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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60 import javax.swing.filechooser.FileFilter;
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61 import javax.swing.plaf.synth.SynthLookAndFeel;
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63 import org.forester.analysis.TaxonomyDataManager;
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64 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
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65 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
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66 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
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67 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
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68 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
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69 import org.forester.archaeopteryx.tools.InferenceManager;
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70 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
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71 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
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72 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
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73 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
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74 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
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75 import org.forester.archaeopteryx.webservices.WebservicesManager;
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76 import org.forester.io.parsers.FastaParser;
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77 import org.forester.io.parsers.GeneralMsaParser;
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78 import org.forester.io.parsers.PhylogenyParser;
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79 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
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80 import org.forester.io.parsers.nhx.NHXParser;
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81 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
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82 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
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83 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
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84 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
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85 import org.forester.io.parsers.tol.TolParser;
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86 import org.forester.io.parsers.util.ParserUtils;
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87 import org.forester.io.writers.PhylogenyWriter;
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88 import org.forester.io.writers.SequenceWriter;
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89 import org.forester.msa.Msa;
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90 import org.forester.msa.MsaFormatException;
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91 import org.forester.phylogeny.Phylogeny;
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92 import org.forester.phylogeny.PhylogenyMethods;
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93 import org.forester.phylogeny.PhylogenyNode;
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94 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
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95 import org.forester.phylogeny.data.Confidence;
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96 import org.forester.phylogeny.data.PhylogenyDataUtil;
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97 import org.forester.phylogeny.data.Sequence;
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98 import org.forester.phylogeny.data.Taxonomy;
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99 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
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100 import org.forester.phylogeny.factories.PhylogenyFactory;
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101 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
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102 import org.forester.sequence.MolecularSequence;
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103 import org.forester.util.BasicDescriptiveStatistics;
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104 import org.forester.util.BasicTable;
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105 import org.forester.util.BasicTableParser;
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106 import org.forester.util.DescriptiveStatistics;
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107 import org.forester.util.ForesterUtil;
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108 import org.forester.util.WindowsUtils;
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110 public final class MainFrameApplication extends MainFrame {
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112 static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
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113 static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
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114 private final static int FRAME_X_SIZE = 800;
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115 private final static int FRAME_Y_SIZE = 800;
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116 // Filters for the file-open dialog (classes defined in this file)
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117 private final static NHFilter nhfilter = new NHFilter();
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118 private final static NHXFilter nhxfilter = new NHXFilter();
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119 private final static XMLFilter xmlfilter = new XMLFilter();
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120 private final static TolFilter tolfilter = new TolFilter();
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121 private final static NexusFilter nexusfilter = new NexusFilter();
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122 private final static PdfFilter pdffilter = new PdfFilter();
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123 private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
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124 private final static MsaFileFilter msafilter = new MsaFileFilter();
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125 private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
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126 private final static DefaultFilter defaultfilter = new DefaultFilter();
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127 private static final long serialVersionUID = -799735726778865234L;
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128 private static final boolean PREPROCESS_TREES = false;
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129 private final JFileChooser _values_filechooser;
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130 private final JFileChooser _sequences_filechooser;
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131 private final JFileChooser _open_filechooser;
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132 private final JFileChooser _msa_filechooser;
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133 private final JFileChooser _seqs_pi_filechooser;
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134 private final JFileChooser _open_filechooser_for_species_tree;
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135 private final JFileChooser _save_filechooser;
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136 private final JFileChooser _writetopdf_filechooser;
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137 private final JFileChooser _writetographics_filechooser;
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138 // Application-only print menu items
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139 private JMenuItem _print_item;
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140 private JMenuItem _write_to_pdf_item;
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141 private JMenuItem _write_to_jpg_item;
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142 private JMenuItem _write_to_gif_item;
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143 private JMenuItem _write_to_tif_item;
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144 private JMenuItem _write_to_png_item;
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145 private JMenuItem _write_to_bmp_item;
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146 private JMenuItem _collapse_below_threshold;
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147 private JMenuItem _collapse_below_branch_length;
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148 private File _current_dir;
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149 private ButtonGroup _radio_group_1;
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150 private ButtonGroup _radio_group_2;
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152 double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
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153 double _min_not_collapse_bl = 0.001;
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154 // Phylogeny Inference menu
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155 private JMenu _inference_menu;
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156 private JMenuItem _inference_from_msa_item;
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157 private JMenuItem _inference_from_seqs_item;
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158 // Phylogeny Inference
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159 private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
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160 private Msa _msa = null;
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161 private File _msa_file = null;
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162 private List<MolecularSequence> _seqs = null;
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163 private File _seqs_file = null;
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164 JMenuItem _read_values_jmi;
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165 JMenuItem _read_seqs_jmi;
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167 private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
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168 _configuration = config;
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169 if ( _configuration == null ) {
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170 throw new IllegalArgumentException( "configuration is null" );
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172 setVisible( false );
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173 setOptions( Options.createInstance( _configuration ) );
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174 _mainpanel = new MainPanel( _configuration, this );
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175 _open_filechooser = null;
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176 _open_filechooser_for_species_tree = null;
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177 _save_filechooser = null;
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178 _writetopdf_filechooser = null;
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179 _writetographics_filechooser = null;
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180 _msa_filechooser = null;
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181 _seqs_pi_filechooser = null;
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182 _values_filechooser = null;
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183 _sequences_filechooser = null;
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184 _jmenubar = new JMenuBar();
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187 _contentpane = getContentPane();
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188 _contentpane.setLayout( new BorderLayout() );
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189 _contentpane.add( _mainpanel, BorderLayout.CENTER );
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191 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
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192 // The window listener
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193 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
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194 addWindowListener( new WindowAdapter() {
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197 public void windowClosing( final WindowEvent e ) {
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201 // setVisible( true );
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202 if ( ( phys != null ) && ( phys.length > 0 ) ) {
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203 AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
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205 getMainPanel().getControlPanel().showWholeAll();
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206 getMainPanel().getControlPanel().showWhole();
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208 //activateSaveAllIfNeeded();
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209 // ...and its children
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210 _contentpane.repaint();
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213 private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
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214 this( phys, config, title, null );
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217 private MainFrameApplication( final Phylogeny[] phys,
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218 final Configuration config,
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219 final String title,
