X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=e88007a8bda8bfbe5a8a6e5d4d9625782e71e3a4;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=44f9feffa638f11dc82a40649526cd6a144e0f76;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 44f9fef..e88007a 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,10 +20,16 @@ */ package jalview.gui; +import java.util.Locale; + 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.ViewBasedAnalysisI; +import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.OrderCommand; @@ -31,17 +37,18 @@ 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.HiddenColumns; import jalview.datamodel.NodeTransformI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.datamodel.SequenceNode; +import jalview.gui.ImageExporter.ImageWriterI; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.NewickFile; import jalview.jbgui.GTreePanel; -import jalview.schemes.ResidueProperties; +import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@ -49,16 +56,18 @@ 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.File; 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; @@ -70,87 +79,66 @@ import org.jibble.epsgraphics.EpsGraphics2D; */ public class TreePanel extends GTreePanel { - String type; + String treeType; + + String scoreModelName; // if tree computed + + String treeTitle; // if tree loaded - String pwtype; + SimilarityParamsI similarityParams; - TreeCanvas treeCanvas; + private TreeCanvas treeCanvas; - NJTree tree; + TreeModel tree; - AlignViewport av; + private AlignViewport av; /** * Creates a new TreePanel object. * - * @param av - * DOCUMENT ME! - * @param seqVector - * DOCUMENT ME! + * @param ap * @param type - * DOCUMENT ME! - * @param pwtype - * DOCUMENT ME! - * @param s - * DOCUMENT ME! - * @param e - * DOCUMENT ME! + * @param modelName + * @param options */ - public TreePanel(AlignmentPanel ap, String type, String pwtype) + public TreePanel(AlignmentPanel ap, String type, String modelName, + SimilarityParamsI options) { super(); - initTreePanel(ap, type, pwtype, null, 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); } - /** - * 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) + 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 AlignmentViewport getViewPort() { - return treeCanvas.av; + // @Mungo - Why don't we return our own viewport ??? + return getTreeCanvas().getViewport(); } - void initTreePanel(AlignmentPanel ap, String type, String pwtype, + void initTreePanel(AlignmentPanel ap, String type, String modelName, NewickFile newTree, AlignmentView inputData) { av = ap.av; - this.type = type; - this.pwtype = pwtype; + this.treeType = type; + this.scoreModelName = modelName; treeCanvas = new TreeCanvas(this, ap, scrollPane); scrollPane.setViewportView(treeCanvas); @@ -159,8 +147,49 @@ public class TreePanel extends GTreePanel 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 (av != null) + { + av.removePropertyChangeListener(listener); + } + releaseReferences(); + } + }); + + TreeLoader tl = new TreeLoader(newTree, inputData); + tl.start(); + + } + + /** + * Ensure any potentially large object references are nulled + */ + public void releaseReferences() + { + this.tree = null; + this.treeCanvas.tree = null; + this.treeCanvas.nodeHash = null; + this.treeCanvas.nameHash = null; + } + + /** + * @return + */ + protected PropertyChangeListener addAlignmentListener() + { + final PropertyChangeListener listener = new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) @@ -175,27 +204,22 @@ public class TreePanel extends GTreePanel } 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((List) evt.getNewValue()); + 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(); - + }; + av.addPropertyChangeListener(listener); + return listener; } + @Override public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -203,9 +227,9 @@ public class TreePanel extends GTreePanel void buildAssociatedViewMenu() { - AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av - .getSequenceSetId()); - if (aps.length == 1 && treeCanvas.ap == aps[0]) + AlignmentPanel[] aps = PaintRefresher + .getAssociatedPanels(av.getSequenceSetId()); + if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0]) { associateLeavesMenu.setVisible(false); return; @@ -213,7 +237,8 @@ public class TreePanel extends GTreePanel associateLeavesMenu.setVisible(true); - if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) + if ((viewMenu + .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) { viewMenu.insertSeparator(viewMenu.getItemCount() - 1); } @@ -227,15 +252,17 @@ public class TreePanel extends GTreePanel 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 == treeCanvas.getAssociatedPanel()); buttonGroup.add(item); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = false; - treeCanvas.ap = ap; - treeCanvas.av = ap.av; + treeCanvas.setAssociatedPanel(ap); + treeCanvas.setViewport(ap.av); PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId()); } }); @@ -249,6 +276,7 @@ public class TreePanel extends GTreePanel itemf.setSelected(treeCanvas.applyToAllViews); itemf.