2 // FORESTER -- software libraries and applications
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3 // for evolutionary biology research and applications.
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5 // Copyright (C) 2008-2009 Christian M. Zmasek
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6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
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7 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
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8 // All rights reserved
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10 // This library is free software; you can redistribute it and/or
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11 // modify it under the terms of the GNU Lesser General Public
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12 // License as published by the Free Software Foundation; either
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13 // version 2.1 of the License, or (at your option) any later version.
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15 // This library is distributed in the hope that it will be useful,
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16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
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17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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18 // Lesser General Public License for more details.
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20 // You should have received a copy of the GNU Lesser General Public
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21 // License along with this library; if not, write to the Free Software
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22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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24 // Contact: phylosoft @ gmail . com
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25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
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27 package org.forester.archaeopteryx;
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29 import java.awt.BorderLayout;
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30 import java.awt.Font;
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31 import java.awt.event.ActionEvent;
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32 import java.awt.event.ComponentAdapter;
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33 import java.awt.event.ComponentEvent;
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34 import java.awt.event.WindowAdapter;
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35 import java.awt.event.WindowEvent;
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36 import java.io.File;
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37 import java.io.FileInputStream;
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38 import java.io.IOException;
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39 import java.io.InputStream;
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40 import java.net.MalformedURLException;
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41 import java.net.URL;
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42 import java.util.ArrayList;
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43 import java.util.HashSet;
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44 import java.util.List;
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45 import java.util.Set;
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47 import javax.swing.ButtonGroup;
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48 import javax.swing.JCheckBoxMenuItem;
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49 import javax.swing.JFileChooser;
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50 import javax.swing.JMenu;
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51 import javax.swing.JMenuBar;
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52 import javax.swing.JMenuItem;
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53 import javax.swing.JOptionPane;
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54 import javax.swing.JRadioButtonMenuItem;
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55 import javax.swing.UIManager;
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56 import javax.swing.UnsupportedLookAndFeelException;
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57 import javax.swing.WindowConstants;
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58 import javax.swing.event.ChangeEvent;
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59 import javax.swing.event.ChangeListener;
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61 import org.forester.analysis.TaxonomyDataManager;
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62 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
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63 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
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64 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
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65 import org.forester.archaeopteryx.tools.InferenceManager;
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66 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
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67 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
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68 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
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69 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
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70 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
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71 import org.forester.archaeopteryx.webservices.WebservicesManager;
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72 import org.forester.io.parsers.FastaParser;
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73 import org.forester.io.parsers.GeneralMsaParser;
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74 import org.forester.io.parsers.PhylogenyParser;
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75 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
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76 import org.forester.io.parsers.nhx.NHXParser;
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77 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
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78 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
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79 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
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80 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
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81 import org.forester.io.parsers.tol.TolParser;
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82 import org.forester.io.parsers.util.ParserUtils;
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83 import org.forester.io.writers.SequenceWriter;
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84 import org.forester.msa.Msa;
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85 import org.forester.msa.MsaFormatException;
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86 import org.forester.phylogeny.Phylogeny;
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87 import org.forester.phylogeny.PhylogenyMethods;
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88 import org.forester.phylogeny.PhylogenyNode;
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89 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
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90 import org.forester.phylogeny.data.Confidence;
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91 import org.forester.phylogeny.data.PhylogenyDataUtil;
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92 import org.forester.phylogeny.data.Sequence;
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93 import org.forester.phylogeny.data.Taxonomy;
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94 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
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95 import org.forester.phylogeny.factories.PhylogenyFactory;
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96 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
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97 import org.forester.sequence.MolecularSequence;
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98 import org.forester.util.BasicDescriptiveStatistics;
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99 import org.forester.util.BasicTable;
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100 import org.forester.util.BasicTableParser;
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101 import org.forester.util.DescriptiveStatistics;
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102 import org.forester.util.ForesterUtil;
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104 public final class MainFrameApplication extends MainFrame {
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106 private final static int FRAME_X_SIZE = 800;
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107 private final static int FRAME_Y_SIZE = 800;
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108 // Filters for the file-open dialog (classes defined in this file)
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109 private static final long serialVersionUID = -799735726778865234L;
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110 private static final boolean PREPROCESS_TREES = false;
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111 private final JFileChooser _values_filechooser;
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112 private final JFileChooser _sequences_filechooser;
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113 private final JFileChooser _open_filechooser;
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114 private final JFileChooser _msa_filechooser;
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115 private final JFileChooser _seqs_pi_filechooser;
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116 private final JFileChooser _open_filechooser_for_species_tree;
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117 // Application-only print menu items
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118 private JMenuItem _collapse_below_threshold;
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119 private JMenuItem _collapse_below_branch_length;
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120 private ButtonGroup _radio_group_1;
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121 private ButtonGroup _radio_group_2;
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123 double _min_not_collapse = AptxConstants.MIN_NOT_COLLAPSE_DEFAULT;
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124 double _min_not_collapse_bl = 0.001;
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125 // Phylogeny Inference menu
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126 private JMenu _inference_menu;
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127 private JMenuItem _inference_from_msa_item;
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128 private JMenuItem _inference_from_seqs_item;
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129 // Phylogeny Inference
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130 private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
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131 private Msa _msa = null;
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132 private File _msa_file = null;
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133 private List<MolecularSequence> _seqs = null;
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134 private File _seqs_file = null;
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135 JMenuItem _read_values_jmi;
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136 JMenuItem _read_seqs_jmi;
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138 private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
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139 _configuration = config;
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140 if ( _configuration == null ) {
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141 throw new IllegalArgumentException( "configuration is null" );
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143 setVisible( false );
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144 setOptions( Options.createInstance( _configuration ) );
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145 _mainpanel = new MainPanel( _configuration, this );
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146 _open_filechooser = null;
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147 _open_filechooser_for_species_tree = null;
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148 _save_filechooser = null;
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149 _writetopdf_filechooser = null;
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150 _writetographics_filechooser = null;
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151 _msa_filechooser = null;
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152 _seqs_pi_filechooser = null;
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153 _values_filechooser = null;
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154 _sequences_filechooser = null;
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155 _jmenubar = new JMenuBar();
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158 _contentpane = getContentPane();
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159 _contentpane.setLayout( new BorderLayout() );
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160 _contentpane.add( _mainpanel, BorderLayout.CENTER );
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162 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
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163 // The window listener
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164 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
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165 addWindowListener( new WindowAdapter() {
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168 public void windowClosing( final WindowEvent e ) {
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172 // setVisible( true );
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173 if ( ( phys != null ) && ( phys.length > 0 ) ) {
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174 AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
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176 getMainPanel().getControlPanel().showWholeAll();
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177 getMainPanel().getControlPanel().showWhole();
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179 //activateSaveAllIfNeeded();
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180 // ...and its children
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181 _contentpane.repaint();
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184 private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
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185 this( phys, config, title, null );
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188 private MainFrameApplication( final Phylogeny[] phys,
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189 final Configuration config,
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190 final String title,
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191 final File current_dir ) {
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193 _configuration = config;
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194 if ( _configuration == null ) {
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195 throw new IllegalArgumentException( "configuration is null" );
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198 if ( _configuration.isUseNativeUI() ) {
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199 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
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202 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
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205 catch ( final UnsupportedLookAndFeelException e ) {
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206 AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
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208 catch ( final ClassNotFoundException e ) {
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209 AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
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211 catch ( final InstantiationException e ) {
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212 AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
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214 catch ( final IllegalAccessException e ) {
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215 AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
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217 if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
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218 setCurrentDir( current_dir );
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220 // hide until everything is ready
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221 setVisible( false );
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222 setOptions( Options.createInstance( _configuration ) );
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223 setInferenceManager( InferenceManager.createInstance( _configuration ) );
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224 setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
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226 setTitle( AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + " (" + AptxConstants.PRG_DATE + ")" );
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227 _mainpanel = new MainPanel( _configuration, this );
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228 // The file dialogs
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229 _open_filechooser = new JFileChooser();
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230 _open_filechooser.setMultiSelectionEnabled( true );
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231 _open_filechooser.addChoosableFileFilter( MainFrame.xmlfilter );
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232 _open_filechooser.addChoosableFileFilter( MainFrame.nhxfilter );
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233 _open_filechooser.addChoosableFileFilter( MainFrame.nhfilter );
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234 _open_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );
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235 _open_filechooser.addChoosableFileFilter( MainFrame.tolfilter );
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236 _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
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237 _open_filechooser.setFileFilter( MainFrame.defaultfilter );
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238 _open_filechooser_for_species_tree = new JFileChooser();
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239 _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
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240 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.xmlfilter );
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241 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.tolfilter );
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242 _open_filechooser_for_species_tree.setFileFilter( MainFrame.xmlfilter );
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244 _msa_filechooser = new JFileChooser();
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245 _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
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246 _msa_filechooser.setMultiSelectionEnabled( false );
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247 _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
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248 _msa_filechooser.addChoosableFileFilter( MainFrame.msafilter );
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250 _seqs_pi_filechooser = new JFileChooser();
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251 _seqs_pi_filechooser.setName( "Read Sequences File" );
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252 _seqs_pi_filechooser.setMultiSelectionEnabled( false );
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253 _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );
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254 _seqs_pi_filechooser.addChoosableFileFilter( MainFrame.seqsfilter );
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256 _values_filechooser = new JFileChooser();
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257 _values_filechooser.setMultiSelectionEnabled( false );
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259 _sequences_filechooser = new JFileChooser();
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260 _sequences_filechooser.setMultiSelectionEnabled( false );
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262 final String home_dir = System.getProperty( "user.home" );
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263 _open_filechooser.setCurrentDirectory( new File( home_dir ) );
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264 _open_filechooser_for_species_tree.setCurrentDirectory( new File( home_dir ) );
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265 _msa_filechooser.setCurrentDirectory( new File( home_dir ) );
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266 _seqs_pi_filechooser.setCurrentDirectory( new File( home_dir ) );
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267 _values_filechooser.setCurrentDirectory( new File( home_dir ) );
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268 _sequences_filechooser.setCurrentDirectory( new File( home_dir ) );
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270 catch ( final Exception e ) {
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271 e.printStackTrace();
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272 // Do nothing. Not important.
