X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=857e77c4fd5460205cfcda46ea985e06cef7edc2;hb=74c5bd7b1f98214a6d57d7c64d0548013530d397;hp=087d3727000ef791834505f4707f9e2dc9d6af1c;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 087d372..857e77c 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 2.8.2b1) - * Copyright (C) 2014 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. * @@ -22,6 +22,8 @@ package jalview.gui; import jalview.analysis.AlignmentSorter; import jalview.analysis.NJTree; +import jalview.analysis.scoremodels.ScoreModels; +import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.ViewBasedAnalysisI; import jalview.bin.Cache; @@ -41,8 +43,9 @@ import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.NewickFile; import jalview.jbgui.GTreePanel; -import jalview.schemes.ResidueProperties; +import jalview.util.ImageMaker; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; import java.awt.Font; import java.awt.Graphics; @@ -105,27 +108,6 @@ public class TreePanel extends GTreePanel // 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) { @@ -138,7 +120,7 @@ public class TreePanel extends GTreePanel return treeCanvas.av.getAlignment(); } - public AlignViewport getViewPort() + public AlignmentViewport getViewPort() { return treeCanvas.av; } @@ -160,6 +142,7 @@ public class TreePanel extends GTreePanel av.addPropertyChangeListener(new java.beans.PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) @@ -178,7 +161,7 @@ public class TreePanel extends GTreePanel .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(); @@ -195,6 +178,7 @@ public class TreePanel extends GTreePanel } + @Override public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -230,6 +214,7 @@ public class TreePanel extends GTreePanel buttonGroup.add(item); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = false; @@ -242,11 +227,13 @@ public class TreePanel extends GTreePanel 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.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = itemf.isSelected(); @@ -274,6 +261,7 @@ public class TreePanel extends GTreePanel } } + @Override public void run() { @@ -313,26 +301,8 @@ public class TreePanel extends GTreePanel 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 = configureScoreModel(pwtype); + tree = new NJTree(av, type, sm, SimilarityParams.Jalview); showDistances(true); } @@ -343,7 +313,7 @@ public class TreePanel extends GTreePanel av.setCurrentTree(tree); if (av.getSortByTree()) { - sortByTree_actionPerformed(null); + sortByTree_actionPerformed(); } } } @@ -387,37 +357,19 @@ 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 "); - } + String newTitle = getPanelTitle(type, pwtype); - if (pwtype.equals("BL")) - { - buffer.append("BLOSUM62"); - } - else - { - buffer.append("PID"); - } - - 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); @@ -432,12 +384,14 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void saveAsNewick_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick")); + chooser.setDialogTitle(MessageManager + .getString("label.save_tree_as_newick")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(null); @@ -452,8 +406,8 @@ public class TreePanel extends GTreePanel { 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); @@ -471,12 +425,14 @@ 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()) @@ -508,8 +464,8 @@ public class TreePanel extends GTreePanel { // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); - Alignment al = new Alignment((SequenceI[]) alAndColsel[0]); - Alignment dataset = (av != null && av.getAlignment() != null) ? av + AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); + AlignmentI dataset = (av != null && av.getAlignment() != null) ? av .getAlignment().getDataset() : null; if (dataset != null) { @@ -531,8 +487,8 @@ public class TreePanel extends GTreePanel // msaorder); Desktop.addInternalFrame(af, MessageManager.formatMessage( - "label.original_data_for_params", new String[] - { this.title }), AlignFrame.DEFAULT_WIDTH, + "label.original_data_for_params", + new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } } @@ -544,6 +500,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void fitToWindow_actionPerformed(ActionEvent e) { treeCanvas.fitToWindow = fitToWindow.isSelected(); @@ -555,7 +512,8 @@ public class TreePanel extends GTreePanel * * @param e */ - public void sortByTree_actionPerformed(ActionEvent e) + @Override + public void sortByTree_actionPerformed() { if (treeCanvas.applyToAllViews) @@ -617,7 +575,7 @@ public class TreePanel extends GTreePanel public CommandI sortAlignmentIn(AlignmentPanel ap) { - AlignViewport av = ap.av; + AlignmentViewport av = ap.av; SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); AlignmentSorter.sortByTree(av.getAlignment(), tree); CommandI undo; @@ -633,6 +591,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { if (treeCanvas == null) @@ -662,6 +621,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void distanceMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowDistances(distanceMenu.isSelected()); @@ -673,6 +633,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void bootstrapMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); @@ -684,6 +645,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void placeholdersMenu_actionPerformed(ActionEvent e) { treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); @@ -695,6 +657,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void epsTree_actionPerformed(ActionEvent e) { boolean accurateText = true; @@ -728,23 +691,22 @@ public class TreePanel extends GTreePanel 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(MessageManager.getString("label.create_eps_from_tree")); + 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()); EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height); @@ -767,6 +729,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void pngTree_actionPerformed(ActionEvent e) { int width = treeCanvas.getWidth(); @@ -774,13 +737,12 @@ public class TreePanel extends GTreePanel 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(MessageManager.getString("label.create_png_from_tree")); + chooser.setDialogTitle(MessageManager + .getString("label.create_png_from_tree")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -822,6 +784,7 @@ public class TreePanel extends GTreePanel tree.applyToNodes(new NodeTransformI() { + @Override public void transform(BinaryNode node) { if (node instanceof SequenceNode @@ -834,8 +797,8 @@ public class TreePanel extends GTreePanel { // search dbrefs, features and annotation DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs( - sq.getDBRef(), new String[] - { labelClass.toUpperCase() }); + sq.getDBRefs(), + new String[] { labelClass.toUpperCase() }); if (refs != null) { for (int i = 0; i < refs.length; i++) @@ -879,4 +842,68 @@ public class TreePanel extends GTreePanel } }); } + + /** + * Formats a localised title for the tree panel, like + *

+ * Neighbour Joining Using BLOSUM62 + *

+ * For a tree loaded from file, just uses the file name + * + * @param treeType + * NJ or AV or FromFile + * @param modelOrFileName + * @return + */ + public static String getPanelTitle(String treeType, String modelOrFileName) + { + if (NJTree.FROM_FILE.equals(treeType)) + { + return modelOrFileName; + } + + /* + * i18n description of Neighbour Joining or Average Distance method + */ + String treecalcnm = MessageManager.getString("label.tree_calc_" + + treeType.toLowerCase()); + + /* + * i18n description (if any) of score model used + */ + String smn = MessageManager.getStringOrReturn("label.score_model_", + modelOrFileName); + + /* + * put them together as Using + */ + final String ttl = MessageManager.formatMessage("label.treecalc_title", + treecalcnm, smn); + return ttl; + } + + /** + * Gets the score model for the given name. If the score model is one that + * requires to get state data from the current view, allow it to do so + * + * @param sm + * @return + */ + protected ScoreModelI configureScoreModel(String modelName) + { + ScoreModelI sm = ScoreModels.getInstance().forName(modelName); + 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()); + } + } + return sm; + } }