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220 final File current_dir ) {
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222 _configuration = config;
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223 if ( _configuration == null ) {
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224 throw new IllegalArgumentException( "configuration is null" );
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227 boolean synth_exception = false;
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228 if ( Constants.__SYNTH_LF ) {
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230 final SynthLookAndFeel synth = new SynthLookAndFeel();
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231 synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
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232 MainFrameApplication.class );
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233 UIManager.setLookAndFeel( synth );
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235 catch ( final Exception ex ) {
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236 synth_exception = true;
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237 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
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238 "could not create synth look and feel: "
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239 + ex.getLocalizedMessage() );
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242 if ( !Constants.__SYNTH_LF || synth_exception ) {
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243 if ( _configuration.isUseNativeUI() ) {
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244 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
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247 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
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250 //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
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252 catch ( final UnsupportedLookAndFeelException e ) {
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253 AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
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255 catch ( final ClassNotFoundException e ) {
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256 AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
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258 catch ( final InstantiationException e ) {
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259 AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
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261 catch ( final IllegalAccessException e ) {
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262 AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
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264 if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
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265 setCurrentDir( current_dir );
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267 // hide until everything is ready
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268 setVisible( false );
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269 setOptions( Options.createInstance( _configuration ) );
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270 setInferenceManager( InferenceManager.createInstance( _configuration ) );
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271 setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
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272 // _textframe = null; #~~~~
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274 setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
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275 _mainpanel = new MainPanel( _configuration, this );
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276 // The file dialogs
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277 _open_filechooser = new JFileChooser();
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278 _open_filechooser.setCurrentDirectory( new File( "." ) );
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279 _open_filechooser.setMultiSelectionEnabled( false );
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280 _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );
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281 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
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282 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
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283 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
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284 _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );
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285 _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
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286 _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );
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287 _open_filechooser_for_species_tree = new JFileChooser();
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288 _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );
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289 _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
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290 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );
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291 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );
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292 _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );
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293 _save_filechooser = new JFileChooser();
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294 _save_filechooser.setCurrentDirectory( new File( "." ) );
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295 _save_filechooser.setMultiSelectionEnabled( false );
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296 _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
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297 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
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298 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
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299 _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
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300 _writetopdf_filechooser = new JFileChooser();
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301 _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );
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302 _writetographics_filechooser = new JFileChooser();
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303 _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );
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305 _msa_filechooser = new JFileChooser();
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306 _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
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307 _msa_filechooser.setCurrentDirectory( new File( "." ) );
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308 _msa_filechooser.setMultiSelectionEnabled( false );
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309 _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
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310 _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );
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312 _seqs_pi_filechooser = new JFileChooser();
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313 _seqs_pi_filechooser.setName( "Read Sequences File" );
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314 _seqs_pi_filechooser.setCurrentDirectory( new File( "." ) );
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315 _seqs_pi_filechooser.setMultiSelectionEnabled( false );
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316 _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );
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317 _seqs_pi_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
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319 _values_filechooser = new JFileChooser();
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320 _values_filechooser.setCurrentDirectory( new File( "." ) );
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321 _values_filechooser.setMultiSelectionEnabled( false );
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323 _sequences_filechooser = new JFileChooser();
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324 _sequences_filechooser.setCurrentDirectory( new File( "." ) );
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325 _sequences_filechooser.setMultiSelectionEnabled( false );
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326 // build the menu bar
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327 _jmenubar = new JMenuBar();
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328 if ( !_configuration.isUseNativeUI() ) {
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329 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
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332 if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
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333 buildPhylogeneticInferenceMenu();
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335 buildAnalysisMenu();
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338 buildFontSizeMenu();
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339 buildOptionsMenu();
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342 setJMenuBar( _jmenubar );
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343 _jmenubar.add( _help_jmenu );
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344 _contentpane = getContentPane();
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345 _contentpane.setLayout( new BorderLayout() );
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346 _contentpane.add( _mainpanel, BorderLayout.CENTER );
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348 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
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349 // addWindowFocusListener( new WindowAdapter() {
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352 // public void windowGainedFocus( WindowEvent e ) {
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353 // requestFocusInWindow();
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356 // The window listener
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357 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
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358 addWindowListener( new WindowAdapter() {
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361 public void windowClosing( final WindowEvent e ) {
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362 if ( isUnsavedDataPresent() ) {
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363 final int r = JOptionPane.showConfirmDialog( null,
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364 "Exit despite potentially unsaved changes?",
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366 JOptionPane.YES_NO_OPTION );
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367 if ( r != JOptionPane.YES_OPTION ) {
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372 final int r = JOptionPane.showConfirmDialog( null,
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373 "Exit Archaeopteryx?",
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375 JOptionPane.YES_NO_OPTION );
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376 if ( r != JOptionPane.YES_OPTION ) {
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383 // The component listener
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384 addComponentListener( new ComponentAdapter() {
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387 public void componentResized( final ComponentEvent e ) {
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388 if ( _mainpanel.getCurrentTreePanel() != null ) {
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389 _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
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391 _mainpanel.getCurrentTreePanel()
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396 requestFocusInWindow();
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397 // addKeyListener( this );
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398 setVisible( true );
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399 if ( ( phys != null ) && ( phys.length > 0 ) ) {
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400 AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
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402 getMainPanel().getControlPanel().showWholeAll();
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403 getMainPanel().getControlPanel().showWhole();
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405 activateSaveAllIfNeeded();
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406 // ...and its children
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407 _contentpane.repaint();
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411 private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
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412 // Reads the config file (false, false => not url, not applet):
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413 this( phys, new Configuration( config_file, false, false, true ), title );
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417 public void actionPerformed( final ActionEvent e ) {
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419 super.actionPerformed( e );
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420 final Object o = e.getSource();
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421 // Handle app-specific actions here:
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422 if ( o == _open_item ) {
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423 readPhylogeniesFromFile();
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425 if ( o == _open_url_item ) {
