X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=ee070a981d21990b5af44077ed62be213402acd4;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=d6c0069480292a4cb9080240a93ff2619dba9c88;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java old mode 100755 new mode 100644 index d6c0069..ee070a9 --- a/src/jalview/appletgui/TreePanel.java +++ b/src/jalview/appletgui/TreePanel.java @@ -1,30 +1,30 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 The Jalview Authors * - * 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 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * 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 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. + * + * 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 + * You should have received a copy of the GNU General Public License 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.*; +import jalview.util.MessageManager; public class TreePanel extends EmbmenuFrame implements ActionListener, ItemListener @@ -43,6 +43,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener, NJTree tree; + AlignmentPanel ap; + AlignViewport av; public NJTree getTree() @@ -50,23 +52,30 @@ public class TreePanel extends EmbmenuFrame implements ActionListener, return tree; } + public void finalize() throws Throwable + { + ap = null; + av = null; + super.finalize(); + } + /** * Creates a new TreePanel object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! * @param seqVector - * DOCUMENT ME! + * DOCUMENT ME! * @param type - * DOCUMENT ME! + * DOCUMENT ME! * @param pwtype - * DOCUMENT ME! + * DOCUMENT ME! * @param s - * DOCUMENT ME! + * DOCUMENT ME! * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ - public TreePanel(AlignViewport av, String type, String pwtype) + public TreePanel(AlignmentPanel ap, String type, String pwtype) { try { @@ -77,24 +86,24 @@ public class TreePanel extends EmbmenuFrame implements ActionListener, ex.printStackTrace(); } - initTreePanel(av, type, pwtype, null); + initTreePanel(ap, type, pwtype, null); } /** * Creates a new TreePanel object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! * @param seqVector - * DOCUMENT ME! + * DOCUMENT ME! * @param newtree - * DOCUMENT ME! + * DOCUMENT ME! * @param type - * DOCUMENT ME! + * DOCUMENT ME! * @param pwtype - * DOCUMENT ME! + * DOCUMENT ME! */ - public TreePanel(AlignViewport av, String type, String pwtype, + public TreePanel(AlignmentPanel ap, String type, String pwtype, NewickFile newtree) { try @@ -106,18 +115,19 @@ public class TreePanel extends EmbmenuFrame implements ActionListener, e.printStackTrace(); } - initTreePanel(av, type, pwtype, newtree); + initTreePanel(ap, type, pwtype, newtree); } - void initTreePanel(AlignViewport av, String type, String pwtype, + 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(av, scrollPane); + treeCanvas = new TreeCanvas(ap, scrollPane); TreeLoader tl = new TreeLoader(newTree); tl.start(); embedMenuIfNeeded(treeCanvas); @@ -179,11 +189,11 @@ public class TreePanel extends EmbmenuFrame implements ActionListener, { if (odata == null) { - tree = new NJTree(av.alignment.getSequencesArray(), newtree); + tree = new NJTree(av.getAlignment().getSequencesArray(), newtree); } else { - tree = new NJTree(av.alignment.getSequencesArray(), odata, + tree = new NJTree(av.getAlignment().getSequencesArray(), odata, newtree); } @@ -192,19 +202,21 @@ public class TreePanel extends EmbmenuFrame implements ActionListener, { int start, end; SequenceI[] seqs; - AlignmentView seqStrings = av.getAlignmentView(av - .getSelectionGroup() != null); - if (av.getSelectionGroup() == null) + boolean selview = (av.getSelectionGroup() != null) + && (av.getSelectionGroup().getSize() > 1); + AlignmentView seqStrings = av.getAlignmentView(selview); + if (!selview) { start = 0; - end = av.alignment.getWidth(); - seqs = av.alignment.getSequencesArray(); + end = av.getAlignment().getWidth(); + seqs = av.getAlignment().getSequencesArray(); } else { start = av.getSelectionGroup().getStartRes(); end = av.getSelectionGroup().getEndRes() + 1; - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); + seqs = av.getSelectionGroup().getSequencesInOrder( + av.getAlignment()); } tree = new NJTree(seqs, seqStrings, type, pwtype, start, end); @@ -215,10 +227,20 @@ public class TreePanel extends EmbmenuFrame implements ActionListener, 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(); @@ -271,8 +293,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener, 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); @@ -331,22 +353,22 @@ public class TreePanel extends EmbmenuFrame implements ActionListener, 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);