2 // FORESTER -- software libraries and applications
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3 // for evolutionary biology research and applications.
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5 // Copyright (C) 2008-2010 Christian M. Zmasek
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6 // All rights reserved
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8 // This library is free software; you can redistribute it and/or
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9 // modify it under the terms of the GNU Lesser General Public
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10 // License as published by the Free Software Foundation; either
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11 // version 2.1 of the License, or (at your option) any later version.
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13 // This library is distributed in the hope that it will be useful,
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14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
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15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 // Lesser General Public License for more details.
\r
18 // You should have received a copy of the GNU Lesser General Public
\r
19 // License along with this library; if not, write to the Free Software
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20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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22 // Contact: phylosoft @ gmail . com
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23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
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25 package org.forester.archaeopteryx;
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27 import java.awt.Color;
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28 import java.awt.Component;
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29 import java.awt.Container;
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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.ActionListener;
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33 import java.io.File;
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34 import java.io.IOException;
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35 import java.util.ArrayList;
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36 import java.util.HashSet;
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37 import java.util.LinkedList;
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38 import java.util.List;
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39 import java.util.Locale;
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40 import java.util.NoSuchElementException;
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41 import java.util.Set;
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43 import javax.swing.Box;
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44 import javax.swing.JApplet;
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45 import javax.swing.JCheckBoxMenuItem;
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46 import javax.swing.JFrame;
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47 import javax.swing.JLabel;
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48 import javax.swing.JMenu;
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49 import javax.swing.JMenuBar;
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50 import javax.swing.JMenuItem;
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51 import javax.swing.JOptionPane;
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52 import javax.swing.JPanel;
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53 import javax.swing.JRadioButtonMenuItem;
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54 import javax.swing.JTextField;
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55 import javax.swing.SwingUtilities;
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57 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
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58 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
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59 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
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60 import org.forester.archaeopteryx.tools.InferenceManager;
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61 import org.forester.archaeopteryx.tools.ProcessPool;
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62 import org.forester.archaeopteryx.tools.ProcessRunning;
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63 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
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64 import org.forester.phylogeny.Phylogeny;
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65 import org.forester.phylogeny.PhylogenyMethods;
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66 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
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67 import org.forester.phylogeny.PhylogenyNode;
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68 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
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69 import org.forester.phylogeny.data.Annotation;
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70 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
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71 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
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72 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
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73 import org.forester.sdi.GSDI;
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74 import org.forester.sdi.GSDIR;
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75 import org.forester.sdi.SDIException;
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76 import org.forester.util.ForesterConstants;
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77 import org.forester.util.ForesterUtil;
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79 public abstract class MainFrame extends JFrame implements ActionListener {
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81 static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
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82 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
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83 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
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84 private static final long serialVersionUID = 3655000897845508358L;
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85 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
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88 static final String TYPE_MENU_HEADER = "Type";
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89 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
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90 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
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91 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
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92 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
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93 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
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94 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
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95 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
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96 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
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97 static final String OPTIONS_HEADER = "Options";
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98 static final String SEARCH_SUBHEADER = "Search:";
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99 static final String DISPLAY_SUBHEADER = "Display:";
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100 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
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101 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
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102 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
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103 static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Branch Length Values";
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104 static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";
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105 static final String DISPLAY_SCALE_LABEL = "Scale";
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106 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
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107 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
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108 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
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109 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
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110 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
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111 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
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112 static final String BG_GRAD_LABEL = "Background Color Gradient";
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113 static final String DISPLAY_NODE_BOXES_LABEL_EXT = "External Node Shapes";
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114 static final String DISPLAY_NODE_BOXES_LABEL_INT = "Internal Node Shapes";
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115 static final String SHOW_OVERVIEW_LABEL = "Overview";
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116 static final String FONT_SIZE_MENU_LABEL = "Font Size";
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117 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
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118 static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";
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119 static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";
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120 static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
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121 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
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122 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
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123 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
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124 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
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125 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
