.jibble.epsgraphics.*; -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; +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 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 org.jibble.epsgraphics.EpsGraphics2D; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class TreePanel - extends GTreePanel +public class TreePanel extends GTreePanel { - String type; - String pwtype; - TreeCanvas treeCanvas; - NJTree tree; - AlignViewport av; + String treeType; - /** - * 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); + String scoreModelName; // if tree computed - // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default - // showDistances(true); - } + String treeTitle; // if tree loaded + + SimilarityParamsI similarityParams; + + private TreeCanvas treeCanvas; + + TreeModel tree; + + private AlignViewport av; /** * 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! + * + * @param ap + * @param type + * @param modelName + * @param options */ - public TreePanel(AlignmentPanel ap, - String type, - String pwtype, - NewickFile newtree) + public TreePanel(AlignmentPanel ap, String type, String modelName, + SimilarityParamsI options) { super(); - initTreePanel(ap, type, pwtype, newtree, null); + this.similarityParams = options; + initTreePanel(ap, type, modelName, null, null); + + // We know this tree has distances. JBPNote TODO: prolly should add this as + // a userdefined default + // showDistances(true); } - public TreePanel(AlignmentPanel av, - String type, - String pwtype, - NewickFile newtree, AlignmentView inputData) + public TreePanel(AlignmentPanel alignPanel, NewickFile newtree, + String theTitle, AlignmentView inputData) { super(); - initTreePanel(av, type, pwtype, newtree, inputData); + this.treeTitle = theTitle; + initTreePanel(alignPanel, null, null, newtree, inputData); } public AlignmentI getAlignment() { - return treeCanvas.av.getAlignment(); + return getTreeCanvas().getViewport().getAlignment(); } - public AlignViewport getViewPort() + public AlignmentViewport getViewPort() { - return treeCanvas.av; + 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(this, ap, scrollPane); - scrollPane.setViewportView(treeCanvas); + scrollPane.setViewportView(getTreeCanvas()); PaintRefresher.Register(this, ap.av.getSequenceSetId()); buildAssociatedViewMenu(); - av.addPropertyChangeListener(new java.beans.PropertyChangeListener() + final PropertyChangeListener listener = addAlignmentListener(); + + /* + * remove listener when window is closed, so that this + * panel can be garbage collected + */ + addInternalFrameListener(new InternalFrameAdapter() { + @Override + public void internalFrameClosed(InternalFrameEvent evt) + { + if (getViewport() != null) + { + getViewport().removePropertyChangeListener(listener); + } + } + }); + + TreeLoader tl = new TreeLoader(newTree, inputData); + tl.start(); + + } + + /** + * @return + */ + protected PropertyChangeListener addAlignmentListener() + { + final PropertyChangeListener listener = new PropertyChangeListener() + { + @Override public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) @@ -129,28 +182,29 @@ public class TreePanel 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"); + 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 + tree.updatePlaceHolders((List) evt.getNewValue()); + getTreeCanvas().nameHash.clear(); // reset the mapping between canvas + // rectangles and leafnodes repaint(); } } - }); - - TreeLoader tl = new TreeLoader(newTree); - if (inputData != null) - { - tl.odata = inputData; - } - tl.start(); - + }; + getViewport().addPropertyChangeListener(listener); + return listener; } + @Override public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -158,9 +212,9 @@ public class TreePanel void buildAssociatedViewMenu() { - AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av. - getSequenceSetId()); - if (aps.length == 1 && treeCanvas.ap == aps[0]) + AlignmentPanel[] aps = PaintRefresher + .getAssociatedPanels(getViewport().getSequenceSetId()); + if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0]) { associateLeavesMenu.setVisible(false); return; @@ -168,7 +222,8 @@ public class TreePanel associateLeavesMenu.setVisible(true); - if ( (viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) + if ((viewMenu + .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) { viewMenu.insertSeparator(viewMenu.getItemCount() - 1); } @@ -182,15 +237,16 @@ public class TreePanel for (i = 0; i < iSize; i++) { final AlignmentPanel ap = aps[i]; - item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap); + item = new JRadioButtonMenuItem(ap.av.getViewName(), ap == getTreeCanvas().getAssociatedPanel()); buttonGroup.add(item); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { - treeCanvas.applyToAllViews = false; - treeCanvas.ap = ap; - treeCanvas.av = ap.av; + getTreeCanvas().applyToAllViews = false; + getTreeCanvas().setAssociatedPanel(ap); + getTreeCanvas().setViewport(ap.av); PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId()); } }); @@ -198,169 +254,148 @@ public class TreePanel associateLeavesMenu.add(item); } - final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views"); + final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem( + MessageManager.getString("label.all_views")); buttonGroup.add(itemf); - itemf.setSelected(treeCanvas.applyToAllViews); + itemf.setSelected(getTreeCanvas().applyToAllViews); itemf.