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426 readPhylogeniesFromURL();
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428 else if ( o == _save_item ) {
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429 writeToFile( _mainpanel.getCurrentPhylogeny() );
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430 // If subtree currently displayed, save it, instead of complete
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433 else if ( o == _new_item ) {
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436 else if ( o == _save_all_item ) {
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439 else if ( o == _close_item ) {
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440 closeCurrentPane();
\r
442 else if ( o == _write_to_pdf_item ) {
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443 writeToPdf( _mainpanel.getCurrentPhylogeny() );
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445 else if ( o == _write_to_jpg_item ) {
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446 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
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448 else if ( o == _write_to_png_item ) {
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449 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
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451 else if ( o == _write_to_gif_item ) {
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452 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
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454 else if ( o == _write_to_tif_item ) {
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455 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
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457 else if ( o == _write_to_bmp_item ) {
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458 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
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460 else if ( o == _print_item ) {
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463 else if ( o == _load_species_tree_item ) {
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464 readSpeciesTreeFromFile();
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466 else if ( o == _lineage_inference ) {
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467 if ( isSubtreeDisplayed() ) {
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468 JOptionPane.showMessageDialog( this,
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469 "Subtree is shown.",
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470 "Cannot infer ancestral taxonomies",
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471 JOptionPane.ERROR_MESSAGE );
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474 executeLineageInference();
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476 else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
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477 if ( isSubtreeDisplayed() ) {
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480 obtainDetailedTaxonomicInformation();
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482 else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
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483 if ( isSubtreeDisplayed() ) {
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486 obtainDetailedTaxonomicInformationDelete();
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488 else if ( o == _obtain_seq_information_jmi ) {
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489 obtainSequenceInformation();
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491 else if ( o == _read_values_jmi ) {
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492 if ( isSubtreeDisplayed() ) {
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495 addExpressionValuesFromFile();
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497 else if ( o == _read_seqs_jmi ) {
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498 if ( isSubtreeDisplayed() ) {
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501 addSequencesFromFile();
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503 else if ( o == _move_node_names_to_tax_sn_jmi ) {
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504 moveNodeNamesToTaxSn();
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506 else if ( o == _move_node_names_to_seq_names_jmi ) {
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507 moveNodeNamesToSeqNames();
\r
509 else if ( o == _extract_tax_code_from_node_names_jmi ) {
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510 extractTaxDataFromNodeNames();
\r
512 else if ( o == _graphics_export_visible_only_cbmi ) {
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513 updateOptions( getOptions() );
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515 else if ( o == _antialias_print_cbmi ) {
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516 updateOptions( getOptions() );
\r
518 else if ( o == _print_black_and_white_cbmi ) {
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519 updateOptions( getOptions() );
\r
521 else if ( o == _print_using_actual_size_cbmi ) {
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522 updateOptions( getOptions() );
\r
524 else if ( o == _graphics_export_using_actual_size_cbmi ) {
\r
525 updateOptions( getOptions() );
\r
527 else if ( o == _print_size_mi ) {
\r
530 else if ( o == _choose_pdf_width_mi ) {
\r
533 else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
\r
534 updateOptions( getOptions() );
\r
536 else if ( o == _replace_underscores_cbmi ) {
\r
537 if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
\r
538 _extract_taxonomy_no_rbmi.setSelected( true );
\r
540 updateOptions( getOptions() );
\r
542 else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {
\r
543 updateOptions( getOptions() );
\r
545 else if ( o == _collapse_below_threshold ) {
\r
546 if ( isSubtreeDisplayed() ) {
\r
549 collapseBelowThreshold();
\r
551 else if ( o == _collapse_below_branch_length ) {
\r
552 if ( isSubtreeDisplayed() ) {
\r
555 collapseBelowBranchLengthThreshold();
\r
557 else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )
\r
558 || ( o == _extract_taxonomy_agressive_rbmi ) ) {
\r
559 if ( _replace_underscores_cbmi != null ) {
\r
560 _replace_underscores_cbmi.setSelected( false );
\r
562 updateOptions( getOptions() );
\r
564 else if ( o == _extract_taxonomy_no_rbmi ) {
\r
565 updateOptions( getOptions() );
\r
567 else if ( o == _inference_from_msa_item ) {
\r
568 executePhyleneticInference( false );
\r
570 else if ( o == _inference_from_seqs_item ) {
\r
571 executePhyleneticInference( true );
\r
573 _contentpane.repaint();
\r
575 catch ( final Exception ex ) {
\r
576 AptxUtil.unexpectedException( ex );
\r
578 catch ( final Error err ) {
\r
579 AptxUtil.unexpectedError( err );
\r
583 public void end() {
\r
584 _mainpanel.terminate();
\r
585 _contentpane.removeAll();
\r
586 setVisible( false );
\r
591 public MainPanel getMainPanel() {
\r
595 public Msa getMsa() {
\r
599 public File getMsaFile() {
\r
603 public List<MolecularSequence> getSeqs() {
\r
607 public File getSeqsFile() {
\r
611 public void readMsaFromFile() {
\r
612 // Set an initial directory if none set yet
\r
613 final File my_dir = getCurrentDir();
\r
614 _msa_filechooser.setMultiSelectionEnabled( false );
\r
615 // Open file-open dialog and set current directory
\r
616 if ( my_dir != null ) {
\r
617 _msa_filechooser.setCurrentDirectory( my_dir );
\r
619 final int result = _msa_filechooser.showOpenDialog( _contentpane );
\r
620 // All done: get the msa
\r
621 final File file = _msa_filechooser.getSelectedFile();
\r
622 setCurrentDir( _msa_filechooser.getCurrentDirectory() );
\r
623 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
624 setMsaFile( null );
\r
628 final InputStream is = new FileInputStream( file );
\r
629 if ( FastaParser.isLikelyFasta( file ) ) {
\r
630 msa = FastaParser.parseMsa( is );
\r
633 msa = GeneralMsaParser.parse( is );
\r
636 catch ( final MsaFormatException e ) {
\r
638 JOptionPane.showMessageDialog( this,
\r
639 e.getLocalizedMessage(),
\r
640 "Multiple sequence alignment format error",
\r
641 JOptionPane.ERROR_MESSAGE );
\r
644 catch ( final IOException e ) {
\r
646 JOptionPane.showMessageDialog( this,
\r
647 e.getLocalizedMessage(),
\r
648 "Failed to read multiple sequence alignment",
\r
649 JOptionPane.ERROR_MESSAGE );
\r
652 catch ( final IllegalArgumentException e ) {
\r
654 JOptionPane.showMessageDialog( this,
\r
655 e.getLocalizedMessage(),
\r
656 "Unexpected error during reading of multiple sequence alignment",
\r
657 JOptionPane.ERROR_MESSAGE );
\r
660 catch ( final Exception e ) {
\r
662 e.printStackTrace();
\r
663 JOptionPane.showMessageDialog( this,
\r
664 e.getLocalizedMessage(),
\r
665 "Unexpected error during reading of multiple sequence alignment",
\r
666 JOptionPane.ERROR_MESSAGE );
\r
669 if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
\r
670 JOptionPane.showMessageDialog( this,
\r
671 "Multiple sequence alignment is empty",
\r
672 "Illegal Multiple Sequence Alignment",
\r
673 JOptionPane.ERROR_MESSAGE );
\r
676 if ( msa.getNumberOfSequences() < 4 ) {
\r
677 JOptionPane.showMessageDialog( this,
\r
678 "Multiple sequence alignment needs to contain at least 3 sequences",
\r
679 "Illegal multiple sequence alignment",
\r
680 JOptionPane.ERROR_MESSAGE );
\r
683 if ( msa.getLength() < 2 ) {
\r
684 JOptionPane.showMessageDialog( this,
\r
685 "Multiple sequence alignment needs to contain at least 2 residues",
\r
686 "Illegal multiple sequence alignment",
\r
687 JOptionPane.ERROR_MESSAGE );
\r
691 setMsaFile( _msa_filechooser.getSelectedFile() );
\r
696 public void readSeqsFromFileforPI() {
\r
697 // Set an initial directory if none set yet
\r
698 final File my_dir = getCurrentDir();
\r
699 _seqs_pi_filechooser.setMultiSelectionEnabled( false );
\r
700 // Open file-open dialog and set current directory
\r
701 if ( my_dir != null ) {
\r
702 _seqs_pi_filechooser.setCurrentDirectory( my_dir );
\r
704 final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );
\r
705 // All done: get the seqs
\r
706 final File file = _seqs_pi_filechooser.getSelectedFile();
\r
707 setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );
\r
708 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
709 setSeqsFile( null );
\r
711 List<MolecularSequence> seqs = null;
\r
713 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
\r
714 seqs = FastaParser.parse( new FileInputStream( file ) );
\r
715 for( final MolecularSequence seq : seqs ) {
\r
716 System.out.println( SequenceWriter.toFasta( seq, 60 ) );
\r
723 catch ( final MsaFormatException e ) {
\r
725 JOptionPane.showMessageDialog( this,
\r
726 e.getLocalizedMessage(),
\r
727 "Multiple sequence file format error",
\r
728 JOptionPane.ERROR_MESSAGE );
\r
731 catch ( final IOException e ) {
\r
733 JOptionPane.showMessageDialog( this,
\r
734 e.getLocalizedMessage(),
\r
735 "Failed to read multiple sequence file",
\r
736 JOptionPane.ERROR_MESSAGE );
\r
739 catch ( final IllegalArgumentException e ) {
\r
741 JOptionPane.showMessageDialog( this,
\r
742 e.getLocalizedMessage(),
\r
743 "Unexpected error during reading of multiple sequence file",
\r
744 JOptionPane.ERROR_MESSAGE );
\r
747 catch ( final Exception e ) {
\r
749 e.printStackTrace();
\r
750 JOptionPane.showMessageDialog( this,
\r
751 e.getLocalizedMessage(),
\r
752 "Unexpected error during reading of multiple sequence file",
\r
753 JOptionPane.ERROR_MESSAGE );
\r
756 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
\r
757 JOptionPane.showMessageDialog( this,
\r
758 "Multiple sequence file is empty",
\r
759 "Illegal multiple sequence file",
\r
760 JOptionPane.ERROR_MESSAGE );
\r
763 if ( seqs.size() < 4 ) {
\r
764 JOptionPane.showMessageDialog( this,
\r
765 "Multiple sequence file needs to contain at least 3 sequences",
\r
766 "Illegal multiple sequence file",
\r
767 JOptionPane.ERROR_MESSAGE );
\r
770 // if ( msa.getLength() < 2 ) {
\r
771 // JOptionPane.showMessageDialog( this,
\r
772 // "Multiple sequence alignment needs to contain at least 2 residues",
\r
773 // "Illegal multiple sequence file",
\r
774 // JOptionPane.ERROR_MESSAGE );
\r
778 setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
\r
783 void buildAnalysisMenu() {
\r
784 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
\r
785 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
\r
786 _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
\r
787 _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
\r
788 customizeJMenuItem( _gsdi_item );
\r
789 customizeJMenuItem( _gsdir_item );
\r
790 customizeJMenuItem( _load_species_tree_item );
\r
791 _analysis_menu.addSeparator();
\r
792 _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
\r
793 customizeJMenuItem( _lineage_inference );
\r
794 _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
\r
795 _jmenubar.add( _analysis_menu );
\r
799 void buildFileMenu() {
\r
800 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
\r
801 _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
\r
802 _file_jmenu.addSeparator();
\r
803 _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
\r
804 _file_jmenu.addSeparator();
\r
805 final WebservicesManager webservices_manager = WebservicesManager.getInstance();
\r
806 _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
\r
807 .getAvailablePhylogeniesWebserviceClients().size() ];
\r
808 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
\r
809 final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
\r
810 _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
\r
811 _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
\r
813 if ( getConfiguration().isEditable() ) {
\r
814 _file_jmenu.addSeparator();
\r
815 _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
\r
816 _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
\r
818 _file_jmenu.addSeparator();
\r
819 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
\r
820 _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
\r
821 _save_all_item.setToolTipText( "Write all phylogenies to one file." );
\r
822 _save_all_item.setEnabled( false );
\r
823 _file_jmenu.addSeparator();
\r
824 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
\r
825 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
\r