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274 // build the menu bar
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275 _jmenubar = new JMenuBar();
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276 if ( !_configuration.isUseNativeUI() ) {
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277 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
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280 if ( AptxConstants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
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281 buildPhylogeneticInferenceMenu();
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283 buildAnalysisMenu();
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286 buildFontSizeMenu();
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287 buildOptionsMenu();
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290 setJMenuBar( _jmenubar );
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291 _jmenubar.add( _help_jmenu );
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292 _contentpane = getContentPane();
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293 _contentpane.setLayout( new BorderLayout() );
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294 _contentpane.add( _mainpanel, BorderLayout.CENTER );
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296 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
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297 // addWindowFocusListener( new WindowAdapter() {
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300 // public void windowGainedFocus( WindowEvent e ) {
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301 // requestFocusInWindow();
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304 // The window listener
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305 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
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306 addWindowListener( new WindowAdapter() {
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309 public void windowClosing( final WindowEvent e ) {
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310 if ( isUnsavedDataPresent() ) {
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311 final int r = JOptionPane.showConfirmDialog( null,
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312 "Exit despite potentially unsaved changes?",
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314 JOptionPane.YES_NO_OPTION );
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315 if ( r != JOptionPane.YES_OPTION ) {
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320 final int r = JOptionPane.showConfirmDialog( null,
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321 "Exit Archaeopteryx?",
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323 JOptionPane.YES_NO_OPTION );
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324 if ( r != JOptionPane.YES_OPTION ) {
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331 // The component listener
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332 addComponentListener( new ComponentAdapter() {
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335 public void componentResized( final ComponentEvent e ) {
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336 if ( _mainpanel.getCurrentTreePanel() != null ) {
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337 _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
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339 _mainpanel.getCurrentTreePanel()
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344 requestFocusInWindow();
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345 // addKeyListener( this );
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346 setVisible( true );
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347 if ( ( phys != null ) && ( phys.length > 0 ) ) {
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348 AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
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350 getMainPanel().getControlPanel().showWholeAll();
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351 getMainPanel().getControlPanel().showWhole();
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353 activateSaveAllIfNeeded();
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354 // ...and its children
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355 _contentpane.repaint();
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359 private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
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360 // Reads the config file (false, false => not url, not applet):
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361 this( phys, new Configuration( config_file, false, false, true ), title );
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365 public void actionPerformed( final ActionEvent e ) {
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367 super.actionPerformed( e );
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368 final Object o = e.getSource();
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369 // Handle app-specific actions here:
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370 if ( o == _open_item ) {
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371 readPhylogeniesFromFile();
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373 if ( o == _open_url_item ) {
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374 readPhylogeniesFromURL();
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376 else if ( o == _new_item ) {
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379 else if ( o == _close_item ) {
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380 closeCurrentPane();
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382 else if ( o == _load_species_tree_item ) {
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383 readSpeciesTreeFromFile();
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385 else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
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386 if ( isSubtreeDisplayed() ) {
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389 obtainDetailedTaxonomicInformation();
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391 else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
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392 if ( isSubtreeDisplayed() ) {
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395 obtainDetailedTaxonomicInformationDelete();
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397 else if ( o == _obtain_seq_information_jmi ) {
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398 obtainSequenceInformation();
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400 else if ( o == _read_values_jmi ) {
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401 if ( isSubtreeDisplayed() ) {
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404 addExpressionValuesFromFile();
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406 else if ( o == _read_seqs_jmi ) {
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407 if ( isSubtreeDisplayed() ) {
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410 addSequencesFromFile();
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412 else if ( o == _move_node_names_to_tax_sn_jmi ) {
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413 moveNodeNamesToTaxSn();
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415 else if ( o == _move_node_names_to_seq_names_jmi ) {
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416 moveNodeNamesToSeqNames();
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418 else if ( o == _extract_tax_code_from_node_names_jmi ) {
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419 extractTaxDataFromNodeNames();
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421 else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
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422 updateOptions( getOptions() );
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424 else if ( o == _replace_underscores_cbmi ) {
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425 if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
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426 _extract_taxonomy_no_rbmi.setSelected( true );
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428 updateOptions( getOptions() );
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430 else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {
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431 updateOptions( getOptions() );
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433 else if ( o == _collapse_below_threshold ) {
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434 if ( isSubtreeDisplayed() ) {
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437 collapseBelowThreshold();
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439 else if ( o == _collapse_below_branch_length ) {
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440 if ( isSubtreeDisplayed() ) {
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443 collapseBelowBranchLengthThreshold();
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445 else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )
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446 || ( o == _extract_taxonomy_agressive_rbmi ) ) {
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447 if ( _replace_underscores_cbmi != null ) {