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { - treeCanvas.applyToAllViews = itemf.isSelected(); + getTreeCanvas().applyToAllViews = itemf.isSelected(); } }); associateLeavesMenu.add(itemf); } - class TreeLoader - extends Thread + class TreeLoader extends Thread { - NewickFile newtree; - jalview.datamodel.AlignmentView odata = null; - public TreeLoader(NewickFile newtree) + private NewickFile newtree; + + private AlignmentView odata = null; + + public TreeLoader(NewickFile newickFile, AlignmentView inputData) { - this.newtree = newtree; - if (newtree != null) + this.newtree = newickFile; + this.odata = inputData; + + if (newickFile != null) { // Must be outside run(), as Jalview2XML tries to // update distance/bootstrap visibility at the same time - showBootstrap(newtree.HasBootstrap()); - showDistances(newtree.HasDistances()); + showBootstrap(newickFile.HasBootstrap()); + showDistances(newickFile.HasDistances()); } } + @Override public void run() { if (newtree != null) { - if (odata == null) - { - tree = new NJTree(av.alignment.getSequencesArray(), - newtree); - } - else + tree = new TreeModel(getViewport().getAlignment().getSequencesArray(), odata, + newtree); + if (tree.getOriginalData() == null) { - tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree); - } - if (!tree.hasOriginalSequenceData()) - { - allowOriginalSeqData(false); + originalSeqData.setVisible(false); } } else { - int start, end; - SequenceI[] seqs; - AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup() != null); - if (av.getSelectionGroup() == null) - { - start = 0; - end = av.alignment.getWidth(); - seqs = av.alignment.getSequencesArray(); - } - else - { - start = av.getSelectionGroup().getStartRes(); - end = av.getSelectionGroup().getEndRes() + 1; - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); - } - - tree = new NJTree(seqs, seqStrings, type, pwtype, start, end); + 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); } tree.reCount(tree.getTopNode()); tree.findHeight(tree.getTopNode()); - treeCanvas.setTree(tree); - treeCanvas.repaint(); - av.setCurrentTree(tree); - + getTreeCanvas().setTree(tree); + getTreeCanvas().repaint(); + getViewport().setCurrentTree(tree); + if (getViewport().getSortByTree()) + { + sortByTree_actionPerformed(); + } } } public void showDistances(boolean b) { - treeCanvas.setShowDistances(b); + getTreeCanvas().setShowDistances(b); distanceMenu.setSelected(b); } public void showBootstrap(boolean b) { - treeCanvas.setShowBootstrap(b); + getTreeCanvas().setShowBootstrap(b); bootstrapMenu.setSelected(b); } public void showPlaceholders(boolean b) { placeholdersMenu.setState(b); - treeCanvas.setMarkPlaceholders(b); - } - - private void allowOriginalSeqData(boolean b) - { - originalSeqData.setVisible(b); + getTreeCanvas().setMarkPlaceholders(b); } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ - public NJTree getTree() + public TreeModel getTree() { return tree; } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void textbox_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); - StringBuffer buffer = new StringBuffer(); + String newTitle = getPanelTitle(); - if (type.equals("AV")) - { - buffer.append("Average distance tree using "); - } - else - { - buffer.append("Neighbour joining tree using "); - } - - if (pwtype.equals("BL")) + NewickFile fout = new NewickFile(tree.getTopNode()); + try { - buffer.append("BLOSUM62"); - } - else + cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(), + tree.hasRootDistance())); + Desktop.addInternalFrame(cap, newTitle, 500, 100); + } catch (OutOfMemoryError oom) { - buffer.append("PID"); + new OOMWarning("generating newick tree file", oom); + cap.dispose(); } - 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())); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void saveAsNewick_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty( - "LAST_DIRECTORY")); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save tree as newick file"); - chooser.setToolTipText("Save"); + chooser.setDialogTitle( + MessageManager.getString("label.save_tree_as_newick")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(null); @@ -368,20 +403,19 @@ public class TreePanel { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); + 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)); + 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) + } catch (Exception ex) { ex.printStackTrace(); } @@ -390,35 +424,54 @@ public class TreePanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void printMenu_actionPerformed(ActionEvent e) { - //Putting in a thread avoids Swing painting problems - treeCanvas.startPrinting(); + // Putting in a thread avoids Swing painting problems + getTreeCanvas().startPrinting(); } + @Override public void originalSeqData_actionPerformed(ActionEvent e) { - if (!tree.hasOriginalSequenceData()) + AlignmentView originalData = tree.getOriginalData(); + if (originalData == null) { - jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); + 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) + // 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()); + 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(); + + } catch (Exception ex) + { + } + + Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) { // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); - Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]); - Alignment dataset = av.getAlignment().getDataset(); + AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); + AlignmentI dataset = (getViewport() != null && getViewport().getAlignment() != null) + ? getViewport().getAlignment().getDataset() + : null; if (dataset != null) { al.setDataset(dataset); @@ -427,43 +480,126 @@ public class TreePanel if (true) { // make a new frame! - AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1], - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT - ); + AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1], + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - //>>>This is a fix for the moment, until a better solution is found!!<<< + // >>>This is a fix for the moment, until a better solution is + // found!!