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126 static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";
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127 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
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128 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
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129 static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";
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130 JMenuBar _jmenubar;
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134 JMenu _options_jmenu;
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135 JMenu _font_size_menu;
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137 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
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139 JMenu _analysis_menu;
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140 JMenuItem _load_species_tree_item;
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141 JMenuItem _gsdi_item;
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142 JMenuItem _gsdir_item;
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143 JMenuItem _lineage_inference;
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145 JMenuItem _open_item;
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146 JMenuItem _open_url_item;
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147 JMenuItem _save_item;
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148 JMenuItem _save_all_item;
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149 JMenuItem _close_item;
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150 JMenuItem _exit_item;
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151 JMenuItem _new_item;
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153 JMenuItem _midpoint_root_item;
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154 JMenuItem _taxcolor_item;
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155 JMenuItem _confcolor_item;
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156 JMenuItem _color_rank_jmi;
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157 JMenuItem _collapse_species_specific_subtrees;
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158 JMenuItem _collapse_below_threshold; //TODO implememt me
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159 JMenuItem _obtain_detailed_taxonomic_information_jmi;
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160 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
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161 JMenuItem _obtain_seq_information_jmi;
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162 JMenuItem _move_node_names_to_tax_sn_jmi;
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163 JMenuItem _move_node_names_to_seq_names_jmi;
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164 JMenuItem _extract_tax_code_from_node_names_jmi;
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165 JMenuItem _annotate_item;
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166 JMenuItem _remove_branch_color_item;
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167 JMenuItem _remove_visual_styles_item;
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168 JMenuItem _delete_selected_nodes_item;
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169 JMenuItem _delete_not_selected_nodes_item;
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171 JMenuItem _super_tiny_fonts_item;
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172 JMenuItem _tiny_fonts_item;
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173 JMenuItem _small_fonts_item;
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174 JMenuItem _medium_fonts_item;
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175 JMenuItem _large_fonts_item;
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177 // _ screen and print
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178 JMenuItem _choose_font_mi;
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179 JMenuItem _switch_colors_mi;
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180 JCheckBoxMenuItem _label_direction_cbmi;
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181 // _ screen display
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182 JCheckBoxMenuItem _screen_antialias_cbmi;
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183 JCheckBoxMenuItem _background_gradient_cbmi;
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184 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
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185 JRadioButtonMenuItem _uniform_cladograms_rbmi;
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186 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
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187 JCheckBoxMenuItem _show_branch_length_values_cbmi;
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188 JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
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189 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
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190 JCheckBoxMenuItem _show_overview_cbmi;
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191 JCheckBoxMenuItem _show_domain_labels;
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192 JCheckBoxMenuItem _show_annotation_ref_source;
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193 JCheckBoxMenuItem _abbreviate_scientific_names;
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194 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
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195 JMenuItem _overview_placment_mi;
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196 JMenuItem _choose_minimal_confidence_mi;
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197 JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
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198 JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
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199 JMenuItem _cycle_node_shape_mi;
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200 JMenuItem _cycle_node_fill_mi;
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201 JMenuItem _choose_node_size_mi;
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202 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
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204 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
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205 JCheckBoxMenuItem _antialias_print_cbmi;
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206 JCheckBoxMenuItem _print_black_and_white_cbmi;
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207 JCheckBoxMenuItem _print_using_actual_size_cbmi;
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208 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
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209 JMenuItem _print_size_mi;
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210 JMenuItem _choose_pdf_width_mi;
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212 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
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213 JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
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214 JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
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215 JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
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216 JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
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217 JCheckBoxMenuItem _replace_underscores_cbmi;
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218 JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
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219 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
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220 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
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222 JCheckBoxMenuItem _search_case_senstive_cbmi;
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223 JCheckBoxMenuItem _search_whole_words_only_cbmi;
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224 JCheckBoxMenuItem _inverse_search_result_cbmi;
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227 JCheckBoxMenuItem _rectangular_type_cbmi;
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228 JCheckBoxMenuItem _triangular_type_cbmi;
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229 JCheckBoxMenuItem _curved_type_cbmi;
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230 JCheckBoxMenuItem _convex_type_cbmi;
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231 JCheckBoxMenuItem _euro_type_cbmi;
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232 JCheckBoxMenuItem _rounded_type_cbmi;
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233 JCheckBoxMenuItem _unrooted_type_cbmi;
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234 JCheckBoxMenuItem _circular_type_cbmi;
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235 // view as text menu:
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236 JMenuItem _view_as_NH_item;
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237 JMenuItem _view_as_XML_item;
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238 JMenuItem _view_as_nexus_item;
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239 JMenuItem _display_basic_information_item;
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241 JMenuItem _about_item;
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242 JMenuItem _help_item;
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243 JMenuItem _website_item;
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244 JMenuItem _phyloxml_website_item;
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245 JMenuItem _phyloxml_ref_item;
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246 JMenuItem _aptx_ref_item;
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248 JMenu _process_menu;
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249 // Handy pointers to child components:
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250 MainPanel _mainpanel;
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251 Container _contentpane;
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252 final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
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253 Configuration _configuration;
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255 private Phylogeny _species_tree;
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256 InferenceManager _inference_manager;
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257 final ProcessPool _process_pool;
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258 private String _previous_node_annotation_ref;
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261 _process_pool = ProcessPool.createInstance();
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265 * Action performed.