826 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
\r
828 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
\r
829 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
\r
830 if ( AptxUtil.canWriteFormat( "gif" ) ) {
\r
831 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
\r
833 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
\r
834 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
\r
836 _file_jmenu.addSeparator();
\r
837 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
\r
838 _file_jmenu.addSeparator();
\r
839 _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
\r
840 _close_item.setToolTipText( "To close the current pane." );
\r
841 _close_item.setEnabled( true );
\r
842 _file_jmenu.addSeparator();
\r
843 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
\r
844 customizeJMenuItem( _open_item );
\r
846 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
\r
847 customizeJMenuItem( _open_url_item );
\r
848 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
\r
849 customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
\r
851 customizeJMenuItem( _save_item );
\r
852 if ( getConfiguration().isEditable() ) {
\r
853 customizeJMenuItem( _new_item );
\r
855 customizeJMenuItem( _close_item );
\r
856 customizeJMenuItem( _save_all_item );
\r
857 customizeJMenuItem( _write_to_pdf_item );
\r
858 customizeJMenuItem( _write_to_png_item );
\r
859 customizeJMenuItem( _write_to_jpg_item );
\r
860 customizeJMenuItem( _write_to_gif_item );
\r
861 customizeJMenuItem( _write_to_tif_item );
\r
862 customizeJMenuItem( _write_to_bmp_item );
\r
863 customizeJMenuItem( _print_item );
\r
864 customizeJMenuItem( _exit_item );
\r
865 _jmenubar.add( _file_jmenu );
\r
868 void buildOptionsMenu() {
\r
869 _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
\r
870 _options_jmenu.addChangeListener( new ChangeListener() {
\r
873 public void stateChanged( final ChangeEvent e ) {
\r
874 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
\r
875 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
\r
877 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
\r
878 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
\r
879 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
\r
880 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
\r
881 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
\r
882 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
\r
883 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
\r
884 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
\r
886 getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
\r
887 getMainPanel().getControlPanel().setVisibilityOfX();
\r
889 catch ( final Exception ignore ) {
\r
890 // do nothing, not important.
\r
894 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
\r
896 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
\r
897 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
\r
898 _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
\r
899 _radio_group_1 = new ButtonGroup();
\r
900 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
\r
901 _radio_group_1.add( _uniform_cladograms_rbmi );
\r
902 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
\r
903 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
\r
904 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
\r
906 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
\r
908 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
\r
910 .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
\r
911 _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
\r
912 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
\r
913 _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
\r
914 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
\r
916 _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
\r
917 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
\r
918 _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
\r
919 _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
\r
920 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
\r
921 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
\r
922 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
\r
923 _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
\r
924 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
\r
925 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
\r
926 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
\r
927 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
\r
928 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
\r
929 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
\r
930 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
\r
931 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
\r
932 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
\r
933 _options_jmenu.addSeparator();
\r
934 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
\r
935 _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
\r
936 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
\r
937 _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
\r
938 _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
\r
939 _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
\r
940 _options_jmenu.addSeparator();
\r
941 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
\r
942 getConfiguration() ) );
\r
943 _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
\r
944 _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
\r
946 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
\r
948 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
\r
950 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
\r
951 _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
\r
952 _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
\r
953 _options_jmenu.addSeparator();
\r
954 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
\r
956 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
\r
957 _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
\r
959 .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
\r
960 _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
\r
962 .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
\r
964 .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
\r
966 .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
\r
967 _extract_taxonomy_pfam_strict_rbmi
\r
968 .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
969 _extract_taxonomy_pfam_relaxed_rbmi
\r
970 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
\r
971 _extract_taxonomy_agressive_rbmi
\r
972 .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
973 _radio_group_2 = new ButtonGroup();
\r
974 _radio_group_2.add( _extract_taxonomy_no_rbmi );
\r
975 _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
\r
976 _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );
\r
977 _radio_group_2.add( _extract_taxonomy_agressive_rbmi );
\r
978 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
\r
980 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
\r
981 _use_brackets_for_conf_in_nh_export_cbmi
\r
982 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
\r
984 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
\r
985 customizeJMenuItem( _choose_font_mi );
\r
986 customizeJMenuItem( _choose_minimal_confidence_mi );
\r
987 customizeJMenuItem( _switch_colors_mi );
\r
988 customizeJMenuItem( _print_size_mi );
\r
989 customizeJMenuItem( _choose_pdf_width_mi );
\r
990 customizeJMenuItem( _overview_placment_mi );
\r
991 customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
\r
992 .isShowDefaultNodeShapesExternal() );
\r
993 customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
\r
994 .isShowDefaultNodeShapesInternal() );
\r
995 customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
\r
996 .isShowDefaultNodeShapesForMarkedNodes() );
\r
997 customizeJMenuItem( _cycle_node_shape_mi );
\r
998 customizeJMenuItem( _cycle_node_fill_mi );
\r
999 customizeJMenuItem( _choose_node_size_mi );
\r
1000 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
\r
1001 customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
\r
1002 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
\r
1003 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
\r
1004 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
\r
1005 customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
\r
1006 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
\r
1007 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
\r
1008 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
\r
1009 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
\r
1010 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
\r
1011 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
\r
1012 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
\r
1013 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
\r
1014 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
\r
1015 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
\r
1016 customizeCheckBoxMenuItem( _label_direction_cbmi,
\r
1017 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
\r
1018 customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
\r
1019 customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
\r
1020 customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
\r
1021 .isInternalNumberAreConfidenceForNhParsing() );
\r
1022 customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
\r
1023 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
\r
1024 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
\r
1025 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
\r
1026 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,
\r
1027 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
\r
1028 customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
\r
1029 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1030 customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
\r
1031 customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()
\r
1032 .isReplaceUnderscoresInNhParsing() );
\r
1033 customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
\r
1034 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
\r
1035 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
\r
1036 customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
\r
1037 customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
\r
1038 customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
\r
1039 .isGraphicsExportUsingActualSize() );
\r
1040 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
\r
1041 customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
\r
1042 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
\r
1043 customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
\r
1044 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
\r
1045 customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
\r
1046 customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
\r
1047 _jmenubar.add( _options_jmenu );
\r
1050 void buildPhylogeneticInferenceMenu() {
\r
1051 final InferenceManager im = getInferenceManager();
\r
1052 _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
\r
1053 _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
\r
1054 customizeJMenuItem( _inference_from_msa_item );
\r
1055 _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
\r
1056 if ( im.canDoMsa() ) {
\r
1057 _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
\r
1058 customizeJMenuItem( _inference_from_seqs_item );
\r
1059 _inference_from_seqs_item
\r
1060 .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
\r
1064 .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
\r
1065 customizeJMenuItem( _inference_from_seqs_item );
\r
1066 _inference_from_seqs_item.setEnabled( false );
\r
1068 _jmenubar.add( _inference_menu );
\r
1071 void buildToolsMenu() {
\r
1072 _tools_menu = createMenu( "Tools", getConfiguration() );
\r
1073 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
\r
1074 customizeJMenuItem( _confcolor_item );
\r
1075 _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
\r
1076 customizeJMenuItem( _color_rank_jmi );
\r
1077 _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
\r
1078 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
\r
1079 customizeJMenuItem( _taxcolor_item );
\r
1080 _tools_menu.addSeparator();
\r
1081 _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
\r
1082 _remove_visual_styles_item
\r
1083 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );
\r
1084 customizeJMenuItem( _remove_visual_styles_item );
\r
1085 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
\r
1086 _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );
\r
1087 customizeJMenuItem( _remove_branch_color_item );
\r
1088 _tools_menu.addSeparator();
\r
1089 _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
\r
1090 customizeJMenuItem( _annotate_item );
\r
1091 _tools_menu.addSeparator();
\r
1092 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
\r
1093 customizeJMenuItem( _midpoint_root_item );
\r
1094 _tools_menu.addSeparator();
\r
1095 _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );
\r
1096 _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );
\r
1097 customizeJMenuItem( _delete_selected_nodes_item );
\r
1098 _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );
\r
1099 _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );
\r
1100 customizeJMenuItem( _delete_not_selected_nodes_item );
\r
1101 _tools_menu.addSeparator();
\r
1102 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
\r
1103 customizeJMenuItem( _collapse_species_specific_subtrees );
\r
1104 _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );
\r
1106 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
\r
1107 customizeJMenuItem( _collapse_below_threshold );
\r
1108 _collapse_below_threshold
\r
1109 .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
1112 .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );
\r
1113 customizeJMenuItem( _collapse_below_branch_length );
\r
1114 _collapse_below_branch_length
\r
1115 .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );
\r
1117 _tools_menu.addSeparator();
\r
1119 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
\r
1120 customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
\r
1121 _extract_tax_code_from_node_names_jmi
\r
1122 .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