<<< // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer()); - // af.addSortByOrderMenuItem(ServiceName + " Ordering", - // msaorder); + // af.addSortByOrderMenuItem(ServiceName + " Ordering", + // msaorder); - Desktop.addInternalFrame(af, "Original Data for " + this.title, - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + 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! + * + * @param e + * DOCUMENT ME! */ + @Override public void fitToWindow_actionPerformed(ActionEvent e) { - treeCanvas.fitToWindow = fitToWindow.isSelected(); + getTreeCanvas().fitToWindow = fitToWindow.isSelected(); repaint(); } /** + * sort the associated alignment view by the current tree. + * + * @param e + */ + @Override + public void sortByTree_actionPerformed() + { + + if (getTreeCanvas().applyToAllViews) + { + 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) + { + 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(getViewport().getSequenceSetId())) + { + // ensure all the alignFrames refresh their GI after adding an undo item + ap.alignFrame.updateEditMenuBar(); + } + } + else + { + getTreeCanvas().getAssociatedPanel().alignFrame + .addHistoryItem(sortAlignmentIn(getTreeCanvas().getAssociatedPanel())); + } + + } + + 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! + * + * @param e + * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { - if (treeCanvas == null) + if (getTreeCanvas() == null) { return; } @@ -473,65 +609,72 @@ public class TreePanel public Font getTreeFont() { - return treeCanvas.font; + return getTreeCanvas().font; } - public void setTreeFont(Font font) + public void setTreeFont(Font f) { - if (treeCanvas != null) + if (getTreeCanvas() != null) { - treeCanvas.setFont(font); + getTreeCanvas().setFont(f); } } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void distanceMenu_actionPerformed(ActionEvent e) { - treeCanvas.setShowDistances(distanceMenu.isSelected()); + getTreeCanvas().setShowDistances(distanceMenu.isSelected()); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void bootstrapMenu_actionPerformed(ActionEvent e) { - treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); + getTreeCanvas().setShowBootstrap(bootstrapMenu.isSelected()); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void placeholdersMenu_actionPerformed(ActionEvent e) { - treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); + getTreeCanvas().setMarkPlaceholders(placeholdersMenu.isSelected()); } /** * DOCUMENT ME! - * - * @param e 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"); + "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"))) + && !(System.getProperty("java.awt.headless") != null && System + .getProperty("java.awt.headless").equals("true"))) { EPSOptions eps = new EPSOptions(); renderStyle = eps.getValue(); @@ -548,44 +691,40 @@ public class TreePanel accurateText = false; } - int width = treeCanvas.getWidth(); - int height = treeCanvas.getHeight(); + int width = getTreeCanvas().getWidth(); + int height = getTreeCanvas().getHeight(); 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"); + 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")); int value = chooser.showSaveDialog(this); - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + if (value != JalviewFileChooser.APPROVE_OPTION) { return; } - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); + Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); - FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); + FileOutputStream out = new FileOutputStream( + chooser.getSelectedFile()); EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, - height); + height); pg.setAccurateTextMode(accurateText); - treeCanvas.draw(pg, width, height); + getTreeCanvas().draw(pg, width, height); pg.flush(); pg.close(); - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } @@ -593,27 +732,25 @@ public class TreePanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void pngTree_actionPerformed(ActionEvent e) { - int width = treeCanvas.getWidth(); - int height = treeCanvas.getHeight(); + int width = getTreeCanvas().getWidth(); + int height = getTreeCanvas().getHeight(); try { - 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"); + JalviewFileChooser chooser = new JalviewFileChooser( + ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Create PNG image from tree"); - chooser.setToolTipText("Save"); + chooser.setDialogTitle( + MessageManager.getString("label.create_png_from_tree")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -623,22 +760,142 @@ public class TreePanel } jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); + chooser.getSelectedFile().getParent()); - FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); + FileOutputStream out = new FileOutputStream( + chooser.getSelectedFile()); BufferedImage bi = new BufferedImage(width, height, - BufferedImage.TYPE_INT_RGB); + BufferedImage.TYPE_INT_RGB); Graphics png = bi.getGraphics(); - treeCanvas.draw(png, width, height); + getTreeCanvas().draw(png, width, height); ImageIO.write(bi, "png", out); out.close(); - } - catch (Exception ex) + } 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() + { + + @Override + 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 = jalview.util.DBRefUtils + .selectRefs(sq.getDBRefs(), 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) + { + 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; + } + + /* + * i18n description of Neighbour Joining or Average Distance method + */ + String treecalcnm = MessageManager + .getString("label.tree_calc_" + treeType.toLowerCase()); + + /* + * short score model name (long description can be too long) + */ + String smn = scoreModelName; + + /* + * put them together as Using + */ + final String ttl = MessageManager.formatMessage("label.calc_title", + treecalcnm, smn); + return ttl; + } + + public AlignViewport getViewport() + { + return av; + } + + public void setViewport(AlignViewport av) + { + this.av = av; + } + + public TreeCanvas getTreeCanvas() + { + return treeCanvas; + } }