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448 _replace_underscores_cbmi.setSelected( false );
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450 updateOptions( getOptions() );
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452 else if ( o == _extract_taxonomy_no_rbmi ) {
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453 updateOptions( getOptions() );
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455 else if ( o == _inference_from_msa_item ) {
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456 executePhyleneticInference( false );
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458 else if ( o == _inference_from_seqs_item ) {
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459 executePhyleneticInference( true );
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461 _contentpane.repaint();
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463 catch ( final Exception ex ) {
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464 AptxUtil.unexpectedException( ex );
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466 catch ( final Error err ) {
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467 AptxUtil.unexpectedError( err );
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471 public void end() {
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472 _mainpanel.terminate();
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473 _contentpane.removeAll();
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474 setVisible( false );
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479 public MainPanel getMainPanel() {
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483 public Msa getMsa() {
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487 public File getMsaFile() {
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491 public List<MolecularSequence> getSeqs() {
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495 public File getSeqsFile() {
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499 public void readMsaFromFile() {
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500 // Set an initial directory if none set yet
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501 final File my_dir = getCurrentDir();
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502 _msa_filechooser.setMultiSelectionEnabled( false );
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503 // Open file-open dialog and set current directory
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504 if ( my_dir != null ) {
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505 _msa_filechooser.setCurrentDirectory( my_dir );
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507 final int result = _msa_filechooser.showOpenDialog( _contentpane );
\r
508 // All done: get the msa
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509 final File file = _msa_filechooser.getSelectedFile();
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510 setCurrentDir( _msa_filechooser.getCurrentDirectory() );
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511 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
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512 setMsaFile( null );
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516 final InputStream is = new FileInputStream( file );
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517 if ( FastaParser.isLikelyFasta( file ) ) {
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518 msa = FastaParser.parseMsa( is );
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521 msa = GeneralMsaParser.parse( is );
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524 catch ( final MsaFormatException e ) {
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526 JOptionPane.showMessageDialog( this,
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527 e.getLocalizedMessage(),
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528 "Multiple sequence alignment format error",
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529 JOptionPane.ERROR_MESSAGE );
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532 catch ( final IOException e ) {
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534 JOptionPane.showMessageDialog( this,
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535 e.getLocalizedMessage(),
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536 "Failed to read multiple sequence alignment",
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537 JOptionPane.ERROR_MESSAGE );
\r
540 catch ( final IllegalArgumentException e ) {
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542 JOptionPane.showMessageDialog( this,
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543 e.getLocalizedMessage(),
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544 "Unexpected error during reading of multiple sequence alignment",
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545 JOptionPane.ERROR_MESSAGE );
\r
548 catch ( final Exception e ) {
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550 e.printStackTrace();
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551 JOptionPane.showMessageDialog( this,
\r
552 e.getLocalizedMessage(),
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553 "Unexpected error during reading of multiple sequence alignment",
\r
554 JOptionPane.ERROR_MESSAGE );
\r
557 if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
\r
558 JOptionPane.showMessageDialog( this,
\r
559 "Multiple sequence alignment is empty",
\r
560 "Illegal Multiple Sequence Alignment",
\r
561 JOptionPane.ERROR_MESSAGE );
\r
564 if ( msa.getNumberOfSequences() < 4 ) {
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565 JOptionPane.showMessageDialog( this,
\r
566 "Multiple sequence alignment needs to contain at least 3 sequences",
\r
567 "Illegal multiple sequence alignment",
\r
568 JOptionPane.ERROR_MESSAGE );
\r
571 if ( msa.getLength() < 2 ) {
\r
572 JOptionPane.showMessageDialog( this,
\r
573 "Multiple sequence alignment needs to contain at least 2 residues",
\r
574 "Illegal multiple sequence alignment",
\r
575 JOptionPane.ERROR_MESSAGE );
\r
579 setMsaFile( _msa_filechooser.getSelectedFile() );
\r
584 public void readSeqsFromFileforPI() {
\r
585 // Set an initial directory if none set yet
\r
586 final File my_dir = getCurrentDir();
\r
587 _seqs_pi_filechooser.setMultiSelectionEnabled( false );
\r
588 // Open file-open dialog and set current directory
\r
589 if ( my_dir != null ) {
\r
590 _seqs_pi_filechooser.setCurrentDirectory( my_dir );
\r
592 final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );
\r
593 // All done: get the seqs
\r
594 final File file = _seqs_pi_filechooser.getSelectedFile();
\r
595 setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );
\r
596 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
597 setSeqsFile( null );
\r
599 List<MolecularSequence> seqs = null;
\r
601 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
\r
602 seqs = FastaParser.parse( new FileInputStream( file ) );
\r
603 for( final MolecularSequence seq : seqs ) {
\r
604 System.out.println( SequenceWriter.toFasta( seq, 60 ) );
\r
611 catch ( final MsaFormatException e ) {
\r
613 JOptionPane.showMessageDialog( this,
\r
614 e.getLocalizedMessage(),
\r
615 "Multiple sequence file format error",
\r
616 JOptionPane.ERROR_MESSAGE );
\r
619 catch ( final IOException e ) {
\r
621 JOptionPane.showMessageDialog( this,
\r
622 e.getLocalizedMessage(),
\r
623 "Failed to read multiple sequence file",
\r
624 JOptionPane.ERROR_MESSAGE );
\r
627 catch ( final IllegalArgumentException e ) {
\r
629 JOptionPane.showMessageDialog( this,
\r
630 e.getLocalizedMessage(),
\r
631 "Unexpected error during reading of multiple sequence file",
\r
632 JOptionPane.ERROR_MESSAGE );
\r
635 catch ( final Exception e ) {
\r
637 e.printStackTrace();
\r
638 JOptionPane.showMessageDialog( this,
\r
639 e.getLocalizedMessage(),
\r
640 "Unexpected error during reading of multiple sequence file",
\r
641 JOptionPane.ERROR_MESSAGE );
\r
644 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
\r
645 JOptionPane.showMessageDialog( this,
\r
646 "Multiple sequence file is empty",
\r
647 "Illegal multiple sequence file",
\r
648 JOptionPane.ERROR_MESSAGE );
\r
651 if ( seqs.size() < 4 ) {
\r
652 JOptionPane.showMessageDialog( this,
\r
653 "Multiple sequence file needs to contain at least 3 sequences",
\r
654 "Illegal multiple sequence file",
\r
655 JOptionPane.ERROR_MESSAGE );
\r
658 // if ( msa.getLength() < 2 ) {
\r
659 // JOptionPane.showMessageDialog( this,
\r
660 // "Multiple sequence alignment needs to contain at least 2 residues",
\r
661 // "Illegal multiple sequence file",
\r
662 // JOptionPane.ERROR_MESSAGE );
\r
666 setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
\r
671 private void addExpressionValuesFromFile() {
\r
672 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
\r
673 JOptionPane.showMessageDialog( this,
\r
674 "Need to load evolutionary tree first",
\r
675 "Can Not Read Expression Values",
\r
676 JOptionPane.WARNING_MESSAGE );
\r
679 final File my_dir = getCurrentDir();
\r
680 if ( my_dir != null ) {
\r
681 _values_filechooser.setCurrentDirectory( my_dir );
\r
683 final int result = _values_filechooser.showOpenDialog( _contentpane );
\r
684 final File file = _values_filechooser.getSelectedFile();
\r
685 if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
686 BasicTable<String> t = null;
\r
688 t = BasicTableParser.parse( file, '\t' );
\r
