X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=d73540219a4d7d967575ffc9899933f22a3b8399;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=d4c6009acdd70d964de8b8d5d5546d3139374c70;hpb=2ff143c5a47bd7bde7409ce1457bf84e332660a8;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index d4c6009..d735402 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -20,32 +20,36 @@ */ 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.SimilarityParamsI; -import jalview.api.analysis.ViewBasedAnalysisI; import jalview.bin.Cache; +import jalview.bin.Console; 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.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.util.ImageMaker; +import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@ -53,16 +57,18 @@ 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; @@ -76,32 +82,32 @@ public class TreePanel extends GTreePanel { String treeType; - ScoreModelI scoreModel; // if tree computed + String scoreModelName; // if tree computed String treeTitle; // if tree loaded SimilarityParamsI similarityParams; - TreeCanvas treeCanvas; + private TreeCanvas treeCanvas; TreeModel tree; - AlignViewport av; + private AlignViewport av; /** * Creates a new TreePanel object. * * @param ap * @param type - * @param sm + * @param modelName * @param options */ - public TreePanel(AlignmentPanel ap, String type, ScoreModelI sm, + public TreePanel(AlignmentPanel ap, String type, String modelName, SimilarityParamsI options) { super(); this.similarityParams = options; - initTreePanel(ap, type, sm, null, null); + initTreePanel(ap, type, modelName, null, null); // We know this tree has distances. JBPNote TODO: prolly should add this as // a userdefined default @@ -118,21 +124,22 @@ public class TreePanel extends GTreePanel 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, ScoreModelI sm, + void initTreePanel(AlignmentPanel ap, String type, String modelName, NewickFile newTree, AlignmentView inputData) { av = ap.av; this.treeType = type; - this.scoreModel = sm; + this.scoreModelName = modelName; treeCanvas = new TreeCanvas(this, ap, scrollPane); scrollPane.setViewportView(treeCanvas); @@ -141,7 +148,47 @@ 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) @@ -158,8 +205,8 @@ 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()); @@ -168,11 +215,9 @@ public class TreePanel extends GTreePanel repaint(); } } - }); - - TreeLoader tl = new TreeLoader(newTree, inputData); - tl.start(); - + }; + av.addPropertyChangeListener(listener); + return listener; } @Override @@ -183,9 +228,9 @@ 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; @@ -193,7 +238,8 @@ 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); } @@ -207,7 +253,8 @@ 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() { @@ -215,8 +262,8 @@ public class TreePanel extends GTreePanel 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()); } }); @@ -275,10 +322,11 @@ public class TreePanel extends GTreePanel } else { - ScoreModelI sm = configureScoreModel(); - TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree( - av, sm, similarityParams) : new AverageDistanceTree(av, sm, - similarityParams); + 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); } @@ -359,11 +407,12 @@ public class TreePanel extends GTreePanel @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); @@ -371,15 +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.hasBootstrap(), - tree.hasDistances(), tree.hasRootDistance()); + 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); @@ -410,8 +459,8 @@ public class TreePanel extends GTreePanel AlignmentView originalData = tree.getOriginalData(); if (originalData == null) { - jalview.bin.Cache.log - .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); + Console.info( + "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); return; } // decide if av alignment is sufficiently different to original data to @@ -431,16 +480,16 @@ public class TreePanel extends GTreePanel { } - Object[] alAndColsel = originalData - .getAlignmentAndColumnSelection(gc); + Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) { // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); - AlignmentI dataset = (av != null && av.getAlignment() != null) ? av - .getAlignment().getDataset() : null; + AlignmentI dataset = (av != null && av.getAlignment() != null) + ? av.getAlignment().getDataset() + : null; if (dataset != null) { al.setDataset(dataset); @@ -449,9 +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!!<<< @@ -461,8 +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); } } @@ -492,9 +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())); } @@ -532,8 +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(); @@ -541,21 +589,22 @@ 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) { + // 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); + ap.paintAlignment(true, false); return undo; } @@ -626,123 +675,28 @@ public class TreePanel extends GTreePanel } /** - * 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"); - - // 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( - 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 != 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! + * 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. */ @Override - public void pngTree_actionPerformed(ActionEvent e) + public void writeTreeImage(TYPE imageFormat) { int width = treeCanvas.getWidth(); int height = treeCanvas.getHeight(); - - try + ImageWriterI writer = new ImageWriterI() { - JalviewFileChooser chooser = new JalviewFileChooser( - ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION); - - 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) + @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()); - - 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)); } /** @@ -770,38 +724,36 @@ public class TreePanel extends GTreePanel if (sq != null) { // search dbrefs, features and annotation - DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs( - sq.getDBRefs(), - 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(); } } } @@ -823,6 +775,7 @@ public class TreePanel extends GTreePanel * Neighbour Joining Using BLOSUM62 *

* For a tree loaded from file, just uses the file name + * * @return */ public String getPanelTitle() @@ -835,44 +788,63 @@ public class TreePanel extends GTreePanel /* * i18n description of Neighbour Joining or Average Distance method */ - String treecalcnm = MessageManager.getString("label.tree_calc_" - + treeType.toLowerCase()); + String treecalcnm = MessageManager.getString( + "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT)); /* - * i18n description (if available) of score model used + * short score model name (long description can be too long) */ - String smn = MessageManager.getStringOrReturn("label.score_model_", - scoreModel.getName()); + String smn = scoreModelName; /* * put them together as Using */ - final String ttl = MessageManager.formatMessage("label.treecalc_title", + final String ttl = MessageManager.formatMessage("label.calc_title", treecalcnm, smn); return ttl; } /** - * If the score model is one that requires to get state data from the current - * view, create and configure a new instance of it + * Builds an EPS image and writes it to the specified file. * - * @return + * @param outFile + * @param textOption + * true for Text character rendering, false for Lineart */ - protected ScoreModelI configureScoreModel() + protected void writeEpsFile(File outFile, boolean textOption) { - if (scoreModel instanceof ViewBasedAnalysisI) + try { - try - { - scoreModel = scoreModel.getClass().newInstance(); - ((ViewBasedAnalysisI) scoreModel) - .configureFromAlignmentView(treeCanvas.ap); - } catch (Exception q) - { - Cache.log.error("Couldn't create a scoremodel instance for " - + scoreModel.getName()); - } + 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(); } - return scoreModel; + } + + public AlignViewport getViewport() + { + return av; + } + + public void setViewport(AlignViewport av) + { + this.av = av; + } + + public TreeCanvas getTreeCanvas() + { + return treeCanvas; } }