1124 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
\r
1125 customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
\r
1126 _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
\r
1127 _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
\r
1128 customizeJMenuItem( _move_node_names_to_seq_names_jmi );
\r
1129 _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
\r
1130 _tools_menu.addSeparator();
\r
1131 _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
\r
1132 customizeJMenuItem( _obtain_seq_information_jmi );
\r
1133 _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
\r
1135 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
\r
1136 customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
\r
1137 _obtain_detailed_taxonomic_information_jmi
\r
1138 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
\r
1140 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
\r
1141 customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
\r
1142 _obtain_detailed_taxonomic_information_deleting_jmi
\r
1143 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
\r
1144 _tools_menu.addSeparator();
\r
1145 _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
\r
1146 customizeJMenuItem( _read_values_jmi );
\r
1147 _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
\r
1148 _jmenubar.add( _tools_menu );
\r
1149 _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
\r
1150 customizeJMenuItem( _read_seqs_jmi );
\r
1152 .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
\r
1153 _jmenubar.add( _tools_menu );
\r
1158 if ( isUnsavedDataPresent() ) {
\r
1159 final int r = JOptionPane.showConfirmDialog( this,
\r
1160 "Exit despite potentially unsaved changes?",
\r
1162 JOptionPane.YES_NO_OPTION );
\r
1163 if ( r != JOptionPane.YES_OPTION ) {
\r
1170 void executeLineageInference() {
\r
1171 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
\r
1174 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
\r
1175 JOptionPane.showMessageDialog( this,
\r
1176 "Phylogeny is not rooted.",
\r
1177 "Cannot infer ancestral taxonomies",
\r
1178 JOptionPane.ERROR_MESSAGE );
\r
1181 final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
\r
1182 _mainpanel.getCurrentTreePanel(),
\r
1183 _mainpanel.getCurrentPhylogeny()
\r
1185 new Thread( inferrer ).start();
\r
1189 removeAllTextFrames();
\r
1190 _mainpanel.terminate();
\r
1191 _contentpane.removeAll();
\r
1192 setVisible( false );
\r
1197 void readPhylogeniesFromURL() {
\r
1199 Phylogeny[] phys = null;
\r
1200 final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
\r
1201 final String url_string = JOptionPane.showInputDialog( this,
\r
1203 "Use URL/webservice to obtain a phylogeny",
\r
1204 JOptionPane.QUESTION_MESSAGE );
\r
1205 boolean nhx_or_nexus = false;
\r
1206 if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
\r
1208 url = new URL( url_string );
\r
1209 PhylogenyParser parser = null;
\r
1210 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
\r
1211 parser = new TolParser();
\r
1214 parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
\r
1215 .isValidatePhyloXmlAgainstSchema() );
\r
1217 if ( parser instanceof NexusPhylogeniesParser ) {
\r
1218 nhx_or_nexus = true;
\r
1220 else if ( parser instanceof NHXParser ) {
\r
1221 nhx_or_nexus = true;
\r
1223 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1224 _mainpanel.getCurrentTreePanel().setWaitCursor();
\r
1227 _mainpanel.setWaitCursor();
\r
1229 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
\r
1230 phys = factory.create( url.openStream(), parser );
\r
1232 catch ( final MalformedURLException e ) {
\r
1233 JOptionPane.showMessageDialog( this,
\r
1234 "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
\r
1236 JOptionPane.ERROR_MESSAGE );
\r
1238 catch ( final IOException e ) {
\r
1239 JOptionPane.showMessageDialog( this,
\r
1240 "Could not read from " + url + "\n"
\r
1241 + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
1242 "Failed to read URL",
\r
1243 JOptionPane.ERROR_MESSAGE );
\r
1245 catch ( final Exception e ) {
\r
1246 JOptionPane.showMessageDialog( this,
\r
1247 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
1248 "Unexpected Exception",
\r
1249 JOptionPane.ERROR_MESSAGE );
\r
1252 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1253 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
1256 _mainpanel.setArrowCursor();
\r
1259 if ( ( phys != null ) && ( phys.length > 0 ) ) {
\r
1260 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
\r
1261 for( final Phylogeny phy : phys ) {
\r
1262 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
\r
1265 AptxUtil.addPhylogeniesToTabs( phys,
\r
1266 new File( url.getFile() ).getName(),
\r
1267 new File( url.getFile() ).toString(),
\r
1268 getConfiguration(),
\r
1270 _mainpanel.getControlPanel().showWhole();
\r
1273 activateSaveAllIfNeeded();
\r
1277 void setMsa( final Msa msa ) {
\r
1281 void setMsaFile( final File msa_file ) {
\r
1282 _msa_file = msa_file;
\r
1285 void setSeqs( final List<MolecularSequence> seqs ) {
\r
1289 void setSeqsFile( final File seqs_file ) {
\r
1290 _seqs_file = seqs_file;
\r
1293 void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
\r
1294 _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
\r
1295 _mainpanel.getCurrentTreePanel().getHeight() );
\r
1296 String file_written_to = "";
\r
1297 boolean error = false;
\r
1299 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
\r
1300 _mainpanel.getCurrentTreePanel().getWidth(),
\r
1301 _mainpanel.getCurrentTreePanel().getHeight(),
\r
1302 _mainpanel.getCurrentTreePanel(),
\r
1303 _mainpanel.getControlPanel(),
\r
1307 catch ( final IOException e ) {
\r
1309 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
\r
1312 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
\r
1313 JOptionPane.showMessageDialog( this,
\r
1314 "Wrote image to: " + file_written_to,
\r
1315 "Graphics Export",
\r
1316 JOptionPane.INFORMATION_MESSAGE );
\r
1319 JOptionPane.showMessageDialog( this,
\r
1320 "There was an unknown problem when attempting to write to an image file: \""
\r
1321 + file_name + "\"",
\r
1323 JOptionPane.ERROR_MESSAGE );
\r
1326 _contentpane.repaint();
\r
1329 private void addExpressionValuesFromFile() {
\r
1330 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
\r
1331 JOptionPane.showMessageDialog( this,
\r
1332 "Need to load evolutionary tree first",
\r
1333 "Can Not Read Expression Values",
\r
1334 JOptionPane.WARNING_MESSAGE );
\r
1337 final File my_dir = getCurrentDir();
\r
1338 if ( my_dir != null ) {
\r
1339 _values_filechooser.setCurrentDirectory( my_dir );
\r
1341 final int result = _values_filechooser.showOpenDialog( _contentpane );
\r
1342 final File file = _values_filechooser.getSelectedFile();
\r
1343 if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
1344 BasicTable<String> t = null;
\r
1346 t = BasicTableParser.parse( file, '\t' );
\r
1347 if ( t.getNumberOfColumns() < 2 ) {
\r
1348 t = BasicTableParser.parse( file, ',' );
\r
1350 if ( t.getNumberOfColumns() < 2 ) {
\r
1351 t = BasicTableParser.parse( file, ' ' );
\r
1354 catch ( final IOException e ) {
\r
1355 JOptionPane.showMessageDialog( this,
\r
1357 "Could Not Read Expression Value Table",
\r
1358 JOptionPane.ERROR_MESSAGE );
\r
1361 if ( t.getNumberOfColumns() < 2 ) {
\r
1362 JOptionPane.showMessageDialog( this,
\r
1363 "Table contains " + t.getNumberOfColumns() + " column(s)",
\r
1364 "Problem with Expression Value Table",
\r
1365 JOptionPane.ERROR_MESSAGE );
\r
1368 if ( t.getNumberOfRows() < 1 ) {
\r
1369 JOptionPane.showMessageDialog( this,
\r
1370 "Table contains zero rows",
\r
1371 "Problem with Expression Value Table",
\r
1372 JOptionPane.ERROR_MESSAGE );
\r
1375 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1376 if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
\r
1377 JOptionPane.showMessageDialog( this,
\r
1378 "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
\r
1379 + phy.getNumberOfExternalNodes() + " external nodes",
\r
1381 JOptionPane.WARNING_MESSAGE );
\r
1383 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
\r
1384 int not_found = 0;
\r
1385 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
\r
1386 final PhylogenyNode node = iter.next();
\r
1387 final String node_name = node.getName();
\r
1388 if ( !ForesterUtil.isEmpty( node_name ) ) {
\r
1391 row = t.findRow( node_name );
\r
1393 catch ( final IllegalArgumentException e ) {
\r
1395 .showMessageDialog( this,
\r
1397 "Error Mapping Node Identifiers to Expression Value Identifiers",
\r
1398 JOptionPane.ERROR_MESSAGE );
\r
1402 if ( node.isExternal() ) {
\r
1407 final List<Double> l = new ArrayList<Double>();
\r
1408 for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
\r
1411 d = Double.parseDouble( t.getValueAsString( col, row ) );
\r
1413 catch ( final NumberFormatException e ) {
\r
1414 JOptionPane.showMessageDialog( this,
\r
1415 "Could not parse \"" + t.getValueAsString( col, row )
\r
1416 + "\" into a decimal value",
\r
1417 "Issue with Expression Value Table",
\r
1418 JOptionPane.ERROR_MESSAGE );
\r
1421 stats.addValue( d );
\r
1424 if ( !l.isEmpty() ) {
\r
1425 if ( node.getNodeData().getProperties() != null ) {
\r
1426 node.getNodeData().getProperties()
\r
1427 .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
\r
1429 node.getNodeData().setVector( l );
\r
1433 if ( not_found > 0 ) {
\r
1434 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
\r
1435 + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
\r
1437 getCurrentTreePanel().setStatisticsForExpressionValues( stats );
\r
1441 private void addSequencesFromFile() {
\r
1442 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
\r
1443 JOptionPane.showMessageDialog( this,
\r
1444 "Need to load evolutionary tree first",
\r
1445 "Can Not Read Sequences",
\r
1446 JOptionPane.WARNING_MESSAGE );
\r
1449 final File my_dir = getCurrentDir();
\r
1450 if ( my_dir != null ) {
\r
1451 _sequences_filechooser.setCurrentDirectory( my_dir );
\r
1453 final int result = _sequences_filechooser.showOpenDialog( _contentpane );
\r
1454 final File file = _sequences_filechooser.getSelectedFile();
\r
1455 List<MolecularSequence> seqs = null;
\r
1456 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
1458 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
\r
1459 seqs = FastaParser.parse( new FileInputStream( file ) );
\r
1462 JOptionPane.showMessageDialog( this,
\r
1463 "Format does not appear to be Fasta",
\r
1464 "Multiple sequence file format error",
\r
1465 JOptionPane.ERROR_MESSAGE );
\r
1469 catch ( final MsaFormatException e ) {
\r
1471 JOptionPane.showMessageDialog( this,
\r
1472 e.getLocalizedMessage(),
\r
1473 "Multiple sequence file format error",
\r
1474 JOptionPane.ERROR_MESSAGE );
\r
1477 catch ( final IOException e ) {
\r
1479 JOptionPane.showMessageDialog( this,
\r
1480 e.getLocalizedMessage(),
\r
1481 "Failed to read multiple sequence file",
\r
1482 JOptionPane.ERROR_MESSAGE );
\r
1485 catch ( final Exception e ) {
\r
1487 e.printStackTrace();
\r
1488 JOptionPane.showMessageDialog( this,
\r
1489 e.getLocalizedMessage(),
\r
1490 "Unexpected error during reading of multiple sequence file",
\r
1491 JOptionPane.ERROR_MESSAGE );
\r
1494 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
\r
1495 JOptionPane.showMessageDialog( this,
\r
1496 "Multiple sequence file is empty",
\r
1497 "Empty multiple sequence file",
\r
1498 JOptionPane.ERROR_MESSAGE );
\r
1503 if ( seqs != null ) {
\r
1504 for( final MolecularSequence seq : seqs ) {
\r
1505 System.out.println( seq.getIdentifier() );
\r
1507 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1508 int total_counter = 0;
\r
1509 int attached_counter = 0;
\r
1510 for( final MolecularSequence seq : seqs ) {
\r
1512 final String seq_name = seq.getIdentifier();
\r
1513 if ( !ForesterUtil.isEmpty( seq_name ) ) {
\r
1514 List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
\r
1515 if ( nodes.isEmpty() ) {
\r
1516 nodes = phy.getNodesViaSequenceSymbol( seq_name );
\r
1518 if ( nodes.isEmpty() ) {
\r
1519 nodes = phy.getNodesViaGeneName( seq_name );
\r
1521 if ( nodes.isEmpty() ) {
\r
1522 nodes = phy.getNodes( seq_name );
\r
1524 if ( nodes.size() > 1 ) {
\r
1525 JOptionPane.showMessageDialog( this,
\r
1526 "Sequence name \"" + seq_name + "\" is not unique",
\r
1527 "Sequence name not unique",
\r
1528 JOptionPane.ERROR_MESSAGE );
\r
1532 final String[] a = seq_name.split( "\\s" );
\r
1533 if ( nodes.isEmpty() && ( a.length > 1 ) ) {
\r
1534 final String seq_name_split = a[ 0 ];
\r
1535 nodes = phy.getNodesViaSequenceName( seq_name_split );
\r
1536 if ( nodes.isEmpty() ) {
\r
1537 nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
\r
1539 if ( nodes.isEmpty() ) {
\r
1540 nodes = phy.getNodes( seq_name_split );
\r
1542 if ( nodes.size() > 1 ) {
\r
1543 JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
\r
1544 + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
\r
1549 if ( nodes.size() == 1 ) {
\r
1550 ++attached_counter;
\r
1551 final PhylogenyNode n = nodes.get( 0 );
\r
1552 if ( !n.getNodeData().isHasSequence() ) {
\r
1553 n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
\r
1555 n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
\r
1556 if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
\r
1557 n.getNodeData().getSequence().setName( seq_name );
\r
1562 if ( attached_counter > 0 ) {
\r
1563 int ext_nodes = 0;
\r
1564 int ext_nodes_with_seq = 0;
\r
1565 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
\r
1567 final PhylogenyNode n = iter.next();
\r
1568 if ( n.getNodeData().isHasSequence()
\r
1569 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
\r
1570 ++ext_nodes_with_seq;
\r
1574 if ( ext_nodes == ext_nodes_with_seq ) {
\r
1575 s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
\r
1578 s = ext_nodes_with_seq + " out of " + ext_nodes
\r
1579 + " external nodes now have a molecular sequence attached to them.";
\r
1581 if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
\r
1582 JOptionPane.showMessageDialog( this,
\r
1583 "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
\r
1584 "All sequences attached",
\r
1585 JOptionPane.INFORMATION_MESSAGE );
\r
1588 JOptionPane.showMessageDialog( this, "Attached " + attached_counter
\r
1589 + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
\r
1590 + " sequences attached", JOptionPane.WARNING_MESSAGE );
\r
1594 JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