689 if ( t.getNumberOfColumns() < 2 ) {
\r
690 t = BasicTableParser.parse( file, ',' );
\r
692 if ( t.getNumberOfColumns() < 2 ) {
\r
693 t = BasicTableParser.parse( file, ' ' );
\r
696 catch ( final IOException e ) {
\r
697 JOptionPane.showMessageDialog( this,
\r
699 "Could Not Read Expression Value Table",
\r
700 JOptionPane.ERROR_MESSAGE );
\r
703 if ( t.getNumberOfColumns() < 2 ) {
\r
704 JOptionPane.showMessageDialog( this,
\r
705 "Table contains " + t.getNumberOfColumns() + " column(s)",
\r
706 "Problem with Expression Value Table",
\r
707 JOptionPane.ERROR_MESSAGE );
\r
710 if ( t.getNumberOfRows() < 1 ) {
\r
711 JOptionPane.showMessageDialog( this,
\r
712 "Table contains zero rows",
\r
713 "Problem with Expression Value Table",
\r
714 JOptionPane.ERROR_MESSAGE );
\r
717 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
718 if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
\r
719 JOptionPane.showMessageDialog( this,
\r
720 "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
\r
721 + phy.getNumberOfExternalNodes() + " external nodes",
\r
723 JOptionPane.WARNING_MESSAGE );
\r
725 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
\r
727 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
\r
728 final PhylogenyNode node = iter.next();
\r
729 final String node_name = node.getName();
\r
730 if ( !ForesterUtil.isEmpty( node_name ) ) {
\r
733 row = t.findRow( node_name );
\r
735 catch ( final IllegalArgumentException e ) {
\r
737 .showMessageDialog( this,
\r
739 "Error Mapping Node Identifiers to Expression Value Identifiers",
\r
740 JOptionPane.ERROR_MESSAGE );
\r
744 if ( node.isExternal() ) {
\r
749 final List<Double> l = new ArrayList<Double>();
\r
750 for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
\r
753 d = Double.parseDouble( t.getValueAsString( col, row ) );
\r
755 catch ( final NumberFormatException e ) {
\r
756 JOptionPane.showMessageDialog( this,
\r
757 "Could not parse \"" + t.getValueAsString( col, row )
\r
758 + "\" into a decimal value",
\r
759 "Issue with Expression Value Table",
\r
760 JOptionPane.ERROR_MESSAGE );
\r
763 stats.addValue( d );
\r
766 if ( !l.isEmpty() ) {
\r
767 if ( node.getNodeData().getProperties() != null ) {
\r
768 node.getNodeData().getProperties()
\r
769 .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
\r
771 node.getNodeData().setVector( l );
\r
775 if ( not_found > 0 ) {
\r
776 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
\r
777 + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
\r
779 getCurrentTreePanel().setStatisticsForExpressionValues( stats );
\r
783 private void addSequencesFromFile() {
\r
784 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
\r
785 JOptionPane.showMessageDialog( this,
\r
786 "Need to load evolutionary tree first",
\r
787 "Can Not Read Sequences",
\r
788 JOptionPane.WARNING_MESSAGE );
\r
791 final File my_dir = getCurrentDir();
\r
792 if ( my_dir != null ) {
\r
793 _sequences_filechooser.setCurrentDirectory( my_dir );
\r
795 final int result = _sequences_filechooser.showOpenDialog( _contentpane );
\r
796 final File file = _sequences_filechooser.getSelectedFile();
\r
797 List<MolecularSequence> seqs = null;
\r
798 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
800 final FileInputStream fis1 = new FileInputStream( file );
\r
801 if ( FastaParser.isLikelyFasta( fis1 ) ) {
\r
802 final FileInputStream fis2 = new FileInputStream( file );
\r
803 seqs = FastaParser.parse( fis2 );
\r
807 catch ( final Exception e ) {
\r
812 JOptionPane.showMessageDialog( this,
\r
813 "Format does not appear to be Fasta",
\r
814 "Multiple sequence file format error",
\r
815 JOptionPane.ERROR_MESSAGE );
\r
821 catch ( final Exception e ) {
\r
825 catch ( final MsaFormatException e ) {
\r
827 JOptionPane.showMessageDialog( this,
\r
828 e.getLocalizedMessage(),
\r
829 "Multiple sequence file format error",
\r
830 JOptionPane.ERROR_MESSAGE );
\r
833 catch ( final IOException e ) {
\r
835 JOptionPane.showMessageDialog( this,
\r
836 e.getLocalizedMessage(),
\r
837 "Failed to read multiple sequence file",
\r
838 JOptionPane.ERROR_MESSAGE );
\r
841 catch ( final Exception e ) {
\r
843 e.printStackTrace();
\r
844 JOptionPane.showMessageDialog( this,
\r
845 e.getLocalizedMessage(),
\r
846 "Unexpected error during reading of multiple sequence file",
\r
847 JOptionPane.ERROR_MESSAGE );
\r
850 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
\r
851 JOptionPane.showMessageDialog( this,
\r
852 "Multiple sequence file is empty",
\r
853 "Empty multiple sequence file",
\r
854 JOptionPane.ERROR_MESSAGE );
\r
859 if ( seqs != null ) {
\r
860 for( final MolecularSequence seq : seqs ) {
\r
861 System.out.println( seq.getIdentifier() );
\r
863 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
864 int total_counter = 0;
\r
865 int attached_counter = 0;
\r
866 for( final MolecularSequence seq : seqs ) {
\r
868 final String seq_name = seq.getIdentifier();
\r
869 if ( !ForesterUtil.isEmpty( seq_name ) ) {
\r
870 List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
\r
871 if ( nodes.isEmpty() ) {
\r
872 nodes = phy.getNodesViaSequenceSymbol( seq_name );
\r
874 if ( nodes.isEmpty() ) {
\r
875 nodes = phy.getNodesViaGeneName( seq_name );
\r
877 if ( nodes.isEmpty() ) {
\r
878 nodes = phy.getNodes( seq_name );
\r
880 if ( nodes.size() > 1 ) {
\r
881 JOptionPane.showMessageDialog( this,
\r
882 "Sequence name \"" + seq_name + "\" is not unique",
\r
883 "Sequence name not unique",
\r
884 JOptionPane.ERROR_MESSAGE );
\r
888 final String[] a = seq_name.split( "\\s" );
\r
889 if ( nodes.isEmpty() && ( a.length > 1 ) ) {
\r
890 final String seq_name_split = a[ 0 ];
\r
891 nodes = phy.getNodesViaSequenceName( seq_name_split );
\r
892 if ( nodes.isEmpty() ) {
\r
893 nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
\r
895 if ( nodes.isEmpty() ) {
\r
896 nodes = phy.getNodes( seq_name_split );
\r
898 if ( nodes.size() > 1 ) {
\r
899 JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
\r
900 + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
\r
905 if ( nodes.size() == 1 ) {
\r
906 ++attached_counter;
\r
907 final PhylogenyNode n = nodes.get( 0 );
\r
908 if ( !n.getNodeData().isHasSequence() ) {
\r
909 n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
\r
911 n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
\r
912 if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
\r
913 n.getNodeData().getSequence().setName( seq_name );
\r
918 if ( attached_counter > 0 ) {
\r
920 int ext_nodes_with_seq = 0;
\r
921 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
\r
923 final PhylogenyNode n = iter.next();
\r
924 if ( n.getNodeData().isHasSequence()
\r
925 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
\r
926 ++ext_nodes_with_seq;
\r
930 if ( ext_nodes == ext_nodes_with_seq ) {
\r
931 s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
\r
934 s = ext_nodes_with_seq + " out of " + ext_nodes
\r
935 + " external nodes now have a molecular sequence attached to them.";
\r
937 if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
\r
938 JOptionPane.showMessageDialog( this,
\r
939 "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
\r
940 "All sequences attached",
\r
941 JOptionPane.INFORMATION_MESSAGE );
\r
944 JOptionPane.showMessageDialog( this, "Attached " + attached_counter
\r
945 + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
\r
946 + " sequences attached", JOptionPane.WARNING_MESSAGE );
\r
950 JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
\r
951 + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
\r
956 private void closeCurrentPane() {
\r
957 if ( getMainPanel().getCurrentTreePanel() != null ) {
\r
958 if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
\r
959 final int r = JOptionPane.showConfirmDialog( this,
\r
960 "Close tab despite potentially unsaved changes?",
\r
962 JOptionPane.YES_NO_OPTION );
\r
963 if ( r != JOptionPane.YES_OPTION ) {
\r
967 getMainPanel().closeCurrentPane();
\r
968 activateSaveAllIfNeeded();
\r
972 private void collapse( final Phylogeny phy ) {
\r
973 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
974 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
\r
975 double min_support = Double.MAX_VALUE;
\r
976 boolean conf_present = false;
\r
977 while ( it.hasNext() ) {
\r
978 final PhylogenyNode n = it.next();
\r
979 if ( !n.isExternal() && !n.isRoot() ) {
\r
980 final List<Confidence> c = n.getBranchData().getConfidences();
\r
981 if ( ( c != null ) && ( c.size() > 0 ) ) {
\r
982 conf_present = true;
\r
984 for( final Confidence confidence : c ) {
\r
985 if ( confidence.getValue() > max ) {
\r
986 max = confidence.getValue();
\r
989 if ( max < getMinNotCollapseConfidenceValue() ) {
\r
990 to_be_removed.add( n );
\r
992 if ( max < min_support ) {
\r
998 if ( conf_present ) {
\r
999 for( final PhylogenyNode node : to_be_removed ) {
\r
1000 PhylogenyMethods.removeNode( node, phy );
\r
1002 if ( to_be_removed.size() > 0 ) {
\r
1003 phy.externalNodesHaveChanged();
\r
1004 phy.clearHashIdToNodeMap();
\r
1005 phy.recalculateNumberOfExternalDescendants( true );
\r
1006 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
1007 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
\r
1008 getCurrentTreePanel().calculateLongestExtNodeInfo();
\r
1009 getCurrentTreePanel().setNodeInPreorderToNull();
\r
1010 getCurrentTreePanel().recalculateMaxDistanceToRoot();
\r
1011 getCurrentTreePanel().resetPreferredSize();
\r
1012 getCurrentTreePanel().setEdited( true );
\r
1013 getCurrentTreePanel().repaint();
\r
1016 if ( to_be_removed.size() > 0 ) {