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268 public void actionPerformed( final ActionEvent e ) {
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269 final Object o = e.getSource();
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270 boolean is_applet = false;
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271 JApplet applet = null;
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272 if ( getCurrentTreePanel() != null ) {
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273 is_applet = getCurrentTreePanel().isApplet();
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275 applet = getCurrentTreePanel().obtainApplet();
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278 if ( o == _exit_item ) {
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281 else if ( o == _gsdi_item ) {
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282 if ( isSubtreeDisplayed() ) {
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287 else if ( o == _gsdir_item ) {
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288 if ( isSubtreeDisplayed() ) {
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293 else if ( o == _taxcolor_item ) {
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296 else if ( o == _confcolor_item ) {
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299 else if ( o == _color_rank_jmi ) {
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302 else if ( o == _collapse_species_specific_subtrees ) {
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303 if ( isSubtreeDisplayed() ) {
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306 if ( getCurrentTreePanel() != null ) {
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307 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
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310 else if ( o == _remove_branch_color_item ) {
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311 if ( isSubtreeDisplayed() ) {
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314 removeBranchColors();
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316 else if ( o == _remove_visual_styles_item ) {
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317 if ( isSubtreeDisplayed() ) {
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320 removeVisualStyles();
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322 else if ( o == _midpoint_root_item ) {
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323 if ( isSubtreeDisplayed() ) {
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328 else if ( o == _delete_selected_nodes_item ) {
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329 if ( isSubtreeDisplayed() ) {
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332 deleteSelectedNodes( true );
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334 else if ( o == _delete_not_selected_nodes_item ) {
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335 if ( isSubtreeDisplayed() ) {
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338 deleteSelectedNodes( false );
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340 else if ( o == _annotate_item ) {
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341 annotateSequences();
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343 else if ( o == _switch_colors_mi ) {
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346 else if ( o == _display_basic_information_item ) {
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347 displayBasicInformation( getCurrentTreePanel().getTreeFile() );
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349 else if ( o == _view_as_NH_item ) {
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352 else if ( o == _view_as_XML_item ) {
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355 else if ( o == _view_as_nexus_item ) {
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358 else if ( o == _super_tiny_fonts_item ) {
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359 if ( getCurrentTreePanel() != null ) {
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360 getCurrentTreePanel().setSuperTinyFonts();
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361 getCurrentTreePanel().repaint();
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364 else if ( o == _tiny_fonts_item ) {
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365 if ( getCurrentTreePanel() != null ) {
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366 getCurrentTreePanel().setTinyFonts();
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367 getCurrentTreePanel().repaint();
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370 else if ( o == _small_fonts_item ) {
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371 if ( getCurrentTreePanel() != null ) {
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372 getCurrentTreePanel().setSmallFonts();
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373 getCurrentTreePanel().repaint();
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376 else if ( o == _medium_fonts_item ) {
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377 if ( getCurrentTreePanel() != null ) {
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378 getCurrentTreePanel().setMediumFonts();
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379 getCurrentTreePanel().repaint();
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382 else if ( o == _large_fonts_item ) {
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383 if ( getCurrentTreePanel() != null ) {
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384 getCurrentTreePanel().setLargeFonts();
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385 getCurrentTreePanel().repaint();
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388 else if ( o == _choose_font_mi ) {
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391 else if ( o == _choose_minimal_confidence_mi ) {
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392 chooseMinimalConfidence();
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394 else if ( o == _choose_node_size_mi ) {
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395 chooseNodeSize( getOptions(), this );
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397 else if ( o == _overview_placment_mi ) {
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398 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
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400 else if ( o == _cycle_node_fill_mi ) {
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401 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
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403 else if ( o == _cycle_node_shape_mi ) {
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404 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
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406 else if ( o == _screen_antialias_cbmi ) {
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407 updateOptions( getOptions() );
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408 updateScreenTextAntialias( getMainPanel().getTreePanels() );
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410 else if ( o == _background_gradient_cbmi ) {
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411 updateOptions( getOptions() );
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413 else if ( o == _show_domain_labels ) {
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414 updateOptions( getOptions() );
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416 else if ( o == _show_annotation_ref_source ) {
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417 updateOptions( getOptions() );
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419 else if ( o == _abbreviate_scientific_names ) {
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420 updateOptions( getOptions() );
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422 else if ( o == _color_labels_same_as_parent_branch ) {