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = itemf.isSelected(); @@ -260,81 +288,46 @@ public class TreePanel extends GTreePanel class TreeLoader extends Thread { - NewickFile newtree; + private NewickFile newtree; - jalview.datamodel.AlignmentView odata = null; + private AlignmentView odata = null; - public TreeLoader(NewickFile newtree) + 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 TreeModel(av.getAlignment().getSequencesArray(), odata, + newtree); + if (tree.getOriginalData() == null) { - tree = new NJTree(av.getAlignment().getSequencesArray(), newtree); - } - else - { - tree = new NJTree(av.getAlignment().getSequencesArray(), odata, - newtree); - } - if (!tree.hasOriginalSequenceData()) - { - allowOriginalSeqData(false); + originalSeqData.setVisible(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); - } + ScoreModelI sm = ScoreModels.getInstance() + .getScoreModel(scoreModelName, + treeCanvas.getAssociatedPanel()); + TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) + ? new NJTree(av, sm, similarityParams) + : new AverageDistanceTree(av, sm, similarityParams); + tree = new TreeModel(njtree); showDistances(true); } @@ -368,17 +361,12 @@ public class TreePanel extends GTreePanel treeCanvas.setMarkPlaceholders(b); } - private void allowOriginalSeqData(boolean b) - { - originalSeqData.setVisible(b); - } - /** * DOCUMENT ME! * * @return DOCUMENT ME! */ - public NJTree getTree() + public TreeModel getTree() { return tree; } @@ -389,37 +377,19 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override 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"); - } + String newTitle = getPanelTitle(); - jalview.io.NewickFile fout = new jalview.io.NewickFile( - tree.getTopNode()); + NewickFile fout = new NewickFile(tree.getTopNode()); try { - cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), - tree.isHasRootDistance())); - Desktop.addInternalFrame(cap, buffer.toString(), 500, 100); + 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); @@ -434,13 +404,15 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void saveAsNewick_actionPerformed(ActionEvent e) { + // TODO: JAL-3048 save newick file for Jalview-JS JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.save_tree_as_newick")); + chooser.setDialogTitle( + MessageManager.getString("label.save_tree_as_newick")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(null); @@ -448,15 +420,15 @@ public class TreePanel extends GTreePanel if (value == JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser - .getSelectedFile().getParent()); + 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()); + 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); @@ -474,18 +446,21 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void printMenu_actionPerformed(ActionEvent e) { // Putting in a thread avoids Swing painting problems treeCanvas.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."); + Cache.info( + "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); return; } // decide if av alignment is sufficiently different to original data to @@ -504,16 +479,17 @@ public class TreePanel extends GTreePanel } catch (Exception ex) { } - ; - Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc); + + 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 != null && av.getAlignment() != null) ? av - .getAlignment().getDataset() : null; + AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); + AlignmentI dataset = (av != null && av.getAlignment() != null) + ? av.getAlignment().getDataset() + : null; if (dataset != null) { al.setDataset(dataset); @@ -522,9 +498,8 @@ public class TreePanel extends GTreePanel 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!!<<< @@ -534,8 +509,8 @@ public class TreePanel extends GTreePanel // msaorder); Desktop.addInternalFrame(af, MessageManager.formatMessage( - "label.original_data_for_params", - new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH, + "label.original_data_for_params", new Object[] + { this.title }), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } } @@ -547,6 +522,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void fitToWindow_actionPerformed(ActionEvent e) { treeCanvas.fitToWindow = fitToWindow.isSelected(); @@ -564,9 +540,9 @@ public class TreePanel extends GTreePanel if (treeCanvas.applyToAllViews) { - final ArrayList commands = new ArrayList(); - for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av - .getSequenceSetId())) + final ArrayList commands = new ArrayList<>(); + for (AlignmentPanel ap : PaintRefresher + .getAssociatedPanels(av.getSequenceSetId())) { commands.add(sortAlignmentIn(ap.av.getAlignPanel())); } @@ -604,8 +580,8 @@ public class TreePanel extends GTreePanel } } }); - for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av - .getSequenceSetId())) + for (AlignmentPanel ap : PaintRefresher + .getAssociatedPanels(av.getSequenceSetId())) { // ensure all the alignFrames refresh their GI after adding an undo item ap.alignFrame.updateEditMenuBar(); @@ -613,21 +589,23 @@ public class TreePanel extends GTreePanel } else { - treeCanvas.ap.alignFrame - .addHistoryItem(sortAlignmentIn(treeCanvas.ap)); + treeCanvas.getAssociatedPanel().alignFrame + .addHistoryItem( + sortAlignmentIn(treeCanvas.getAssociatedPanel())); } } public CommandI sortAlignmentIn(AlignmentPanel ap) { - AlignmentViewport av = ap.av; - SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); - AlignmentSorter.sortByTree(av.getAlignment(), tree); + // 