\r
1017 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
\r
1018 + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
\r
1019 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
\r
1022 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
\r
1023 + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
\r
1027 JOptionPane.showMessageDialog( this,
\r
1028 "No branch collapsed because no confidence values present",
\r
1029 "No confidence values present",
\r
1030 JOptionPane.INFORMATION_MESSAGE );
\r
1034 private void collapseBelowBranchLengthThreshold() {
\r
1035 if ( getCurrentTreePanel() != null ) {
\r
1036 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1037 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1038 final String s = ( String ) JOptionPane
\r
1039 .showInputDialog( this,
\r
1040 "Please enter the minimum branch length value\n",
\r
1041 "Minimal Branch Length Value",
\r
1042 JOptionPane.QUESTION_MESSAGE,
\r
1045 getMinNotCollapseBlValue() );
\r
1046 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1047 boolean success = true;
\r
1049 final String m_str = s.trim();
\r
1050 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1052 m = Double.parseDouble( m_str );
\r
1054 catch ( final Exception ex ) {
\r
1061 if ( success && ( m >= 0.0 ) ) {
\r
1062 setMinNotCollapseBlValue( m );
\r
1063 collapseBl( phy );
\r
1070 private void collapseBelowThreshold() {
\r
1071 if ( getCurrentTreePanel() != null ) {
\r
1072 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1073 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1074 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
1075 "Please enter the minimum confidence value\n",
\r
1076 "Minimal Confidence Value",
\r
1077 JOptionPane.QUESTION_MESSAGE,
\r
1080 getMinNotCollapseConfidenceValue() );
\r
1081 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1082 boolean success = true;
\r
1084 final String m_str = s.trim();
\r
1085 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1087 m = Double.parseDouble( m_str );
\r
1089 catch ( final Exception ex ) {
\r
1096 if ( success && ( m >= 0.0 ) ) {
\r
1097 setMinNotCollapseConfidenceValue( m );
\r
1105 private void collapseBl( final Phylogeny phy ) {
\r
1106 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1107 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
\r
1108 double min_bl = Double.MAX_VALUE;
\r
1109 boolean bl_present = false;
\r
1110 while ( it.hasNext() ) {
\r
1111 final PhylogenyNode n = it.next();
\r
1112 if ( !n.isExternal() && !n.isRoot() ) {
\r
1113 final double bl = n.getDistanceToParent();
\r
1114 if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
\r
1115 bl_present = true;
\r
1116 if ( bl < getMinNotCollapseBlValue() ) {
\r
1117 to_be_removed.add( n );
\r
1119 if ( bl < min_bl ) {
\r
1125 if ( bl_present ) {
\r
1126 for( final PhylogenyNode node : to_be_removed ) {
\r
1127 PhylogenyMethods.removeNode( node, phy );
\r
1129 if ( to_be_removed.size() > 0 ) {
\r
1130 phy.externalNodesHaveChanged();
\r
1131 phy.clearHashIdToNodeMap();
\r
1132 phy.recalculateNumberOfExternalDescendants( true );
\r
1133 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
1134 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
\r
1135 getCurrentTreePanel().calculateLongestExtNodeInfo();
\r
1136 getCurrentTreePanel().setNodeInPreorderToNull();
\r
1137 getCurrentTreePanel().recalculateMaxDistanceToRoot();
\r
1138 getCurrentTreePanel().resetPreferredSize();
\r
1139 getCurrentTreePanel().setEdited( true );
\r
1140 getCurrentTreePanel().repaint();
\r
1143 if ( to_be_removed.size() > 0 ) {
\r
1144 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
\r
1145 + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "
\r
1146 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
\r
1149 JOptionPane.showMessageDialog( this,
\r
1150 "No branch collapsed,\nminimum branch length is " + min_bl,
\r
1151 "No branch collapsed",
\r
1152 JOptionPane.INFORMATION_MESSAGE );
\r
1156 JOptionPane.showMessageDialog( this,
\r
1157 "No branch collapsed because no branch length values present",
\r
1158 "No branch length values present",
\r
1159 JOptionPane.INFORMATION_MESSAGE );
\r
1163 private PhyloXmlParser createPhyloXmlParser() {
\r
1164 PhyloXmlParser xml_parser = null;
\r
1165 if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
\r
1167 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
\r
1169 catch ( final Exception e ) {
\r
1170 JOptionPane.showMessageDialog( this,
\r
1171 e.getLocalizedMessage(),
\r
1172 "failed to create validating XML parser",
\r
1173 JOptionPane.WARNING_MESSAGE );
\r
1176 if ( xml_parser == null ) {
\r
1177 xml_parser = PhyloXmlParser.createPhyloXmlParser();
\r
1179 return xml_parser;
\r
1182 private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
\r
1183 final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
\r
1184 getPhylogeneticInferenceOptions(),
\r
1185 from_unaligned_seqs );
\r
1186 dialog.activate();
\r
1187 if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
\r
1188 if ( !from_unaligned_seqs ) {
\r
1189 if ( getMsa() != null ) {
\r
1190 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
\r
1191 getPhylogeneticInferenceOptions()
\r
1193 new Thread( inferrer ).start();
\r
1196 JOptionPane.showMessageDialog( this,
\r
1197 "No multiple sequence alignment selected",
\r
1198 "Phylogenetic Inference Not Launched",
\r
1199 JOptionPane.WARNING_MESSAGE );
\r
1203 if ( getSeqs() != null ) {
\r
1204 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
\r
1205 getPhylogeneticInferenceOptions()
\r
1207 new Thread( inferrer ).start();
\r
1210 JOptionPane.showMessageDialog( this,
\r
1211 "No input sequences selected",
\r
1212 "Phylogenetic Inference Not Launched",
\r
1213 JOptionPane.WARNING_MESSAGE );
\r
1219 private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
\r
1220 final StringBuilder sb = new StringBuilder();
\r
1221 final StringBuilder sb_failed = new StringBuilder();
\r
1223 int counter_failed = 0;
\r
1224 if ( getCurrentTreePanel() != null ) {
\r
1225 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1226 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1227 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
\r
1228 while ( it.hasNext() ) {
\r
1229 final PhylogenyNode n = it.next();
\r
1230 final String name = n.getName().trim();
\r
1231 if ( !ForesterUtil.isEmpty( name ) ) {
\r
1232 final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
\r
1233 TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1234 if ( !ForesterUtil.isEmpty( nt ) ) {
\r
1235 if ( counter < 15 ) {
\r
1236 sb.append( name + ": " + nt + "\n" );
\r
1238 else if ( counter == 15 ) {
\r
1239 sb.append( "...\n" );
\r
1244 if ( counter_failed < 15 ) {
\r
1245 sb_failed.append( name + "\n" );
\r
1247 else if ( counter_failed == 15 ) {
\r
1248 sb_failed.append( "...\n" );
\r
1254 if ( counter > 0 ) {
\r
1255 String failed = "";
\r
1256 String all = "all ";
\r
1257 if ( counter_failed > 0 ) {
\r
1259 failed = "\nCould not extract taxonomic data for " + counter_failed
\r
1260 + " named external nodes:\n" + sb_failed;
\r
1262 JOptionPane.showMessageDialog( this,
\r
1263 "Extracted taxonomic data from " + all + counter
\r
1264 + " named external nodes:\n" + sb.toString() + failed,
\r
1265 "Taxonomic Data Extraction Completed",
\r
1266 counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
\r
1267 : JOptionPane.INFORMATION_MESSAGE );
\r
1271 .showMessageDialog( this,
\r
1272 "Could not extract any taxonomic data.\nMaybe node names are empty\n"
\r
1273 + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
\r
1274 + "or nodes already have taxonomic data?\n",
\r
1275 "No Taxonomic Data Extracted",
\r
1276 JOptionPane.ERROR_MESSAGE );
\r
1282 private double getMinNotCollapseBlValue() {
\r
1283 return _min_not_collapse_bl;
\r
1286 private double getMinNotCollapseConfidenceValue() {
\r
1287 return _min_not_collapse;
\r
1290 private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
\r
1291 if ( _phylogenetic_inference_options == null ) {
\r
1292 _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
\r
1294 return _phylogenetic_inference_options;
\r
1297 private boolean isUnsavedDataPresent() {
\r
1298 final List<TreePanel> tps = getMainPanel().getTreePanels();
\r
1299 for( final TreePanel tp : tps ) {
\r
1300 if ( tp.isEdited() ) {
\r
1307 private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
\r
1308 if ( getCurrentTreePanel() != null ) {
\r
1309 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1310 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1312 .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
\r
1317 private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
\r
1318 if ( getCurrentTreePanel() != null ) {
\r
1319 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1320 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1321 PhylogenyMethods.transferNodeNameToField( phy,
\r
1322 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
\r
1328 private void newTree() {
\r
1329 final Phylogeny[] phys = new Phylogeny[ 1 ];
\r
1330 final Phylogeny phy = new Phylogeny();
\r
1331 final PhylogenyNode node = new PhylogenyNode();
\r
1332 phy.setRoot( node );
\r
1333 phy.setRooted( true );
\r
1335 AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
\r
1336 _mainpanel.getControlPanel().showWhole();
\r
1337 _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1338 _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1339 if ( getMainPanel().getMainFrame() == null ) {
\r
1340 // Must be "E" applet version.