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423 updateOptions( getOptions() );
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425 else if ( o == _show_default_node_shapes_internal_cbmi ) {
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426 updateOptions( getOptions() );
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428 else if ( o == _show_default_node_shapes_external_cbmi ) {
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429 updateOptions( getOptions() );
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431 else if ( o == _non_lined_up_cladograms_rbmi ) {
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432 updateOptions( getOptions() );
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435 else if ( o == _uniform_cladograms_rbmi ) {
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436 updateOptions( getOptions() );
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439 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
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440 updateOptions( getOptions() );
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443 else if ( o == _search_case_senstive_cbmi ) {
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444 updateOptions( getOptions() );
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445 getMainPanel().getControlPanel().search0();
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446 getMainPanel().getControlPanel().search1();
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448 else if ( o == _search_whole_words_only_cbmi ) {
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449 updateOptions( getOptions() );
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450 getMainPanel().getControlPanel().search0();
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451 getMainPanel().getControlPanel().search1();
\r
453 else if ( o == _inverse_search_result_cbmi ) {
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454 updateOptions( getOptions() );
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455 getMainPanel().getControlPanel().search0();
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456 getMainPanel().getControlPanel().search1();
\r
458 else if ( o == _show_scale_cbmi ) {
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459 updateOptions( getOptions() );
\r
461 else if ( o == _show_branch_length_values_cbmi ) {
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462 updateOptions( getOptions() );
\r
464 else if ( o == _color_by_taxonomic_group_cbmi ) {
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465 updateOptions( getOptions() );
\r
467 else if ( o == _show_confidence_stddev_cbmi ) {
\r
468 updateOptions( getOptions() );
\r
470 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
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471 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
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472 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
\r
474 updateOptions( getOptions() );
\r
476 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
\r
477 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
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478 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
\r
480 updateOptions( getOptions() );
\r
482 else if ( o == _label_direction_cbmi ) {
\r
483 updateOptions( getOptions() );
\r
485 else if ( o == _show_overview_cbmi ) {
\r
486 updateOptions( getOptions() );
\r
487 if ( getCurrentTreePanel() != null ) {
\r
488 getCurrentTreePanel().updateOvSizes();
\r
491 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
\r
492 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
\r
493 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
\r
496 else if ( o == _about_item ) {
\r
499 else if ( o == _help_item ) {
\r
502 else if ( o == _website_item ) {
\r
504 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
\r
506 catch ( final IOException e1 ) {
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507 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
510 else if ( o == _phyloxml_website_item ) {
\r
512 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
\r
514 catch ( final IOException e1 ) {
\r
515 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
518 else if ( o == _aptx_ref_item ) {
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520 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
\r
522 catch ( final IOException e1 ) {
\r
523 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
526 else if ( o == _phyloxml_ref_item ) {
\r
528 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
\r
530 catch ( final IOException e1 ) {
\r
531 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
535 if ( _load_phylogeny_from_webservice_menu_items != null ) {
\r
536 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
\r
537 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
\r
538 readPhylogeniesFromWebservice( i );
\r
543 _contentpane.repaint();
\r
546 private void deleteSelectedNodes( boolean delete ) {
\r
547 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
548 if ( phy == null || phy.getNumberOfExternalNodes() < 2 ) {
\r
551 List<PhylogenyNode> nodes = null;
\r
552 if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
553 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
555 String function = "Retain";
\r
557 function = "Delete";
\r
559 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
561 .showMessageDialog( this,
\r
562 "Need to select external nodes, either via direct selection or via the \"Search\" function",
\r
563 "No external nodes selected to " + function.toLowerCase(),
\r
564 JOptionPane.ERROR_MESSAGE );
\r
567 final int todo = nodes.size();
\r
568 final int ext = phy.getNumberOfExternalNodes();
\r
574 JOptionPane.showMessageDialog( this,
\r
575 "Cannot delete all nodes",
\r
576 "Attempt to delete all nodes ",
\r
577 JOptionPane.ERROR_MESSAGE );
\r
580 final int result = JOptionPane.showConfirmDialog( null, function + " " + todo
\r
581 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res
\r
582 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );
\r
583 if ( result == JOptionPane.OK_OPTION ) {
\r
585 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
\r
586 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
\r
587 final PhylogenyNode n = it.next();
\r
588 if ( !nodes.contains( n ) ) {
\r
589 to_delete.add( n );
\r
592 for( final PhylogenyNode n : to_delete ) {
\r
593 phy.deleteSubtree( n, true );
\r
597 for( final PhylogenyNode n : nodes ) {
\r
598 phy.deleteSubtree( n, true );
\r
602 getCurrentTreePanel().setNodeInPreorderToNull();
\r
603 phy.externalNodesHaveChanged();
\r
604 phy.clearHashIdToNodeMap();
\r
605 phy.recalculateNumberOfExternalDescendants( true );
\r
606 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
607 getCurrentTreePanel().setEdited( true );
\r
612 void resetSearch() {
\r
613 getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
\r
614 getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
\r
615 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );
\r
616 getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );
\r
617 getMainPanel().getControlPanel().getSearchTextField0().setText( "" );
\r
618 getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );
\r
619 getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );
\r
620 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );
\r
621 getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );
\r
622 getMainPanel().getControlPanel().getSearchTextField1().setText( "" );
\r
623 getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );
\r
624 getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );
\r
627 public Configuration getConfiguration() {
\r
628 return _configuration;
\r
632 * This method returns the current external node data which
\r
633 * has been selected by the user by clicking the "Return ..."
