X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=a163c1548ab4862336cfd2e7d8e013cb0e1f16d3;hb=2604ed9c9ad23a7c97b5d885249d81948cbac130;hp=35998eb440506407485b5a82bb243bcf1ed361c9;hpb=3c75c089a56859ec8e7f674d7054e82af41e4b77;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 35998eb..a163c15 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -20,15 +20,13 @@ */ 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.bin.Cache; +import jalview.bin.Console; import jalview.commands.CommandI; import jalview.commands.OrderCommand; import jalview.datamodel.Alignment; @@ -41,11 +39,12 @@ 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; @@ -53,13 +52,13 @@ 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; @@ -74,9 +73,9 @@ import org.jibble.epsgraphics.EpsGraphics2D; */ public class TreePanel extends GTreePanel { - String treeType; + String substitutionMatrix; - String scoreModelName; // if tree computed + String treeType; String treeTitle; // if tree loaded @@ -86,57 +85,95 @@ public class TreePanel extends GTreePanel TreeModel tree; - AlignViewport av; + private AlignViewport av; /** * Creates a new TreePanel object. * * @param ap - * @param type - * @param modelName - * @param options + * @param tree + * @param treeType + * @param substitutionMatrix */ - public TreePanel(AlignmentPanel ap, String type, String modelName, - SimilarityParamsI options) + public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType, + String substitutionMatrix) { super(); - this.similarityParams = options; - initTreePanel(ap, type, modelName, null, null); + this.treeType = treeType; + this.substitutionMatrix = substitutionMatrix; + this.tree = tree; + initTreePanel(ap, tree); // We know this tree has distances. JBPNote TODO: prolly should add this as // a userdefined default // showDistances(true); } + /** + * Creates a new TreePanel object. + * + * @param alignPanel + * @param newtree + * @param theTitle + * @param inputData + */ public TreePanel(AlignmentPanel alignPanel, NewickFile newtree, String theTitle, AlignmentView inputData) { super(); this.treeTitle = theTitle; - initTreePanel(alignPanel, null, null, newtree, inputData); + initTreePanel(alignPanel, 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(); + } + + /** + * Initialize a tree panel based on a calculated tree + * + * @param ap + * @param tree + */ + void initTreePanel(AlignmentPanel ap, TreeModel tree) + { + buildTreeCanvas(ap); + + TreeLoader tl = new TreeLoader(null, null); + tl.start(); + } - void initTreePanel(AlignmentPanel ap, String type, String modelName, - NewickFile newTree, AlignmentView inputData) + /** + * Initialize a tree panel based on a loaded in tree file. + * + * @param ap + * @param loadedTree + * @param inputData + */ + void initTreePanel(AlignmentPanel ap, + NewickFile loadedTree, AlignmentView inputData) { + buildTreeCanvas(ap); - av = ap.av; - this.treeType = type; - this.scoreModelName = modelName; + TreeLoader tl = new TreeLoader(loadedTree, inputData); + tl.start(); + } + +public void buildTreeCanvas(AlignmentPanel ap) { + av = ap.av; treeCanvas = new TreeCanvas(this, ap, scrollPane); scrollPane.setViewportView(treeCanvas); + PaintRefresher.Register(this, ap.av.getSequenceSetId()); buildAssociatedViewMenu(); @@ -158,8 +195,8 @@ 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()); @@ -170,8 +207,8 @@ public class TreePanel extends GTreePanel } }); - TreeLoader tl = new TreeLoader(newTree, inputData); - tl.start(); + + } @@ -183,9 +220,9 @@ 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 +230,8 @@ 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 +245,8 @@ 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 +254,8 @@ 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()); } }); @@ -242,57 +281,56 @@ public class TreePanel extends GTreePanel class TreeLoader extends Thread { - private NewickFile newtree; + private NewickFile newTree; private AlignmentView odata = null; public TreeLoader(NewickFile newickFile, AlignmentView inputData) { - this.newtree = newickFile; + this.newTree = newickFile; this.odata = inputData; - if (newickFile != null) + if (newTree != null) { // Must be outside run(), as Jalview2XML tries to // update distance/bootstrap visibility at the same time - showBootstrap(newickFile.HasBootstrap()); - showDistances(newickFile.HasDistances()); + showBootstrap(newTree.hasBootstrap()); + showDistances(newTree.hasDistances()); + } + } @Override public void run() { - if (newtree != null) + if (newTree != null) { tree = new TreeModel(av.getAlignment().getSequencesArray(), odata, - newtree); + newTree); if (tree.getOriginalData() == null) { originalSeqData.setVisible(false); } } - else - { - ScoreModelI sm = ScoreModels.getInstance().getScoreModel( - scoreModelName, treeCanvas.ap); - TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree( - av, sm, similarityParams) : new AverageDistanceTree(av, sm, - similarityParams); - tree = new TreeModel(njtree); - showDistances(true); - } + showTree(tree); + } + + public void showTree(TreeModel tree) + { tree.reCount(tree.getTopNode()); tree.findHeight(tree.getTopNode()); treeCanvas.setTree(tree); treeCanvas.repaint(); + av.setCurrentTree(tree); if (av.getSortByTree()) { sortByTree_actionPerformed(); } + } } @@ -360,11 +398,12 @@ 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); @@ -372,15 +411,15 @@ 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); @@ -411,8 +450,8 @@ 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 @@ -439,8 +478,9 @@ public class TreePanel extends GTreePanel // 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); @@ -450,8 +490,7 @@ public class TreePanel extends GTreePanel { // make a new frame! AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1], - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); // >>>This is a fix for the moment, until a better solution is // found!!<<< @@ -461,8 +500,8 @@ 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); } } @@ -487,14 +526,14 @@ public class TreePanel extends GTreePanel * @param e */ @Override - public void sortByTree_actionPerformed() + public void sortByTree_actionPerformed()// modify for Aptx { 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 +571,8 @@ 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 +580,22 @@ 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 +666,28 @@ public class TreePanel extends GTreePanel } /** - * 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 epsTree_actionPerformed(ActionEvent e) + 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() { - 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! - */ - @Override - public void pngTree_actionPerformed(ActionEvent e) - { - int width = treeCanvas.getWidth(); - int height = treeCanvas.getHeight(); - - try - { - 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 +715,36 @@ 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(); } } } @@ -823,31 +766,78 @@ public class TreePanel extends GTreePanel * Neighbour Joining Using BLOSUM62 *

* For a tree loaded from file, just uses the file name + * * @return */ - public String getPanelTitle() + public String getPanelTitle() // to be moved/fixed { if (treeTitle != null) { return treeTitle; } - + else + { /* * 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)); /* * short score model name (long description can be too long) */ - String smn = scoreModelName; + String smn = substitutionMatrix; /* * 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; + 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; } }