\r
1595 + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
\r
1600 private void choosePdfWidth() {
\r
1601 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
1602 "Please enter the default line width for PDF export.\n"
\r
1603 + "[current value: "
\r
1604 + getOptions().getPrintLineWidth() + "]\n",
\r
1605 "Line Width for PDF Export",
\r
1606 JOptionPane.QUESTION_MESSAGE,
\r
1609 getOptions().getPrintLineWidth() );
\r
1610 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1611 boolean success = true;
\r
1613 final String m_str = s.trim();
\r
1614 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1616 f = Float.parseFloat( m_str );
\r
1618 catch ( final Exception ex ) {
\r
1625 if ( success && ( f > 0.0 ) ) {
\r
1626 getOptions().setPrintLineWidth( f );
\r
1631 private void choosePrintSize() {
\r
1632 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
1633 "Please enter values for width and height,\nseparated by a comma.\n"
\r
1634 + "[current values: "
\r
1635 + getOptions().getPrintSizeX() + ", "
\r
1636 + getOptions().getPrintSizeY() + "]\n"
\r
1637 + "[A4: " + Constants.A4_SIZE_X + ", "
\r
1638 + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
\r
1639 + Constants.US_LETTER_SIZE_X + ", "
\r
1640 + Constants.US_LETTER_SIZE_Y + "]",
\r
1641 "Default Size for Graphics Export",
\r
1642 JOptionPane.QUESTION_MESSAGE,
\r
1645 getOptions().getPrintSizeX() + ", "
\r
1646 + getOptions().getPrintSizeY() );
\r
1647 if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
\r
1648 boolean success = true;
\r
1651 final String[] str_ary = s.split( "," );
\r
1652 if ( str_ary.length == 2 ) {
\r
1653 final String x_str = str_ary[ 0 ].trim();
\r
1654 final String y_str = str_ary[ 1 ].trim();
\r
1655 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
\r
1657 x = Integer.parseInt( x_str );
\r
1658 y = Integer.parseInt( y_str );
\r
1660 catch ( final Exception ex ) {
\r
1671 if ( success && ( x > 1 ) && ( y > 1 ) ) {
\r
1672 getOptions().setPrintSizeX( x );
\r
1673 getOptions().setPrintSizeY( y );
\r
1678 private void closeCurrentPane() {
\r
1679 if ( getMainPanel().getCurrentTreePanel() != null ) {
\r
1680 if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
\r
1681 final int r = JOptionPane.showConfirmDialog( this,
\r
1682 "Close tab despite potentially unsaved changes?",
\r
1684 JOptionPane.YES_NO_OPTION );
\r
1685 if ( r != JOptionPane.YES_OPTION ) {
\r
1689 getMainPanel().closeCurrentPane();
\r
1690 activateSaveAllIfNeeded();
\r
1694 private void collapseBl( final Phylogeny phy ) {
\r
1695 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1696 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
\r
1697 double min_bl = Double.MAX_VALUE;
\r
1698 boolean bl_present = false;
\r
1699 while ( it.hasNext() ) {
\r
1700 final PhylogenyNode n = it.next();
\r
1701 if ( !n.isExternal() && !n.isRoot() ) {
\r
1702 final double bl = n.getDistanceToParent();
\r
1703 if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
\r
1704 bl_present = true;
\r
1705 if ( bl < getMinNotCollapseBlValue() ) {
\r
1706 to_be_removed.add( n );
\r
1708 if ( bl < min_bl ) {
\r
1714 if ( bl_present ) {
\r
1715 for( final PhylogenyNode node : to_be_removed ) {
\r
1716 PhylogenyMethods.removeNode( node, phy );
\r
1718 if ( to_be_removed.size() > 0 ) {
\r
1719 phy.externalNodesHaveChanged();
\r
1720 phy.clearHashIdToNodeMap();
\r
1721 phy.recalculateNumberOfExternalDescendants( true );
\r
1722 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
1723 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
\r
1724 getCurrentTreePanel().calculateLongestExtNodeInfo();
\r
1725 getCurrentTreePanel().setNodeInPreorderToNull();
\r
1726 getCurrentTreePanel().recalculateMaxDistanceToRoot();
\r
1727 getCurrentTreePanel().resetPreferredSize();
\r
1728 getCurrentTreePanel().setEdited( true );
\r
1729 getCurrentTreePanel().repaint();
\r
1732 if ( to_be_removed.size() > 0 ) {
\r
1733 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
\r
1734 + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "
\r
1735 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
\r
1738 JOptionPane.showMessageDialog( this,
\r
1739 "No branch collapsed,\nminimum branch length is " + min_bl,
\r
1740 "No branch collapsed",
\r
1741 JOptionPane.INFORMATION_MESSAGE );
\r
1745 JOptionPane.showMessageDialog( this,
\r
1746 "No branch collapsed because no branch length values present",
\r
1747 "No branch length values present",
\r
1748 JOptionPane.INFORMATION_MESSAGE );
\r
1752 private void collapse( final Phylogeny phy ) {
\r
1753 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1754 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
\r
1755 double min_support = Double.MAX_VALUE;
\r
1756 boolean conf_present = false;
\r
1757 while ( it.hasNext() ) {
\r
1758 final PhylogenyNode n = it.next();
\r
1759 if ( !n.isExternal() && !n.isRoot() ) {
\r
1760 final List<Confidence> c = n.getBranchData().getConfidences();
\r
1761 if ( ( c != null ) && ( c.size() > 0 ) ) {
\r
1762 conf_present = true;
\r
1764 for( final Confidence confidence : c ) {
\r
1765 if ( confidence.getValue() > max ) {
\r
1766 max = confidence.getValue();
\r
1769 if ( max < getMinNotCollapseConfidenceValue() ) {
\r
1770 to_be_removed.add( n );
\r
1772 if ( max < min_support ) {
\r
1773 min_support = max;
\r
1778 if ( conf_present ) {
\r
1779 for( final PhylogenyNode node : to_be_removed ) {
\r
1780 PhylogenyMethods.removeNode( node, phy );
\r
1782 if ( to_be_removed.size() > 0 ) {
\r
1783 phy.externalNodesHaveChanged();
\r
1784 phy.clearHashIdToNodeMap();
\r
1785 phy.recalculateNumberOfExternalDescendants( true );
\r
1786 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
1787 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
\r
1788 getCurrentTreePanel().calculateLongestExtNodeInfo();
\r
1789 getCurrentTreePanel().setNodeInPreorderToNull();
\r
1790 getCurrentTreePanel().recalculateMaxDistanceToRoot();
\r
1791 getCurrentTreePanel().resetPreferredSize();
\r
1792 getCurrentTreePanel().setEdited( true );
\r
1793 getCurrentTreePanel().repaint();
\r
1796 if ( to_be_removed.size() > 0 ) {
\r
1797 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
\r
1798 + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
\r
1799 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
\r
1802 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
\r
1803 + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
\r
1807 JOptionPane.showMessageDialog( this,
\r
1808 "No branch collapsed because no confidence values present",
\r
1809 "No confidence values present",
\r
1810 JOptionPane.INFORMATION_MESSAGE );
\r
1814 private void collapseBelowThreshold() {
\r
1815 if ( getCurrentTreePanel() != null ) {
\r
1816 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1817 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1818 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
1819 "Please enter the minimum confidence value\n",
\r
1820 "Minimal Confidence Value",
\r
1821 JOptionPane.QUESTION_MESSAGE,
\r
1824 getMinNotCollapseConfidenceValue() );
\r
1825 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1826 boolean success = true;
\r
1828 final String m_str = s.trim();
\r
1829 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1831 m = Double.parseDouble( m_str );
\r
1833 catch ( final Exception ex ) {
\r
1840 if ( success && ( m >= 0.0 ) ) {
\r
1841 setMinNotCollapseConfidenceValue( m );
\r
1849 private void collapseBelowBranchLengthThreshold() {
\r
1850 if ( getCurrentTreePanel() != null ) {
\r
1851 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1852 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1853 final String s = ( String ) JOptionPane
\r
1854 .showInputDialog( this,
\r
1855 "Please enter the minimum branch length value\n",
\r
1856 "Minimal Branch Length Value",
\r
1857 JOptionPane.QUESTION_MESSAGE,
\r
1860 getMinNotCollapseBlValue() );
\r
1861 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1862 boolean success = true;
\r
1864 final String m_str = s.trim();
\r
1865 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1867 m = Double.parseDouble( m_str );
\r
1869 catch ( final Exception ex ) {
\r
1876 if ( success && ( m >= 0.0 ) ) {
\r
1877 setMinNotCollapseBlValue( m );
\r
1878 collapseBl( phy );
\r
1885 private PhyloXmlParser createPhyloXmlParser() {
\r
1886 PhyloXmlParser xml_parser = null;
\r
1887 if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
\r
1889 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
\r
1891 catch ( final Exception e ) {
\r
1892 JOptionPane.showMessageDialog( this,
\r
1893 e.getLocalizedMessage(),
\r
1894 "failed to create validating XML parser",
\r
1895 JOptionPane.WARNING_MESSAGE );
\r
1898 if ( xml_parser == null ) {
\r
1899 xml_parser = PhyloXmlParser.createPhyloXmlParser();
\r
1901 return xml_parser;
\r
1904 private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
\r
1905 final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
\r
1906 getPhylogeneticInferenceOptions(),
\r
1907 from_unaligned_seqs );
\r
1908 dialog.activate();
\r
1909 if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
\r
1910 if ( !from_unaligned_seqs ) {
\r
1911 if ( getMsa() != null ) {
\r
1912 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
\r
1913 getPhylogeneticInferenceOptions()
\r
1915 new Thread( inferrer ).start();
\r
1918 JOptionPane.showMessageDialog( this,
\r
1919 "No multiple sequence alignment selected",
\r
1920 "Phylogenetic Inference Not Launched",
\r
1921 JOptionPane.WARNING_MESSAGE );
\r
1925 if ( getSeqs() != null ) {
\r
1926 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
\r
1927 getPhylogeneticInferenceOptions()
\r
1929 new Thread( inferrer ).start();
\r
1932 JOptionPane.showMessageDialog( this,
\r
1933 "No input sequences selected",
\r
1934 "Phylogenetic Inference Not Launched",
\r
1935 JOptionPane.WARNING_MESSAGE );
\r
1941 private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
\r
1942 final StringBuilder sb = new StringBuilder();
\r
1943 final StringBuilder sb_failed = new StringBuilder();
\r
1945 int counter_failed = 0;
\r
1946 if ( getCurrentTreePanel() != null ) {
\r
1947 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1948 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1949 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
\r
1950 while ( it.hasNext() ) {
\r
1951 final PhylogenyNode n = it.next();
\r
1952 final String name = n.getName().trim();
\r
1953 if ( !ForesterUtil.isEmpty( name ) ) {
\r
1954 final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
\r
1955 TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1956 if ( !ForesterUtil.isEmpty( nt ) ) {
\r
1957 if ( counter < 15 ) {
\r
1958 sb.append( name + ": " + nt + "\n" );
\r
1960 else if ( counter == 15 ) {
\r
1961 sb.append( "...\n" );
\r
1966 if ( counter_failed < 15 ) {
\r
1967 sb_failed.append( name + "\n" );
\r
1969 else if ( counter_failed == 15 ) {
\r
1970 sb_failed.append( "...\n" );
\r
1976 if ( counter > 0 ) {
\r
1977 String failed = "";
\r
1978 String all = "all ";
\r
1979 if ( counter_failed > 0 ) {
\r
1981 failed = "\nCould not extract taxonomic data for " + counter_failed
\r
1982 + " named external nodes:\n" + sb_failed;
\r
1984 JOptionPane.showMessageDialog( this,
\r
1985 "Extracted taxonomic data from " + all + counter
\r
1986 + " named external nodes:\n" + sb.toString() + failed,
\r
1987 "Taxonomic Data Extraction Completed",
\r
1988 counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
\r
1989 : JOptionPane.INFORMATION_MESSAGE );
\r
1993 .showMessageDialog( this,
\r
1994 "Could not extract any taxonomic data.\nMaybe node names are empty\n"
\r
1995 + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
\r
1996 + "or nodes already have taxonomic data?\n",
\r
1997 "No Taxonomic Data Extracted",
\r
1998 JOptionPane.ERROR_MESSAGE );
\r
2004 private ControlPanel getControlPanel() {
\r
2005 return getMainPanel().getControlPanel();
\r
2008 private File getCurrentDir() {
\r
2009 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
\r
2010 if ( ForesterUtil.isWindows() ) {
\r
2012 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
\r
2014 catch ( final Exception e ) {
\r
2015 _current_dir = null;
\r
2019 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
\r
2020 if ( System.getProperty( "user.home" ) != null ) {
\r
2021 _current_dir = new File( System.getProperty( "user.home" ) );
\r
2023 else if ( System.getProperty( "user.dir" ) != null ) {
\r
2024 _current_dir = new File( System.getProperty( "user.dir" ) );
\r
2027 return _current_dir;
\r
2030 private double getMinNotCollapseConfidenceValue() {
\r
2031 return _min_not_collapse;
\r
2034 private double getMinNotCollapseBlValue() {
\r
2035 return _min_not_collapse_bl;
\r
2038 private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
\r
2039 if ( _phylogenetic_inference_options == null ) {
\r
2040 _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
\r
2042 return _phylogenetic_inference_options;
\r
2045 private boolean isUnsavedDataPresent() {
\r
2046 final List<TreePanel> tps = getMainPanel().getTreePanels();
\r
2047 for( final TreePanel tp : tps ) {
\r
2048 if ( tp.isEdited() ) {
\r
2055 private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
\r
2056 if ( getCurrentTreePanel() != null ) {
\r
2057 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
2058 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
2060 .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
\r
2065 private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
\r
2066 if ( getCurrentTreePanel() != null ) {
\r
2067 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
2068 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
2069 PhylogenyMethods.transferNodeNameToField( phy,
\r
2070 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
\r
2076 private void newTree() {
\r
2077 final Phylogeny[] phys = new Phylogeny[ 1 ];
\r
2078 final Phylogeny phy = new Phylogeny();
\r
2079 final PhylogenyNode node = new PhylogenyNode();
\r
2080 phy.setRoot( node );
\r
2081 phy.setRooted( true );
\r
2083 AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
\r
2084 _mainpanel.getControlPanel().showWhole();
\r
2085 _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
2086 _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
2087 if ( getMainPanel().getMainFrame() == null ) {
\r
2088 // Must be "E" applet version.