\r
1341 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
\r
1342 .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1345 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1347 activateSaveAllIfNeeded();
\r
1351 private void obtainDetailedTaxonomicInformation() {
\r
1352 if ( getCurrentTreePanel() != null ) {
\r
1353 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1354 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1355 final TaxonomyDataManager t = new TaxonomyDataManager( this,
\r
1356 _mainpanel.getCurrentTreePanel(),
\r
1360 new Thread( t ).start();
\r
1365 private void obtainDetailedTaxonomicInformationDelete() {
\r
1366 if ( getCurrentTreePanel() != null ) {
\r
1367 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1368 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1369 final TaxonomyDataManager t = new TaxonomyDataManager( this,
\r
1370 _mainpanel.getCurrentTreePanel(),
\r
1374 new Thread( t ).start();
\r
1379 private void obtainSequenceInformation() {
\r
1380 if ( getCurrentTreePanel() != null ) {
\r
1381 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1382 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1383 final SequenceDataRetriver u = new SequenceDataRetriver( this,
\r
1384 _mainpanel.getCurrentTreePanel(),
\r
1386 new Thread( u ).start();
\r
1391 private void preProcessTreesUponReading( final Phylogeny[] phys ) {
\r
1392 for( final Phylogeny phy : phys ) {
\r
1393 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1394 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
\r
1395 final PhylogenyNode n = it.next();
\r
1396 if ( n.isExternal() ) {
\r
1397 if ( n.getNodeData().isHasSequence() ) {
\r
1398 final Sequence s = n.getNodeData().getSequence();
\r
1399 if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) {
\r
1400 if ( ( s.getAccession() != null )
\r
1401 && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) {
\r
1402 s.setGeneName( s.getAccession().getValue() );
\r
1404 else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
\r
1405 s.setGeneName( n.getName() );
\r
1415 private void readPhylogeniesFromFile() {
\r
1416 boolean exception = false;
\r
1417 Phylogeny[] phys = null;
\r
1418 // Set an initial directory if none set yet
\r
1419 final File my_dir = getCurrentDir();
\r
1420 // Open file-open dialog and set current directory
\r
1421 if ( my_dir != null ) {
\r
1422 _open_filechooser.setCurrentDirectory( my_dir );
\r
1424 final int result = _open_filechooser.showOpenDialog( _contentpane );
\r
1425 // All done: get the file
\r
1426 final File[] files = _open_filechooser.getSelectedFiles();
\r
1427 setCurrentDir( _open_filechooser.getCurrentDirectory() );
\r
1428 boolean nhx_or_nexus = false;
\r
1429 if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
1430 for( final File file : files ) {
\r
1431 if ( ( file != null ) && !file.isDirectory() ) {
\r
1432 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1433 _mainpanel.getCurrentTreePanel().setWaitCursor();
\r
1436 _mainpanel.setWaitCursor();
\r
1438 if ( ( _open_filechooser.getFileFilter() == MainFrame.nhfilter )
\r
1439 || ( _open_filechooser.getFileFilter() == MainFrame.nhxfilter ) ) {
\r
1441 final NHXParser nhx = new NHXParser();
\r
1442 setSpecialOptionsForNhxParser( nhx );
\r
1443 phys = PhylogenyMethods.readPhylogenies( nhx, file );
\r
1444 nhx_or_nexus = true;
\r
1446 catch ( final Exception e ) {
\r
1448 exceptionOccuredDuringOpenFile( e );
\r
1451 else if ( _open_filechooser.getFileFilter() == MainFrame.xmlfilter ) {
\r
1452 warnIfNotPhyloXmlValidation( getConfiguration() );
\r
1454 final PhyloXmlParser xml_parser = createPhyloXmlParser();
\r
1455 phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
\r
1457 catch ( final Exception e ) {
\r
1459 exceptionOccuredDuringOpenFile( e );
\r
1462 else if ( _open_filechooser.getFileFilter() == MainFrame.tolfilter ) {
\r
1464 phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
\r
1466 catch ( final Exception e ) {
\r
1468 exceptionOccuredDuringOpenFile( e );
\r
1471 else if ( _open_filechooser.getFileFilter() == MainFrame.nexusfilter ) {
\r
1473 final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
\r
1474 setSpecialOptionsForNexParser( nex );
\r
1475 phys = PhylogenyMethods.readPhylogenies( nex, file );
\r
1476 nhx_or_nexus = true;
\r
1478 catch ( final Exception e ) {
\r
1480 exceptionOccuredDuringOpenFile( e );
\r
1486 final PhylogenyParser parser = ParserUtils
\r
1487 .createParserDependingOnFileType( file, getConfiguration()
\r
1488 .isValidatePhyloXmlAgainstSchema() );
\r
1489 if ( parser instanceof NexusPhylogeniesParser ) {
\r
1490 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
\r
1491 setSpecialOptionsForNexParser( nex );
\r
1492 nhx_or_nexus = true;
\r
1494 else if ( parser instanceof NHXParser ) {
\r
1495 final NHXParser nhx = ( NHXParser ) parser;
\r
1496 setSpecialOptionsForNhxParser( nhx );
\r
1497 nhx_or_nexus = true;
\r
1499 else if ( parser instanceof PhyloXmlParser ) {
\r
1500 warnIfNotPhyloXmlValidation( getConfiguration() );
\r
1502 phys = PhylogenyMethods.readPhylogenies( parser, file );
\r
1504 catch ( final Exception e ) {
\r
1506 exceptionOccuredDuringOpenFile( e );
\r
1509 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1510 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
1513 _mainpanel.setArrowCursor();
\r
1515 if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
\r
1516 boolean one_desc = false;
\r
1517 if ( nhx_or_nexus ) {
\r
1518 for( final Phylogeny phy : phys ) {
\r
1519 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
\r
1520 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
\r
1522 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
\r
1528 if ( PREPROCESS_TREES ) {
\r
1529 preProcessTreesUponReading( phys );
\r
1531 AptxUtil.addPhylogeniesToTabs( phys,
\r
1533 file.getAbsolutePath(),
\r
1534 getConfiguration(),
\r
1536 _mainpanel.getControlPanel().showWhole();
\r
1537 if ( nhx_or_nexus && one_desc ) {
\r
1539 .showMessageDialog( this,
\r
1540 "One or more trees contain (a) node(s) with one descendant, "
\r
1541 + ForesterUtil.LINE_SEPARATOR
\r
1542 + "possibly indicating illegal parentheses within node names.",
\r
1543 "Warning: Possible Error in New Hampshire Formatted Data",
\r
1544 JOptionPane.WARNING_MESSAGE );
\r
1550 activateSaveAllIfNeeded();
\r
1554 private void readSpeciesTreeFromFile() {
\r
1555 Phylogeny t = null;
\r
1556 boolean exception = false;
\r
1557 final File my_dir = getCurrentDir();
\r
1558 _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
\r
1559 if ( my_dir != null ) {
\r
1560 _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
\r
1562 final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
\r
1563 final File file = _open_filechooser_for_species_tree.getSelectedFile();
\r
1564 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
1565 if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {
\r
1567 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
\r
1568 .createPhyloXmlParserXsdValidating(), file );
\r
1571 catch ( final Exception e ) {
\r
1573 exceptionOccuredDuringOpenFile( e );
\r
1576 else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) {
\r
1578 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
\r
1581 catch ( final Exception e ) {
\r
1583 exceptionOccuredDuringOpenFile( e );
\r
1589 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
\r
1590 .createPhyloXmlParserXsdValidating(), file );
\r
1593 catch ( final Exception e ) {
\r
1595 exceptionOccuredDuringOpenFile( e );
\r
1598 if ( !exception && ( t != null ) && !t.isRooted() ) {
\r
1601 JOptionPane.showMessageDialog( this,
\r
1602 "Species tree is not rooted",
\r
1603 "Species tree not loaded",
\r
1604 JOptionPane.ERROR_MESSAGE );
\r
1606 if ( !exception && ( t != null ) ) {
\r
1607 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
\r
1608 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
\r
1609 final PhylogenyNode node = it.next();
\r
1610 if ( !node.getNodeData().isHasTaxonomy() ) {
\r
1614 .showMessageDialog( this,
\r
1615 "Species tree contains external node(s) without taxonomy information",
\r
1616 "Species tree not loaded",
\r
1617 JOptionPane.ERROR_MESSAGE );
\r
1621 if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
\r
1624 JOptionPane.showMessageDialog( this,
\r
1626 + node.getNodeData().getTaxonomy().asSimpleText()
\r
1627 + "] is not unique in species tree",
\r
1628 "Species tree not loaded",
\r
1629 JOptionPane.ERROR_MESSAGE );
\r
1633 tax_set.add( node.getNodeData().getTaxonomy() );
\r
1638 if ( !exception && ( t != null ) ) {
\r
1639 setSpeciesTree( t );
\r
1640 JOptionPane.showMessageDialog( this,
\r
1641 "Species tree successfully loaded",
\r
1642 "Species tree loaded",
\r
1643 JOptionPane.INFORMATION_MESSAGE );
\r
1645 _contentpane.repaint();
\r
1650 private void setArrowCursor() {
\r
1652 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
1654 catch ( final Exception ex ) {
\r
1659 private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {
\r
1660 _min_not_collapse_bl = min_not_collapse_bl;
\r
1663 private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
\r
1664 _min_not_collapse = min_not_collapse;
\r
1667 private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
\r
1668 _phylogenetic_inference_options = phylogenetic_inference_options;
\r
1671 private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
\r
1672 nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
\r
1673 nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
\r
1676 private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
\r
1677 nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
\r
1678 nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
\r
1679 nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );
\r
1682 void buildAnalysisMenu() {
\r
1683 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
\r
1684 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
\r
1685 _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
\r
1686 _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
\r
1687 customizeJMenuItem( _gsdi_item );
\r
1688 customizeJMenuItem( _gsdir_item );
\r
1689 customizeJMenuItem( _load_species_tree_item );
\r
1690 _analysis_menu.addSeparator();
\r
1691 _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
\r
1692 customizeJMenuItem( _lineage_inference );
\r
1693 _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
\r
1694 _jmenubar.add( _analysis_menu );
\r
1698 void buildFileMenu() {
\r
1699 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
\r
1700 _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
\r
1701 _file_jmenu.addSeparator();
\r
1702 _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
\r
1703 _file_jmenu.addSeparator();
\r
1704 final WebservicesManager webservices_manager = WebservicesManager.getInstance();
\r
1705 _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
\r
1706 .getAvailablePhylogeniesWebserviceClients().size() ];
\r
1707 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
\r
1708 final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