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, av.getAlignment()); + undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment()); - ap.paintAlignment(true); + ap.paintAlignment(true, false); return undo; } @@ -637,6 +615,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { if (treeCanvas == null) @@ -652,11 +631,11 @@ public class TreePanel extends GTreePanel return treeCanvas.font; } - public void setTreeFont(Font font) + public void setTreeFont(Font f) { if (treeCanvas != null) { - treeCanvas.setFont(font); + treeCanvas.setFont(f); } } @@ -666,6 +645,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void distanceMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowDistances(distanceMenu.isSelected()); @@ -677,6 +657,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void bootstrapMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); @@ -688,131 +669,34 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void placeholdersMenu_actionPerformed(ActionEvent e) { treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Outputs the Tree in image format (currently EPS or PNG). The user is + * prompted for the file to save to, and for EPS (unless a preference is + * already set) for the choice of Text or Lineart for character rendering. */ - public void epsTree_actionPerformed(ActionEvent e) + @Override + public void writeTreeImage(TYPE imageFormat) { - boolean accurateText = true; - - String renderStyle = jalview.bin.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 + ImageWriterI writer = new ImageWriterI() { - 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(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) + @Override + public void exportImage(Graphics g) throws Exception { - return; + treeCanvas.draw(g, width, height); } - - 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); - - 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 - { - 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(MessageManager - .getString("label.create_png_from_tree")); - chooser.setToolTipText(MessageManager.getString("action.save")); - - int value = chooser.showSaveDialog(this); - - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) - { - return; - } - - 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(); - - treeCanvas.draw(png, width, height); - - ImageIO.write(bi, "png", out); - out.close(); - } catch (Exception ex) - { - ex.printStackTrace(); - } + }; + String tree = MessageManager.getString("label.tree"); + ImageExporter exporter = new ImageExporter(writer, null, imageFormat, + tree); + exporter.doExport(null, this, width, height, tree.toLowerCase(Locale.ROOT)); } /** @@ -828,6 +712,7 @@ public class TreePanel extends GTreePanel tree.applyToNodes(new NodeTransformI() { + @Override public void transform(BinaryNode node) { if (node instanceof SequenceNode @@ -839,50 +724,128 @@ public class TreePanel extends GTreePanel if (sq != null) { // search dbrefs, features and annotation - DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs( - sq.getDBRef(), - new String[] { labelClass.toUpperCase() }); + List refs = jalview.util.DBRefUtils + .selectRefs(sq.getDBRefs(), new String[] + { labelClass.toUpperCase(Locale.ROOT) }); if (refs != null) { - for (int i = 0; i < refs.length; i++) + for (int i = 0, ni = refs.size(); i < ni; i++) { if (newname == null) { - newname = new String(refs[i].getAccessionId()); + newname = new String(refs.get(i).getAccessionId()); } else { - newname = newname + "; " + refs[i].getAccessionId(); + newname += "; " + refs.get(i).getAccessionId(); } } } if (newname == null) { - SequenceFeature sf[] = sq.getSequenceFeatures(); - for (int i = 0; sf != null && i < sf.length; i++) + List features = sq.getFeatures() + .getPositionalFeatures(labelClass); + for (SequenceFeature feature : features) { - if (sf[i].getType().equals(labelClass)) + if (newname == null) + { + newname = feature.getDescription(); + } + else { - if (newname == null) - { - newname = new String(sf[i].getDescription()); - } - else - { - newname = newname + "; " + sf[i].getDescription(); - } + newname = newname + "; " + feature.getDescription(); } } } } if (newname != null) { - String oldname = ((SequenceNode) node).getName(); - // TODO : save in the undo object for this modification. + // 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(Locale.ROOT)); + + /* + * 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; + } + + /** + * Builds an EPS image and writes it to the specified file. + * + * @param outFile + * @param textOption + * true for Text character rendering, false for Lineart + */ + protected void writeEpsFile(File outFile, boolean textOption) + { + try + { + int width = treeCanvas.getWidth(); + int height = treeCanvas.getHeight(); + + FileOutputStream out = new FileOutputStream( + outFile); + EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, + height); + pg.setAccurateTextMode(!textOption); + treeCanvas.draw(pg, width, height); + + pg.flush(); + pg.close(); + } catch (Exception ex) + { + System.err.println("Error writing tree as EPS"); + ex.printStackTrace(); + } + } + + public AlignViewport getViewport() + { + return av; + } + + public void setViewport(AlignViewport av) + { + this.av = av; + } + + public TreeCanvas getTreeCanvas() + { + return treeCanvas; + } }