\r
2089 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
\r
2090 .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
2093 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
2095 activateSaveAllIfNeeded();
\r
2099 private void obtainDetailedTaxonomicInformation() {
\r
2100 if ( getCurrentTreePanel() != null ) {
\r
2101 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
2102 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
2103 final TaxonomyDataManager t = new TaxonomyDataManager( this,
\r
2104 _mainpanel.getCurrentTreePanel(),
\r
2108 new Thread( t ).start();
\r
2113 private void obtainDetailedTaxonomicInformationDelete() {
\r
2114 if ( getCurrentTreePanel() != null ) {
\r
2115 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
2116 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
2117 final TaxonomyDataManager t = new TaxonomyDataManager( this,
\r
2118 _mainpanel.getCurrentTreePanel(),
\r
2122 new Thread( t ).start();
\r
2127 private void obtainSequenceInformation() {
\r
2128 if ( getCurrentTreePanel() != null ) {
\r
2129 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
2130 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
2131 final SequenceDataRetriver u = new SequenceDataRetriver( this,
\r
2132 _mainpanel.getCurrentTreePanel(),
\r
2134 new Thread( u ).start();
\r
2139 private void print() {
\r
2140 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
\r
2141 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
\r
2144 if ( !getOptions().isPrintUsingActualSize() ) {
\r
2145 getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80,
\r
2146 getOptions().getPrintSizeY() - 140 );
\r
2147 getCurrentTreePanel().resetPreferredSize();
\r
2148 getCurrentTreePanel().repaint();
\r
2150 final String job_name = Constants.PRG_NAME;
\r
2151 boolean error = false;
\r
2152 String printer_name = null;
\r
2154 printer_name = Printer.print( getCurrentTreePanel(), job_name );
\r
2156 catch ( final Exception e ) {
\r
2158 JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
\r
2160 if ( !error && ( printer_name != null ) ) {
\r
2161 String msg = "Printing data sent to printer";
\r
2162 if ( printer_name.length() > 1 ) {
\r
2163 msg += " [" + printer_name + "]";
\r
2165 JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
\r
2167 if ( !getOptions().isPrintUsingActualSize() ) {
\r
2168 getControlPanel().showWhole();
\r
2172 private void printPhylogenyToPdf( final String file_name ) {
\r
2173 if ( !getOptions().isPrintUsingActualSize() ) {
\r
2174 getCurrentTreePanel()
\r
2175 .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() );
\r
2176 getCurrentTreePanel().resetPreferredSize();
\r
2177 getCurrentTreePanel().repaint();
\r
2179 String pdf_written_to = "";
\r
2180 boolean error = false;
\r
2182 if ( getOptions().isPrintUsingActualSize() ) {
\r
2183 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
\r
2184 getCurrentTreePanel(),
\r
2185 getCurrentTreePanel().getWidth(),
\r
2186 getCurrentTreePanel().getHeight() );
\r
2189 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
\r
2190 .getPrintSizeX(), getOptions().getPrintSizeY() );
\r
2193 catch ( final IOException e ) {
\r
2195 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
\r
2198 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
\r
2199 JOptionPane.showMessageDialog( this,
\r
2200 "Wrote PDF to: " + pdf_written_to,
\r
2202 JOptionPane.INFORMATION_MESSAGE );
\r
2205 JOptionPane.showMessageDialog( this,
\r
2206 "There was an unknown problem when attempting to write to PDF file: \""
\r
2207 + file_name + "\"",
\r
2209 JOptionPane.ERROR_MESSAGE );
\r
2212 if ( !getOptions().isPrintUsingActualSize() ) {
\r
2213 getControlPanel().showWhole();
\r
2217 private void readPhylogeniesFromFile() {
\r
2218 boolean exception = false;
\r
2219 Phylogeny[] phys = null;
\r
2220 // Set an initial directory if none set yet
\r
2221 final File my_dir = getCurrentDir();
\r
2222 _open_filechooser.setMultiSelectionEnabled( true );
\r
2223 // Open file-open dialog and set current directory
\r
2224 if ( my_dir != null ) {
\r
2225 _open_filechooser.setCurrentDirectory( my_dir );
\r
2227 final int result = _open_filechooser.showOpenDialog( _contentpane );
\r
2228 // All done: get the file
\r
2229 final File[] files = _open_filechooser.getSelectedFiles();
\r
2230 setCurrentDir( _open_filechooser.getCurrentDirectory() );
\r
2231 boolean nhx_or_nexus = false;
\r
2232 if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2233 for( final File file : files ) {
\r
2234 if ( ( file != null ) && !file.isDirectory() ) {
\r
2235 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
2236 _mainpanel.getCurrentTreePanel().setWaitCursor();
\r
2239 _mainpanel.setWaitCursor();
\r
2241 if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
\r
2242 || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
\r
2244 final NHXParser nhx = new NHXParser();
\r
2245 setSpecialOptionsForNhxParser( nhx );
\r
2246 phys = PhylogenyMethods.readPhylogenies( nhx, file );
\r
2247 nhx_or_nexus = true;
\r
2249 catch ( final Exception e ) {
\r
2251 exceptionOccuredDuringOpenFile( e );
\r
2254 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
\r
2255 warnIfNotPhyloXmlValidation( getConfiguration() );
\r
2257 final PhyloXmlParser xml_parser = createPhyloXmlParser();
\r
2258 phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
\r
2260 catch ( final Exception e ) {
\r
2262 exceptionOccuredDuringOpenFile( e );
\r
2265 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
\r
2267 phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
\r
2269 catch ( final Exception e ) {
\r
2271 exceptionOccuredDuringOpenFile( e );
\r
2274 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
\r
2276 final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
\r
2277 setSpecialOptionsForNexParser( nex );
\r
2278 phys = PhylogenyMethods.readPhylogenies( nex, file );
\r
2279 nhx_or_nexus = true;
\r
2281 catch ( final Exception e ) {
\r
2283 exceptionOccuredDuringOpenFile( e );
\r
2289 final PhylogenyParser parser = ParserUtils
\r
2290 .createParserDependingOnFileType( file, getConfiguration()
\r
2291 .isValidatePhyloXmlAgainstSchema() );
\r
2292 if ( parser instanceof NexusPhylogeniesParser ) {
\r
2293 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
\r
2294 setSpecialOptionsForNexParser( nex );
\r
2295 nhx_or_nexus = true;
\r
2297 else if ( parser instanceof NHXParser ) {
\r
2298 final NHXParser nhx = ( NHXParser ) parser;
\r
2299 setSpecialOptionsForNhxParser( nhx );
\r
2300 nhx_or_nexus = true;
\r
2302 else if ( parser instanceof PhyloXmlParser ) {
\r
2303 warnIfNotPhyloXmlValidation( getConfiguration() );
\r
2305 phys = PhylogenyMethods.readPhylogenies( parser, file );
\r
2307 catch ( final Exception e ) {
\r
2309 exceptionOccuredDuringOpenFile( e );
\r
2312 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
2313 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
2316 _mainpanel.setArrowCursor();
\r
2318 if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
\r
2319 boolean one_desc = false;
\r
2320 if ( nhx_or_nexus ) {
\r
2321 for( final Phylogeny phy : phys ) {
\r
2322 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
\r
2323 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
\r
2325 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
\r
2331 if ( PREPROCESS_TREES ) {
\r
2332 preProcessTreesUponReading( phys );
\r
2334 AptxUtil.addPhylogeniesToTabs( phys,
\r
2336 file.getAbsolutePath(),
\r
2337 getConfiguration(),
\r
2339 _mainpanel.getControlPanel().showWhole();
\r
2340 if ( nhx_or_nexus && one_desc ) {
\r
2342 .showMessageDialog( this,
\r
2343 "One or more trees contain (a) node(s) with one descendant, "
\r
2344 + ForesterUtil.LINE_SEPARATOR
\r
2345 + "possibly indicating illegal parentheses within node names.",
\r
2346 "Warning: Possible Error in New Hampshire Formatted Data",
\r
2347 JOptionPane.WARNING_MESSAGE );
\r
2353 activateSaveAllIfNeeded();
\r
2357 private void preProcessTreesUponReading( final Phylogeny[] phys ) {
\r
2358 for( final Phylogeny phy : phys ) {
\r
2359 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
2360 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
\r
2361 final PhylogenyNode n = it.next();
\r
2362 if ( n.isExternal() ) {
\r
2363 if ( n.getNodeData().isHasSequence() ) {
\r
2364 final Sequence s = n.getNodeData().getSequence();
\r
2365 if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) {
\r
2366 if ( ( s.getAccession() != null )
\r
2367 && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) {
\r
2368 s.setGeneName( s.getAccession().getValue() );
\r
2370 else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
\r
2371 s.setGeneName( n.getName() );
\r
2381 private void readSpeciesTreeFromFile() {
\r
2382 Phylogeny t = null;
\r
2383 boolean exception = false;
\r
2384 final File my_dir = getCurrentDir();
\r
2385 _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
\r
2386 if ( my_dir != null ) {
\r
2387 _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
\r
2389 final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
\r
2390 final File file = _open_filechooser_for_species_tree.getSelectedFile();
\r
2391 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2392 if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
\r
2394 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
\r
2395 .createPhyloXmlParserXsdValidating(), file );
\r
2398 catch ( final Exception e ) {
\r
2400 exceptionOccuredDuringOpenFile( e );
\r
2403 else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
\r
2405 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
\r
2408 catch ( final Exception e ) {
\r
2410 exceptionOccuredDuringOpenFile( e );
\r
2416 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
\r
2417 .createPhyloXmlParserXsdValidating(), file );
\r
2420 catch ( final Exception e ) {
\r
2422 exceptionOccuredDuringOpenFile( e );
\r
2425 if ( !exception && ( t != null ) && !t.isRooted() ) {
\r
2428 JOptionPane.showMessageDialog( this,
\r
2429 "Species tree is not rooted",
\r
2430 "Species tree not loaded",
\r
2431 JOptionPane.ERROR_MESSAGE );
\r
2433 if ( !exception && ( t != null ) ) {
\r
2434 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
\r
2435 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
\r
2436 final PhylogenyNode node = it.next();
\r
2437 if ( !node.getNodeData().isHasTaxonomy() ) {
\r
2441 .showMessageDialog( this,
\r
2442 "Species tree contains external node(s) without taxonomy information",
\r
2443 "Species tree not loaded",
\r
2444 JOptionPane.ERROR_MESSAGE );
\r
2448 if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
\r
2451 JOptionPane.showMessageDialog( this,
\r
2453 + node.getNodeData().getTaxonomy().asSimpleText()
\r
2454 + "] is not unique in species tree",
\r
2455 "Species tree not loaded",
\r
2456 JOptionPane.ERROR_MESSAGE );
\r
2460 tax_set.add( node.getNodeData().getTaxonomy() );
\r
2465 if ( !exception && ( t != null ) ) {
\r
2466 setSpeciesTree( t );
\r
2467 JOptionPane.showMessageDialog( this,
\r
2468 "Species tree successfully loaded",
\r
2469 "Species tree loaded",
\r
2470 JOptionPane.INFORMATION_MESSAGE );
\r
2472 _contentpane.repaint();
\r
2477 private void setArrowCursor() {
\r
2479 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
2481 catch ( final Exception ex ) {
\r
2486 private void setCurrentDir( final File current_dir ) {
\r
2487 _current_dir = current_dir;
\r
2490 private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
\r
2491 _min_not_collapse = min_not_collapse;
\r
2494 private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {
\r
2495 _min_not_collapse_bl = min_not_collapse_bl;
\r
2498 private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
\r
2499 _phylogenetic_inference_options = phylogenetic_inference_options;
\r
2502 private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
\r
2503 nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
\r
2504 nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
\r
2507 private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
\r
2508 nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
\r
2509 nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
\r
2510 nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );
\r
2513 private void writeAllToFile() {
\r
2514 if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
\r
2517 final File my_dir = getCurrentDir();
\r
2518 if ( my_dir != null ) {
\r
2519 _save_filechooser.setCurrentDirectory( my_dir );
\r
2521 _save_filechooser.setSelectedFile( new File( "" ) );
\r
2522 final int result = _save_filechooser.showSaveDialog( _contentpane );
\r
2523 final File file = _save_filechooser.getSelectedFile();
\r
2524 setCurrentDir( _save_filechooser.getCurrentDirectory() );
\r
2525 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2526 if ( file.exists() ) {
\r
2527 final int i = JOptionPane.showConfirmDialog( this,