\r
1709 _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
\r
1710 _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
\r
1712 if ( getConfiguration().isEditable() ) {
\r
1713 _file_jmenu.addSeparator();
\r
1714 _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
\r
1715 _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
\r
1717 _file_jmenu.addSeparator();
\r
1718 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
\r
1719 _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
\r
1720 _save_all_item.setToolTipText( "Write all phylogenies to one file." );
\r
1721 _save_all_item.setEnabled( false );
\r
1722 _file_jmenu.addSeparator();
\r
1723 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
\r
1724 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
\r
1725 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
\r
1727 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
\r
1728 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
\r
1729 if ( AptxUtil.canWriteFormat( "gif" ) ) {
\r
1730 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
\r
1732 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
\r
1733 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
\r
1735 _file_jmenu.addSeparator();
\r
1736 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
\r
1737 _file_jmenu.addSeparator();
\r
1738 _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
\r
1739 _close_item.setToolTipText( "To close the current pane." );
\r
1740 _close_item.setEnabled( true );
\r
1741 _file_jmenu.addSeparator();
\r
1742 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
\r
1743 customizeJMenuItem( _open_item );
\r
1745 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
\r
1746 customizeJMenuItem( _open_url_item );
\r
1747 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
\r
1748 customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
\r
1750 customizeJMenuItem( _save_item );
\r
1751 if ( getConfiguration().isEditable() ) {
\r
1752 customizeJMenuItem( _new_item );
\r
1754 customizeJMenuItem( _close_item );
\r
1755 customizeJMenuItem( _save_all_item );
\r
1756 customizeJMenuItem( _write_to_pdf_item );
\r
1757 customizeJMenuItem( _write_to_png_item );
\r
1758 customizeJMenuItem( _write_to_jpg_item );
\r
1759 customizeJMenuItem( _write_to_gif_item );
\r
1760 customizeJMenuItem( _write_to_tif_item );
\r
1761 customizeJMenuItem( _write_to_bmp_item );
\r
1762 customizeJMenuItem( _print_item );
\r
1763 customizeJMenuItem( _exit_item );
\r
1764 _jmenubar.add( _file_jmenu );
\r
1767 void buildOptionsMenu() {
\r
1768 _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
\r
1769 _options_jmenu.addChangeListener( new ChangeListener() {
\r
1772 public void stateChanged( final ChangeEvent e ) {
\r
1773 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
\r
1774 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
\r
1776 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
\r
1777 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
\r
1778 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
\r
1779 // MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
\r
1780 MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
\r
1781 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
\r
1782 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
\r
1783 MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );
\r
1784 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
\r
1786 getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
\r
1787 getMainPanel().getControlPanel().setVisibilityOfX();
\r
1789 catch ( final Exception ignore ) {
\r
1790 // do nothing, not important.
\r
1794 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
\r
1796 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
\r
1797 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
\r
1798 _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
\r
1799 _radio_group_1 = new ButtonGroup();
\r
1800 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
\r
1801 _radio_group_1.add( _uniform_cladograms_rbmi );
\r
1802 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
\r
1803 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
\r
1804 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
\r
1806 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
\r
1808 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
\r
1810 .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
\r
1811 _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
\r
1812 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
\r
1813 _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
\r
1814 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
\r
1816 _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
\r
1817 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
\r
1818 _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
\r
1819 _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
\r
1820 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
\r
1821 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
\r
1822 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
\r
1823 _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
\r
1824 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
\r
1825 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
\r
1826 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
\r
1827 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
\r
1828 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
\r
1829 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
\r
1830 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
\r
1831 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
\r
1832 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
\r
1833 _options_jmenu.addSeparator();
\r
1834 _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );
\r
1835 _options_jmenu.addSeparator();
\r
1836 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
\r
1837 _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
\r
1838 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
\r
1839 _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
\r
1840 _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
\r
1841 _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
\r
1842 _options_jmenu.add( _color_all_found_nodes_when_coloring_subtree_cbmi = new JCheckBoxMenuItem( "Colorize All Found Nodes When Colorizing Subtree(s)" ) );
\r
1843 _options_jmenu.addSeparator();
\r
1844 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
\r
1845 getConfiguration() ) );
\r
1846 _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
\r
1847 _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
\r
1849 //.add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
\r
1851 //.add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
\r
1853 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
\r
1854 // _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
\r
1855 _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
\r
1856 _options_jmenu.addSeparator();
\r
1857 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Read:" ), getConfiguration() ) );
\r
1859 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
\r
1860 _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
\r
1862 .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
\r
1863 _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
\r
1865 .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
\r
1867 .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
\r
1869 .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
\r
1870 _extract_taxonomy_pfam_strict_rbmi
\r
1871 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
\r
1872 _extract_taxonomy_pfam_relaxed_rbmi
\r
1873 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
\r
1874 _extract_taxonomy_agressive_rbmi
\r
1875 .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );
\r
1876 _radio_group_2 = new ButtonGroup();
\r
1877 _radio_group_2.add( _extract_taxonomy_no_rbmi );
\r
1878 _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
\r
1879 _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );
\r
1880 _radio_group_2.add( _extract_taxonomy_agressive_rbmi );
\r
1881 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Save:" ), getConfiguration() ) );
\r
1883 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
\r
1884 _use_brackets_for_conf_in_nh_export_cbmi
\r
1885 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
\r
1887 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
\r
1888 customizeJMenuItem( _choose_font_mi );
\r
1889 customizeJMenuItem( _choose_minimal_confidence_mi );
\r
1890 customizeJMenuItem( _switch_colors_mi );
\r
1891 // customizeJMenuItem( _print_size_mi );
\r
1892 customizeJMenuItem( _choose_pdf_width_mi );
\r
1893 customizeJMenuItem( _overview_placment_mi );
\r
1894 customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
\r
1895 .isShowDefaultNodeShapesExternal() );
\r
1896 customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
\r
1897 .isShowDefaultNodeShapesInternal() );
\r
1898 customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
\r
1899 .isShowDefaultNodeShapesForMarkedNodes() );
\r
1900 customizeJMenuItem( _cycle_node_shape_mi );
\r
1901 customizeJMenuItem( _cycle_node_fill_mi );
\r
1902 customizeJMenuItem( _choose_node_size_mi );
\r
1903 customizeJMenuItem( _cycle_data_return );
\r
1904 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
\r
1905 customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
\r
1906 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
\r
1907 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
\r
1908 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
\r
1909 customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
\r
1910 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
\r
1911 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
\r
1912 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
\r
1913 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
\r
1914 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
\r
1915 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
\r
1916 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
\r
1917 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
\r
1918 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
\r
1919 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
\r
1920 customizeCheckBoxMenuItem( _label_direction_cbmi,
\r
1921 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
\r
1922 customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
\r
1923 customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
\r
1924 customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
\r
1925 .isInternalNumberAreConfidenceForNhParsing() );
\r
1926 customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
\r
1927 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
\r
1928 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
\r
1929 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
\r
1930 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,