\r
634 * menu item. This method is expected to be called from Javascript or
\r
635 * something like it.
\r
637 * @return current external node data as String
\r
639 public String getCurrentExternalNodesDataBuffer() {
\r
640 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
\r
643 public int getCurrentExternalNodesDataBufferChangeCounter() {
\r
644 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
\r
647 public int getCurrentExternalNodesDataBufferLength() {
\r
648 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
\r
651 public InferenceManager getInferenceManager() {
\r
652 return _inference_manager;
\r
655 public MainPanel getMainPanel() {
\r
659 public Options getOptions() {
\r
663 public ProcessPool getProcessPool() {
\r
664 return _process_pool;
\r
667 public void showTextFrame( final String s, final String title ) {
\r
669 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
\r
672 public void showWhole() {
\r
673 _mainpanel.getControlPanel().showWhole();
\r
676 public void updateProcessMenu() {
\r
677 // In general Swing is not thread safe.
\r
678 // See "Swing's Threading Policy".
\r
679 SwingUtilities.invokeLater( new Runnable() {
\r
682 public void run() {
\r
683 doUpdateProcessMenu();
\r
688 void activateSaveAllIfNeeded() {
\r
689 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
\r
690 _save_all_item.setEnabled( true );
\r
693 _save_all_item.setEnabled( false );
\r
697 void buildFileMenu() {
\r
698 _file_jmenu = createMenu( "File", getConfiguration() );
\r
699 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
\r
700 customizeJMenuItem( _exit_item );
\r
701 _jmenubar.add( _file_jmenu );
\r
704 void buildFontSizeMenu() {
\r
705 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
\r
706 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
\r
707 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
\r
708 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
\r
709 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
\r
710 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
\r
711 customizeJMenuItem( _super_tiny_fonts_item );
\r
712 customizeJMenuItem( _tiny_fonts_item );
\r
713 customizeJMenuItem( _small_fonts_item );
\r
714 customizeJMenuItem( _medium_fonts_item );
\r
715 customizeJMenuItem( _large_fonts_item );
\r
716 _jmenubar.add( _font_size_menu );
\r
719 void buildHelpMenu() {
\r
720 _help_jmenu = createMenu( "Help", getConfiguration() );
\r
721 _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
\r
722 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
\r
723 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
\r
724 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
\r
725 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
\r
726 _help_jmenu.addSeparator();
\r
727 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
\r
728 customizeJMenuItem( _help_item );
\r
729 customizeJMenuItem( _website_item );
\r
730 customizeJMenuItem( _phyloxml_website_item );
\r
731 customizeJMenuItem( _aptx_ref_item );
\r
732 customizeJMenuItem( _phyloxml_ref_item );
\r
733 customizeJMenuItem( _about_item );
\r
734 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
\r
735 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
\r
736 _jmenubar.add( _help_jmenu );
\r
739 void buildTypeMenu() {
\r
740 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
\r
741 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
\r
742 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
\r
743 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
\r
744 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
\r
745 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
\r
746 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
\r
747 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
\r
748 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
\r
749 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
\r
750 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
\r
751 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
\r
752 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
\r
753 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
\r
754 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
\r
755 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
\r
756 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
\r
757 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
758 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
759 initializeTypeMenu( getOptions() );
\r
760 _jmenubar.add( _type_menu );
\r
763 void buildViewMenu() {
\r
764 _view_jmenu = createMenu( "View", getConfiguration() );
\r
765 _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
\r
766 _view_jmenu.addSeparator();
\r
767 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
\r
768 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
\r
769 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
\r
770 customizeJMenuItem( _display_basic_information_item );
\r
771 customizeJMenuItem( _view_as_NH_item );
\r
772 customizeJMenuItem( _view_as_XML_item );
\r
773 customizeJMenuItem( _view_as_nexus_item );
\r
774 _jmenubar.add( _view_jmenu );
\r
777 void checkTextFrames() {
\r
778 if ( _textframes.size() > 5 ) {
\r
780 if ( _textframes.getFirst() != null ) {
\r
781 _textframes.getFirst().removeMe();
\r
784 _textframes.removeFirst();
\r