\r
2528 file + " already exists. Overwrite?",
\r
2530 JOptionPane.OK_CANCEL_OPTION,
\r
2531 JOptionPane.WARNING_MESSAGE );
\r
2532 if ( i != JOptionPane.OK_OPTION ) {
\r
2539 catch ( final Exception e ) {
\r
2540 JOptionPane.showMessageDialog( this,
\r
2541 "Failed to delete: " + file,
\r
2543 JOptionPane.WARNING_MESSAGE );
\r
2547 final int count = getMainPanel().getTabbedPane().getTabCount();
\r
2548 final List<Phylogeny> trees = new ArrayList<Phylogeny>();
\r
2549 for( int i = 0; i < count; ++i ) {
\r
2550 final Phylogeny phy = getMainPanel().getPhylogeny( i );
\r
2551 if ( ForesterUtil.isEmpty( phy.getName() )
\r
2552 && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
\r
2553 phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
\r
2556 getMainPanel().getTreePanels().get( i ).setEdited( false );
\r
2558 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2560 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
\r
2562 catch ( final IOException e ) {
\r
2563 JOptionPane.showMessageDialog( this,
\r
2564 "Failed to write to: " + file,
\r
2566 JOptionPane.WARNING_MESSAGE );
\r
2571 private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
\r
2573 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2574 writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );
\r
2576 catch ( final Exception e ) {
\r
2578 exceptionOccuredDuringSaveAs( e );
\r
2583 private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
\r
2585 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2586 writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
\r
2588 catch ( final Exception e ) {
\r
2590 exceptionOccuredDuringSaveAs( e );
\r
2595 private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
\r
2597 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2598 writer.toPhyloXML( file, t, 0 );
\r
2600 catch ( final Exception e ) {
\r
2602 exceptionOccuredDuringSaveAs( e );
\r
2607 private void writeToFile( final Phylogeny t ) {
\r
2608 if ( t == null ) {
\r
2611 String initial_filename = null;
\r
2612 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
\r
2614 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
\r
2616 catch ( final IOException e ) {
\r
2617 initial_filename = null;
\r
2620 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
\r
2621 _save_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2624 _save_filechooser.setSelectedFile( new File( "" ) );
\r
2626 final File my_dir = getCurrentDir();
\r
2627 if ( my_dir != null ) {
\r
2628 _save_filechooser.setCurrentDirectory( my_dir );
\r
2630 final int result = _save_filechooser.showSaveDialog( _contentpane );
\r
2631 final File file = _save_filechooser.getSelectedFile();
\r
2632 setCurrentDir( _save_filechooser.getCurrentDirectory() );
\r
2633 boolean exception = false;
\r
2634 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2635 if ( file.exists() ) {
\r
2636 final int i = JOptionPane.showConfirmDialog( this,
\r
2637 file + " already exists.\nOverwrite?",
\r
2639 JOptionPane.OK_CANCEL_OPTION,
\r
2640 JOptionPane.QUESTION_MESSAGE );
\r
2641 if ( i != JOptionPane.OK_OPTION ) {
\r
2645 final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
\r
2647 ForesterUtil.copyFile( file, to );
\r
2649 catch ( final Exception e ) {
\r
2650 JOptionPane.showMessageDialog( this,
\r
2651 "Failed to create backup copy " + to,
\r
2652 "Failed to Create Backup Copy",
\r
2653 JOptionPane.WARNING_MESSAGE );
\r
2658 catch ( final Exception e ) {
\r
2659 JOptionPane.showMessageDialog( this,
\r
2660 "Failed to delete: " + file,
\r
2661 "Failed to Delete",
\r
2662 JOptionPane.WARNING_MESSAGE );
\r
2666 if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
\r
2667 exception = writeAsNewHampshire( t, exception, file );
\r
2669 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
\r
2670 exception = writeAsPhyloXml( t, exception, file );
\r
2672 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
\r
2673 exception = writeAsNexus( t, exception, file );
\r
2677 final String file_name = file.getName().trim().toLowerCase();
\r
2678 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2679 || file_name.endsWith( ".tree" ) ) {
\r
2680 exception = writeAsNewHampshire( t, exception, file );
\r
2682 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
\r
2683 exception = writeAsNexus( t, exception, file );
\r
2685 // XML is default:
\r
2687 exception = writeAsPhyloXml( t, exception, file );
\r
2690 if ( !exception ) {
\r
2691 getMainPanel().setTitleOfSelectedTab( file.getName() );
\r
2692 getMainPanel().getCurrentTreePanel().setTreeFile( file );
\r
2693 getMainPanel().getCurrentTreePanel().setEdited( false );
\r
2698 private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
\r
2699 if ( ( t == null ) || t.isEmpty() ) {
\r
2702 String initial_filename = "";
\r
2703 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
\r
2704 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
\r
2706 if ( initial_filename.indexOf( '.' ) > 0 ) {
\r
2707 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
\r
2709 initial_filename = initial_filename + "." + type;
\r
2710 _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2711 final File my_dir = getCurrentDir();
\r
2712 if ( my_dir != null ) {
\r
2713 _writetographics_filechooser.setCurrentDirectory( my_dir );
\r
2715 final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
\r
2716 File file = _writetographics_filechooser.getSelectedFile();
\r
2717 setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
\r
2718 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2719 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
\r
2720 file = new File( file.toString() + "." + type );
\r
2722 if ( file.exists() ) {
\r
2723 final int i = JOptionPane.showConfirmDialog( this,
\r
2724 file + " already exists. Overwrite?",
\r
2726 JOptionPane.OK_CANCEL_OPTION,
\r
2727 JOptionPane.WARNING_MESSAGE );
\r
2728 if ( i != JOptionPane.OK_OPTION ) {
\r
2735 catch ( final Exception e ) {
\r
2736 JOptionPane.showMessageDialog( this,
\r
2737 "Failed to delete: " + file,
\r
2739 JOptionPane.WARNING_MESSAGE );
\r
2743 writePhylogenyToGraphicsFile( file.toString(), type );
\r
2747 private void writeToPdf( final Phylogeny t ) {
\r
2748 if ( ( t == null ) || t.isEmpty() ) {
\r
2751 String initial_filename = "";
\r
2752 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
\r
2753 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
\r
2755 if ( initial_filename.indexOf( '.' ) > 0 ) {
\r
2756 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
\r
2758 initial_filename = initial_filename + ".pdf";
\r
2759 _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2760 final File my_dir = getCurrentDir();
\r
2761 if ( my_dir != null ) {
\r
2762 _writetopdf_filechooser.setCurrentDirectory( my_dir );
\r
2764 final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
\r
2765 File file = _writetopdf_filechooser.getSelectedFile();
\r
2766 setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
\r
2767 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2768 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
\r
2769 file = new File( file.toString() + ".pdf" );
\r
2771 if ( file.exists() ) {
\r
2772 final int i = JOptionPane.showConfirmDialog( this,
\r
2773 file + " already exists. Overwrite?",
\r
2775 JOptionPane.OK_CANCEL_OPTION,
\r
2776 JOptionPane.WARNING_MESSAGE );
\r
2777 if ( i != JOptionPane.OK_OPTION ) {
\r
2781 printPhylogenyToPdf( file.toString() );
\r
2785 public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
\r
2786 return new MainFrameApplication( phys, config );
\r
2789 public static MainFrame createInstance( final Phylogeny[] phys,
\r
2790 final Configuration config,
\r
2791 final String title,
\r
2792 final File current_dir ) {
\r
2793 return new MainFrameApplication( phys, config, title, current_dir );
\r
2796 static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
\r
2797 return new MainFrameApplication( phys, config, title );
\r
2800 static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
\r
2801 return new MainFrameApplication( phys, config_file_name, title );
\r
2804 static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
\r
2805 mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
\r
2806 + o.getPrintSizeY() + ")" );
\r
2809 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
\r
2810 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
\r
2813 static void warnIfNotPhyloXmlValidation( final Configuration c ) {
\r
2814 if ( !c.isValidatePhyloXmlAgainstSchema() ) {
\r
2816 .showMessageDialog( null,
\r
2818 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
\r
2821 JOptionPane.WARNING_MESSAGE );
\r
2824 } // MainFrameApplication.
\r
2826 class DefaultFilter extends FileFilter {
\r
2829 public boolean accept( final File f ) {
\r
2830 final String file_name = f.getName().trim().toLowerCase();
\r
2831 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2832 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
\r
2833 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
\r
2834 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
\r
2835 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
\r
2836 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
\r
2837 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
\r
2838 || file_name.endsWith( ".con" ) || f.isDirectory();
\r
2842 public String getDescription() {
\r
2843 return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
\r
2847 class GraphicsFileFilter extends FileFilter {
\r
2850 public boolean accept( final File f ) {
\r
2851 final String file_name = f.getName().trim().toLowerCase();
\r
2852 return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
\r
2853 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
\r
2857 public String getDescription() {
\r
2858 return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
\r
2862 class MsaFileFilter extends FileFilter {
\r
2865 public boolean accept( final File f ) {
\r
2866 final String file_name = f.getName().trim().toLowerCase();
\r
2867 return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
\r
2868 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
\r
2872 public String getDescription() {
\r
2873 return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
\r
2877 class NexusFilter extends FileFilter {
\r
2880 public boolean accept( final File f ) {
\r
2881 final String file_name = f.getName().trim().toLowerCase();
\r
2882 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
\r
2883 || file_name.endsWith( ".tre" ) || f.isDirectory();
\r
2887 public String getDescription() {
\r
2888 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
\r
2892 class NHFilter extends FileFilter {
\r
2895 public boolean accept( final File f ) {
\r
2896 final String file_name = f.getName().trim().toLowerCase();
\r
2897 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2898 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
\r
2899 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
\r
2900 || f.isDirectory();
\r
2904 public String getDescription() {
\r
2905 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
\r
2909 class NHXFilter extends FileFilter {
\r
2912 public boolean accept( final File f ) {
\r
2913 final String file_name = f.getName().trim().toLowerCase();
\r
2914 return file_name.endsWith( ".nhx" ) || f.isDirectory();
\r
2918 public String getDescription() {
\r
2919 return "NHX files (*.nhx) [deprecated]";
\r
2923 class PdfFilter extends FileFilter {
\r
2926 public boolean accept( final File f ) {
\r
2927 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
\r
2931 public String getDescription() {
\r
2932 return "PDF files (*.pdf)";
\r
2936 class SequencesFileFilter extends FileFilter {
\r
2939 public boolean accept( final File f ) {
\r
2940 final String file_name = f.getName().trim().toLowerCase();
\r
2941 return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
\r
2942 || file_name.endsWith( ".seqs" ) || f.isDirectory();
\r
2946 public String getDescription() {
\r
2947 return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
\r
2951 class TolFilter extends FileFilter {
\r
2954 public boolean accept( final File f ) {
\r
2955 final String file_name = f.getName().trim().toLowerCase();
\r
2956 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
\r
2957 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
\r
2961 public String getDescription() {
\r
2962 return "Tree of Life files (*.tol, *.tolxml)";
\r
2966 class XMLFilter extends FileFilter {
\r
2969 public boolean accept( final File f ) {
\r
2970 final String file_name = f.getName().trim().toLowerCase();
\r
2971 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
\r
2972 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
\r
2976 public String getDescription() {
\r
2977 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";
\r
git://source.jalview.org / jalview.git / blob