X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=b5e33425e70fbe1e83a74df8933e0067d14d4629;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=f865bbd1b96a0bbe9bef5d64ac808429db81e95a;hpb=3d136290d42e4f4ae2deeed8ce3b9dae7c6e2eec;p=jalview.git diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java old mode 100755 new mode 100644 index f865bbd..b5e3342 --- a/src/jalview/appletgui/TreePanel.java +++ b/src/jalview/appletgui/TreePanel.java @@ -1,137 +1,167 @@ /* - * 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.appletgui; -import java.awt.*; -import java.awt.event.*; -import java.util.Hashtable; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.io.*; - -public class TreePanel - extends EmbmenuFrame implements ActionListener, ItemListener +import jalview.analysis.AverageDistanceTree; +import jalview.analysis.NJTree; +import jalview.analysis.TreeBuilder; +import jalview.analysis.TreeModel; +import jalview.analysis.scoremodels.ScoreModels; +import jalview.analysis.scoremodels.SimilarityParams; +import jalview.api.analysis.ScoreModelI; +import jalview.datamodel.Alignment; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SequenceI; +import jalview.io.NewickFile; +import jalview.util.MessageManager; + +import java.awt.BorderLayout; +import java.awt.CheckboxMenuItem; +import java.awt.Color; +import java.awt.Menu; +import java.awt.MenuBar; +import java.awt.MenuItem; +import java.awt.ScrollPane; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; + +public class TreePanel extends EmbmenuFrame + implements ActionListener, ItemListener { SequenceI[] seq; + String type; + String pwtype; + int start; + int end; + TreeCanvas treeCanvas; - NJTree tree; + + TreeModel tree; + + AlignmentPanel ap; + AlignViewport av; - public NJTree getTree() + public TreeModel getTree() { return tree; } + @Override + public void finalize() throws Throwable + { + ap = null; + av = null; + super.finalize(); + } + /** * 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(AlignViewport av, String type, String pwtype) + public TreePanel(AlignmentPanel alignPanel, String type, String pwtype) { try { jbInit(); this.setMenuBar(jMenuBar1); - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } - initTreePanel(av, type, pwtype, null); + initTreePanel(alignPanel, type, pwtype, null); } /** * 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(AlignViewport av, - String type, - String pwtype, - NewickFile newtree) + public TreePanel(AlignmentPanel ap, String type, String pwtype, + NewickFile newtree) { try { jbInit(); this.setMenuBar(jMenuBar1); - } - catch (Exception e) + } catch (Exception e) { e.printStackTrace(); } - initTreePanel(av, type, pwtype, newtree); + initTreePanel(ap, type, pwtype, newtree); } - void initTreePanel(AlignViewport av, - String type, - String pwtype, - NewickFile newTree) + + void initTreePanel(AlignmentPanel ap, String type, String pwtype, + NewickFile newTree) { - this.av = av; + this.ap = ap; + this.av = ap.av; this.type = type; this.pwtype = pwtype; - + treeCanvas = new TreeCanvas(ap, scrollPane); TreeLoader tl = new TreeLoader(newTree); tl.start(); - treeCanvas = new TreeCanvas(av, scrollPane); embedMenuIfNeeded(treeCanvas); scrollPane.add(treeCanvas, BorderLayout.CENTER); } + void showOriginalData() { - // 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[]) - if (tree.seqData != null) + if (tree.getOriginalData() != null) { - 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 = av.getGapCharacter(); + } catch (Exception ex) + { + } + + Object[] alAndColsel = tree.getOriginalData() + .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) { - Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]); - AlignFrame af = new AlignFrame(al, - av.applet, - "Original Data for Tree", - false); + Alignment al = new Alignment((SequenceI[]) alAndColsel[0]); + AlignFrame af = new AlignFrame(al, av.applet, + "Original Data for Tree", false); - af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]); + af.viewport.getAlignment() + .setHiddenColumns((HiddenColumns) alAndColsel[1]); } } else @@ -140,10 +170,10 @@ public class TreePanel } } - class TreeLoader - extends Thread + class TreeLoader extends Thread { NewickFile newtree; + jalview.datamodel.AlignmentView odata = null; public TreeLoader(NewickFile newtree) @@ -151,40 +181,23 @@ public class TreePanel this.newtree = newtree; } + @Override public void run() { if (newtree != null) { - if (odata == null) - { - tree = new NJTree(av.alignment.getSequencesArray(), - newtree); - } - else - { - tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree); - } - + tree = new TreeModel(av.getAlignment().getSequencesArray(), odata, + newtree); } 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 sm1 = ScoreModels.getInstance().getScoreModel(pwtype, + treeCanvas.ap); + ScoreModelI sm = sm1; + TreeBuilder njtree = type.equals(TreeBuilder.NEIGHBOUR_JOINING) + ? new NJTree(av, sm, SimilarityParams.Jalview) + : new AverageDistanceTree(av, sm, SimilarityParams.Jalview); + tree = new TreeModel(njtree); } tree.reCount(tree.getTopNode()); @@ -192,10 +205,20 @@ public class TreePanel treeCanvas.setTree(tree); if (newtree != null) { - distanceMenu.setState(newtree.HasDistances()); - bootstrapMenu.setState(newtree.HasBootstrap()); - treeCanvas.setShowBootstrap(newtree.HasBootstrap()); - treeCanvas.setShowDistances(newtree.HasDistances()); + // Set default view, paying lip service to any overriding tree view + // parameter settings + boolean showDist = newtree.HasDistances() + && av.applet.getDefaultParameter("showTreeDistances", + newtree.HasDistances()); + boolean showBoots = newtree.HasBootstrap() + && av.applet.getDefaultParameter("showTreeBootstraps", + newtree.HasBootstrap()); + distanceMenu.setState(showDist); + bootstrapMenu.setState(showBoots); + treeCanvas.setShowBootstrap(showBoots); + treeCanvas.setShowDistances(showDist); + treeCanvas.setMarkPlaceholders(av.applet + .getDefaultParameter("showUnlinkedTreeNodes", false)); } treeCanvas.repaint(); @@ -205,6 +228,7 @@ public class TreePanel } } + @Override public void actionPerformed(ActionEvent evt) { if (evt.getSource() == newickOutput) @@ -221,6 +245,7 @@ public class TreePanel } } + @Override public void itemStateChanged(ItemEvent evt) { if (evt.getSource() == fitToWindow) @@ -248,7 +273,8 @@ public class TreePanel public void newickOutput_actionPerformed() { - jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode()); + jalview.io.NewickFile fout = new jalview.io.NewickFile( + tree.getTopNode()); String output = fout.print(false, true); CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null); cap.setText(output); @@ -279,40 +305,52 @@ public class TreePanel } BorderLayout borderLayout1 = new BorderLayout(); + protected ScrollPane scrollPane = new ScrollPane(); + MenuBar jMenuBar1 = new MenuBar(); + Menu jMenu2 = new Menu(); + protected MenuItem fontSize = new MenuItem(); + protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem(); + protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem(); + protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem(); + protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem(); + Menu fileMenu = new Menu(); + MenuItem newickOutput = new MenuItem(); + MenuItem inputData = new MenuItem(); - private void jbInit() - throws Exception + private void jbInit() throws Exception { setLayout(borderLayout1); this.setBackground(Color.white); this.setFont(new java.awt.Font("Verdana", 0, 12)); - jMenu2.setLabel("View"); - fontSize.setLabel("Font..."); + jMenu2.setLabel(MessageManager.getString("action.view")); + fontSize.setLabel(MessageManager.getString("action.font")); fontSize.addActionListener(this); - bootstrapMenu.setLabel("Show Bootstrap Values"); + bootstrapMenu.setLabel( + MessageManager.getString("label.show_bootstrap_values")); bootstrapMenu.addItemListener(this); - distanceMenu.setLabel("Show Distances"); + distanceMenu.setLabel(MessageManager.getString("label.show_distances")); distanceMenu.addItemListener(this); - placeholdersMenu.setLabel("Mark Unassociated Leaves"); + placeholdersMenu.setLabel( + MessageManager.getString("label.mark_unassociated_leaves")); placeholdersMenu.addItemListener(this); fitToWindow.setState(true); - fitToWindow.setLabel("Fit To Window"); + fitToWindow.setLabel(MessageManager.getString("label.fit_to_window")); fitToWindow.addItemListener(this); - fileMenu.setLabel("File"); - newickOutput.setLabel("Newick Format"); + fileMenu.setLabel(MessageManager.getString("action.file")); + newickOutput.setLabel(MessageManager.getString("label.newick_format")); newickOutput.addActionListener(this); - inputData.setLabel("Input Data..."); + inputData.setLabel(MessageManager.getString("label.input_data")); add(scrollPane, BorderLayout.CENTER); jMenuBar1.add(fileMenu);