787 catch ( final NoSuchElementException e ) {
\r
794 removeAllTextFrames();
\r
795 if ( _mainpanel != null ) {
\r
796 _mainpanel.terminate();
\r
798 if ( _contentpane != null ) {
\r
799 _contentpane.removeAll();
\r
801 setVisible( false );
\r
806 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
807 final String[] ranks = AptxUtil.getAllPossibleRanks();
\r
808 final String rank = ( String ) JOptionPane
\r
809 .showInputDialog( this,
\r
810 "What rank should the colorization be based on",
\r
812 JOptionPane.QUESTION_MESSAGE,
\r
816 if ( !ForesterUtil.isEmpty( rank ) ) {
\r
817 _mainpanel.getCurrentTreePanel().colorRank( rank );
\r
823 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
824 _mainpanel.getCurrentTreePanel().confColor();
\r
828 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
\r
829 if ( item != null ) {
\r
830 item.setFont( MainFrame.menu_font );
\r
831 if ( !getConfiguration().isUseNativeUI() ) {
\r
832 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
833 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
835 item.setSelected( is_selected );
\r
836 item.addActionListener( this );
\r
840 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
\r
841 if ( jmi != null ) {
\r
842 jmi.setFont( MainFrame.menu_font );
\r
843 if ( !getConfiguration().isUseNativeUI() ) {
\r
844 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
845 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
847 jmi.addActionListener( this );
\r
852 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
\r
853 if ( item != null ) {
\r
854 item.setFont( MainFrame.menu_font );
\r
855 if ( !getConfiguration().isUseNativeUI() ) {
\r
856 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
857 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
859 item.setSelected( is_selected );
\r
860 item.addActionListener( this );
\r
864 void displayBasicInformation( final File treefile ) {
\r
865 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
866 String title = "Basic Information";
\r
867 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
868 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
\r
870 showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
\r
874 void exceptionOccuredDuringOpenFile( final Exception e ) {
\r
876 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
878 catch ( final Exception ex ) {
\r
881 JOptionPane.showMessageDialog( this,
\r
882 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
883 "Error during File|Open",
\r
884 JOptionPane.ERROR_MESSAGE );
\r
887 void exceptionOccuredDuringSaveAs( final Exception e ) {
\r
889 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
891 catch ( final Exception ex ) {
\r
894 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
\r
897 void executeGSDI() {
\r
898 if ( !isOKforSDI( false, true ) ) {
\r
901 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
\r
902 JOptionPane.showMessageDialog( this,
\r
903 "Gene tree is not rooted.",
\r
904 "Cannot execute GSDI",
\r
905 JOptionPane.ERROR_MESSAGE );
\r
908 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
909 gene_tree.setAllNodesToNotCollapse();
\r
910 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
912 final Phylogeny species_tree = getSpeciesTree().copy();
\r
914 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
\r
916 catch ( final SDIException e ) {
\r
917 JOptionPane.showMessageDialog( this,
\r
918 e.getLocalizedMessage(),
\r
919 "Error during GSDI",
\r
920 JOptionPane.ERROR_MESSAGE );
\r
923 catch ( final Exception e ) {
\r
924 AptxUtil.unexpectedException( e );
\r
927 gene_tree.setRerootable( false );
\r
928 gene_tree.clearHashIdToNodeMap();
\r
929 gene_tree.recalculateNumberOfExternalDescendants( true );
\r
930 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
\r
931 getMainPanel().getControlPanel().setShowEvents( true );
\r
933 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
934 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
936 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
938 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
939 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
940 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
941 JOptionPane.showMessageDialog( this,
\r
942 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
943 + "Potential duplications: "
\r
944 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
945 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
946 + "Stripped gene tree nodes: "
\r
947 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
948 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
949 + "Number of polytomies in species tree used: " + poly + "\n",
\r
950 "GSDI successfully completed",
\r
951 JOptionPane.WARNING_MESSAGE );
\r
954 JOptionPane.showMessageDialog( this,
\r
955 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
956 + "Potential duplications: "
\r
957 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
958 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
959 + "Stripped gene tree nodes: "
\r
960 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
961 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
962 + "Number of polytomies in species tree used: " + poly + "\n",
\r
963 "GSDI successfully completed",
\r
964 JOptionPane.INFORMATION_MESSAGE );
\r
968 void executeGSDIR() {
\r