\r
1931 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
\r
1932 customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
\r
1933 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1934 customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
\r
1935 customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()
\r
1936 .isReplaceUnderscoresInNhParsing() );
\r
1937 customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
\r
1938 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
\r
1939 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
\r
1940 customizeCheckBoxMenuItem( _color_all_found_nodes_when_coloring_subtree_cbmi, getOptions().isColorAllFoundNodesWhenColoringSubtree() );
\r
1941 customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
\r
1942 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
\r
1943 customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
\r
1944 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
\r
1945 customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
\r
1946 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
\r
1947 customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
\r
1948 customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
\r
1949 _jmenubar.add( _options_jmenu );
\r
1952 void buildPhylogeneticInferenceMenu() {
\r
1953 final InferenceManager im = getInferenceManager();
\r
1954 _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
\r
1955 _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
\r
1956 customizeJMenuItem( _inference_from_msa_item );
\r
1957 _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
\r
1958 if ( im.canDoMsa() ) {
\r
1959 _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
\r
1960 customizeJMenuItem( _inference_from_seqs_item );
\r
1961 _inference_from_seqs_item
\r
1962 .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
\r
1966 .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
\r
1967 customizeJMenuItem( _inference_from_seqs_item );
\r
1968 _inference_from_seqs_item.setEnabled( false );
\r
1970 _jmenubar.add( _inference_menu );
\r
1973 void buildToolsMenu() {
\r
1974 _tools_menu = createMenu( "Tools", getConfiguration() );
\r
1975 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
\r
1976 customizeJMenuItem( _confcolor_item );
\r
1977 _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
\r
1978 customizeJMenuItem( _color_rank_jmi );
\r
1979 _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
\r
1980 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
\r
1981 customizeJMenuItem( _taxcolor_item );
\r
1982 _tools_menu.addSeparator();
\r
1983 _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
\r
1984 _remove_visual_styles_item
\r
1985 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );
\r
1986 customizeJMenuItem( _remove_visual_styles_item );
\r
1987 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
\r
1988 _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );
\r
1989 customizeJMenuItem( _remove_branch_color_item );
\r
1990 _tools_menu.addSeparator();
\r
1991 _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
\r
1992 customizeJMenuItem( _annotate_item );
\r
1993 _tools_menu.addSeparator();
\r
1994 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
\r
1995 customizeJMenuItem( _midpoint_root_item );
\r
1996 _tools_menu.addSeparator();
\r
1997 _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );
\r
1998 _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );
\r
1999 customizeJMenuItem( _delete_selected_nodes_item );
\r
2000 _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );
\r
2001 _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );
\r
2002 customizeJMenuItem( _delete_not_selected_nodes_item );
\r
2003 _tools_menu.addSeparator();
\r
2004 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
\r
2005 customizeJMenuItem( _collapse_species_specific_subtrees );
\r
2006 _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );
\r
2008 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
\r
2009 customizeJMenuItem( _collapse_below_threshold );
\r
2010 _collapse_below_threshold
\r
2011 .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );
\r
2014 .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );
\r
2015 customizeJMenuItem( _collapse_below_branch_length );
\r
2016 _collapse_below_branch_length
\r
2017 .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );
\r
2019 _tools_menu.addSeparator();
\r
2021 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
\r
2022 customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
\r
2023 _extract_tax_code_from_node_names_jmi
\r
2024 .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
\r
2026 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
\r
2027 customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
\r
2028 _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
\r
2029 _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
\r
2030 customizeJMenuItem( _move_node_names_to_seq_names_jmi );
\r
2031 _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
\r
2032 _tools_menu.addSeparator();
\r
2033 _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
\r
2034 customizeJMenuItem( _obtain_seq_information_jmi );
\r
2035 _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
\r
2037 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
\r
2038 customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
\r
2039 _obtain_detailed_taxonomic_information_jmi
\r
2040 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
\r
2042 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
\r
2043 customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
\r
2044 _obtain_detailed_taxonomic_information_deleting_jmi
\r
2045 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
\r
2046 _tools_menu.addSeparator();
\r
2047 _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
\r
2048 customizeJMenuItem( _read_values_jmi );
\r
2049 _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
\r
2050 _jmenubar.add( _tools_menu );
\r
2051 _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
\r
2052 customizeJMenuItem( _read_seqs_jmi );
\r
2054 .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
\r
2055 _jmenubar.add( _tools_menu );
\r
2060 if ( isUnsavedDataPresent() ) {
\r
2061 final int r = JOptionPane.showConfirmDialog( this,
\r
2062 "Exit despite potentially unsaved changes?",
\r
2064 JOptionPane.YES_NO_OPTION );
\r
2065 if ( r != JOptionPane.YES_OPTION ) {
\r
2073 removeAllTextFrames();
\r
2074 _mainpanel.terminate();
\r
2075 _contentpane.removeAll();
\r
2076 setVisible( false );
\r
2078 // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.
\r
2081 void readPhylogeniesFromURL() {
\r
2083 Phylogeny[] phys = null;
\r
2084 final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
\r
2085 final String url_string = JOptionPane.showInputDialog( this,
\r
2087 "Use URL/webservice to obtain a phylogeny",
\r
2088 JOptionPane.QUESTION_MESSAGE );
\r
2089 boolean nhx_or_nexus = false;
\r
2090 if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
\r
2092 url = new URL( url_string );
\r
2093 PhylogenyParser parser = null;
\r
2094 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
\r
2095 parser = new TolParser();
\r
2098 parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
\r
2099 .isValidatePhyloXmlAgainstSchema() );
\r
2101 if ( parser instanceof NexusPhylogeniesParser ) {
\r
2102 nhx_or_nexus = true;
\r
2104 else if ( parser instanceof NHXParser ) {
\r
2105 nhx_or_nexus = true;
\r
2107 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
2108 _mainpanel.getCurrentTreePanel().setWaitCursor();
\r
2111 _mainpanel.setWaitCursor();
\r
2113 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
\r
2114 phys = factory.create( url.openStream(), parser );
\r
2116 catch ( final MalformedURLException e ) {
\r
2117 JOptionPane.showMessageDialog( this,
\r
2118 "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
\r
2120 JOptionPane.ERROR_MESSAGE );
\r
2122 catch ( final IOException e ) {
\r
2123 JOptionPane.showMessageDialog( this,
\r
2124 "Could not read from " + url + "\n"
\r
2125 + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
2126 "Failed to read URL",
\r
2127 JOptionPane.ERROR_MESSAGE );
\r
2129 catch ( final Exception e ) {
\r
2130 JOptionPane.showMessageDialog( this,
\r
2131 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
2132 "Unexpected Exception",
\r
2133 JOptionPane.ERROR_MESSAGE );
\r
2136 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
2137 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
2140 _mainpanel.setArrowCursor();
\r
2143 if ( ( phys != null ) && ( phys.length > 0 ) ) {
\r
2144 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
\r
2145 for( final Phylogeny phy : phys ) {
\r
2146 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
\r
2149 AptxUtil.addPhylogeniesToTabs( phys,
\r
2150 new File( url.getFile() ).getName(),
\r
2151 new File( url.getFile() ).toString(),
\r
2152 getConfiguration(),
\r
2154 _mainpanel.getControlPanel().showWhole();
\r
2157 activateSaveAllIfNeeded();
\r
2161 void setMsa( final Msa msa ) {
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2165 void setMsaFile( final File msa_file ) {
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2166 _msa_file = msa_file;
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2169 void setSeqs( final List<MolecularSequence> seqs ) {
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2173 void setSeqsFile( final File seqs_file ) {
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2174 _seqs_file = seqs_file;
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2177 public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
\r
2178 return new MainFrameApplication( phys, config );
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2181 public static MainFrame createInstance( final Phylogeny[] phys,
\r
2182 final Configuration config,
\r
2183 final String title,
\r
2184 final File current_dir ) {
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2185 return new MainFrameApplication( phys, config, title, current_dir );
\r
2188 static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
\r
2189 return new MainFrameApplication( phys, config, title );
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2192 static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
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2193 return new MainFrameApplication( phys, config_file_name, title );
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2196 static void warnIfNotPhyloXmlValidation( final Configuration c ) {
\r
2197 if ( !c.isValidatePhyloXmlAgainstSchema() ) {
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2199 .showMessageDialog( null,
\r
2201 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
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2204 JOptionPane.WARNING_MESSAGE );
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2207 } // MainFrameApplication.
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git://source.jalview.org / jalview.git / blob