969 if ( !isOKforSDI( false, false ) ) {
\r
972 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
\r
974 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
\r
975 JOptionPane.showMessageDialog( this,
\r
976 "Gene tree is not completely binary",
\r
977 "Cannot execute GSDI",
\r
978 JOptionPane.ERROR_MESSAGE );
\r
981 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
982 gene_tree.setAllNodesToNotCollapse();
\r
983 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
984 GSDIR gsdir = null;
\r
985 final Phylogeny species_tree = getSpeciesTree().copy();
\r
987 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
\r
989 catch ( final SDIException e ) {
\r
990 JOptionPane.showMessageDialog( this,
\r
991 e.getLocalizedMessage(),
\r
992 "Error during GSDIR",
\r
993 JOptionPane.ERROR_MESSAGE );
\r
996 catch ( final Exception e ) {
\r
997 AptxUtil.unexpectedException( e );
\r
1000 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
\r
1001 result_gene_tree.setRerootable( false );
\r
1002 result_gene_tree.clearHashIdToNodeMap();
\r
1003 result_gene_tree.recalculateNumberOfExternalDescendants( true );
\r
1004 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
\r
1005 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
\r
1006 getMainPanel().getControlPanel().setShowEvents( true );
\r
1008 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
1009 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
1011 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
1013 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
1014 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
1015 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
1016 JOptionPane.showMessageDialog( this,
\r
1017 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1018 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1019 + "Stripped gene tree nodes: "
\r
1020 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1021 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1022 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1023 "GSDIR successfully completed",
\r
1024 JOptionPane.WARNING_MESSAGE );
\r
1027 JOptionPane.showMessageDialog( this,
\r
1028 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1029 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1030 + "Stripped gene tree nodes: "
\r
1031 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1032 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1033 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1034 "GSDIR successfully completed",
\r
1035 JOptionPane.INFORMATION_MESSAGE );
\r
1039 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
\r
1040 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
\r
1041 JOptionPane.showMessageDialog( this,
\r
1042 "Gene tree and species tree have no species in common.",
\r
1043 "Error during SDI",
\r
1044 JOptionPane.ERROR_MESSAGE );
\r
1047 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
\r
1048 JOptionPane.showMessageDialog( this,
\r
1049 "Gene tree and species tree have only one species in common.",
\r
1050 "Error during SDI",
\r
1051 JOptionPane.ERROR_MESSAGE );
\r
1059 TreePanel getCurrentTreePanel() {
\r
1060 return getMainPanel().getCurrentTreePanel();
\r
1063 JMenu getHelpMenu() {
\r
1064 return _help_jmenu;
\r
1067 JCheckBoxMenuItem getlabelDirectionCbmi() {
\r
1068 return _label_direction_cbmi;
\r
1071 JMenuBar getMenuBarOfMainFrame() {
\r
1075 final Phylogeny getSpeciesTree() {
\r
1076 return _species_tree;
\r
1080 final StringBuilder sb = new StringBuilder();
\r
1081 sb.append( "Display options\n" );
\r
1082 sb.append( "-------------------\n" );
\r
1083 sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
\r
1084 sb.append( "Clickable tree nodes\n" );
\r
1085 sb.append( "--------------------\n" );
\r
1086 sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
\r
1087 sb.append( "or by right clicking:\n" );
\r
1088 sb.append( "o Display Node Data -- display information for a node\n" );
\r
1089 sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
\r
1090 sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
\r
1091 sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
\r
1092 sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
\r
1093 sb.append( "o Colorize Subtree -- color a subtree\n" );
\r
1094 sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
\r
1095 sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
\r
1096 sb.append( "- there may be additional choices depending on this particular setup\n\n" );
\r
1097 sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
\r
1098 sb.append( "Zooming\n" );
\r
1099 sb.append( "---------\n" );
\r
1100 sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
\r
1101 sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
\r
1102 sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
\r
1103 sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
\r
1104 sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
\r
1105 sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
\r
1106 sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
\r
1107 sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
\r
1108 sb.append( "Quick tree manipulation:\n" );
\r
1109 sb.append( "------------------------\n" );
\r
1110 sb.append( "Order Subtrees -- order the tree by branch length\n" );
\r
1111 sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
\r
1112 sb.append( "Memory problems (Java heap space error)\n" );
\r
1113 sb.append( "---------------------------------------\n" );
\r
1114 sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
\r
1115 sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
\r
1116 sb.append( "the '-Xmx' Java command line option. For example:\n" );
\r
1117 sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
\r
1118 // + "General remarks\n"
\r
1119 // + "---------------\n"
\r
1121 // "o The application version permits copying to the clipboard \n"
\r
1123 // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
\r
1125 // "o Changes made to a subtree affect this subtree and its subtrees,\n"
\r
1126 // + " but not any of its parent tree(s).\n"
\r
1128 // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
\r
1130 // " are likely to be bootstrap values instead of branch length values.\n\n"
\r
1132 // " Remarks regarding SDI (Speciation Duplication Inference):\n"
\r
1134 // "o Each external node of the gene tree (in display) needs to be associated with\n"
\r
1136 // " a species: either directly through the \"Species\" field, or the species\n"
\r
1138 // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
\r
1140 // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
\r
1142 // "o A species tree for each species of the gene tree needs to be loaded with\n"
\r
1144 // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
\r
1146 // "o !External nodes of the gene tree associated with species not present in\n"
\r
1148 // " the species tree are REMOVED prior to SDI execution!\n"
\r
1150 // "o Both the gene tree and the species tree must be completely binary.\n"
\r
1152 // "o Duplications and speciations are a function of the position of the root.\n"
\r
1154 // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
\r
1155 // + " incorrect and need to be inferred again\n"
\r
1157 // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
\r
1158 sb.append( "phyloXML\n" );
\r
1159 sb.append( "-------------------\n" );
\r
1160 sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
\r
1161 sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
\r
1162 sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
\r
1163 sb.append( "\n" );
\r
1164 sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
\r
1165 sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
\r
1166 TextFrame.instantiate( sb.toString(), "Help", _textframes );
\r
1169 void initializeTypeMenu( final Options options ) {
\r
1170 setTypeMenuToAllUnselected();
\r
1171 switch ( options.getPhylogenyGraphicsType() ) {
\r
1173 _convex_type_cbmi.setSelected( true );
\r
1176 _curved_type_cbmi.setSelected( true );
\r
1179 _euro_type_cbmi.setSelected( true );
\r
1182 _rounded_type_cbmi.setSelected( true );
\r
1185 _triangular_type_cbmi.setSelected( true );
\r
1188 _unrooted_type_cbmi.setSelected( true );
\r
1191 _circular_type_cbmi.setSelected( true );
\r
1194 _rectangular_type_cbmi.setSelected( true );
\r
1199 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
\r
1200 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1203 else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
\r
1204 JOptionPane.showMessageDialog( this,
\r
1205 "No species tree loaded",
\r
1206 "Cannot execute GSDI",
\r
1207 JOptionPane.ERROR_MESSAGE );
\r
1210 else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
\r
1211 JOptionPane.showMessageDialog( this,
\r
1212 "Species tree is not completely binary",
\r
1213 "Cannot execute GSDI",
\r
1214 JOptionPane.ERROR_MESSAGE );
\r
1217 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
\r
1218 JOptionPane.showMessageDialog( this,
\r
1219 "Gene tree is not completely binary",
\r
1220 "Cannot execute GSDI",
\r
1221 JOptionPane.ERROR_MESSAGE );
\r
1229 boolean isSubtreeDisplayed() {
\r
1230 if ( getCurrentTreePanel() != null ) {
\r
1231 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
\r
1233 .showMessageDialog( this,
\r
1234 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
\r
1235 "Operation can not be exectuted on a sub-tree",
\r
1236 JOptionPane.WARNING_MESSAGE );
\r
1243 void midpointRoot() {
\r
1244 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1245 _mainpanel.getCurrentTreePanel().midpointRoot();
\r
1249 void readPhylogeniesFromWebservice( final int i ) {
\r
1250 final UrlTreeReader reader = new UrlTreeReader( this, i );
\r
1251 new Thread( reader ).start();
\r
1254 void removeAllTextFrames() {
\r
1255 for( final TextFrame tf : _textframes ) {
\r
1256 if ( tf != null ) {
\r
1260 _textframes.clear();
\r
1263 void setConfiguration( final Configuration configuration ) {
\r
1264 _configuration = configuration;
\r
1267 void setInferenceManager( final InferenceManager i ) {
\r
1268 _inference_manager = i;
\r
1271 void setOptions( final Options options ) {
\r
1272 _options = options;
\r
1275 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
\r
1276 setTypeMenuToAllUnselected();
\r
1279 _circular_type_cbmi.setSelected( true );
\r
1282 _convex_type_cbmi.setSelected( true );
\r
1285 _curved_type_cbmi.setSelected( true );
\r
1288 _euro_type_cbmi.setSelected( true );
\r
1291 _rounded_type_cbmi.setSelected( true );
\r
1294 _rectangular_type_cbmi.setSelected( true );
\r
1297 _triangular_type_cbmi.setSelected( true );
\r
1300 _unrooted_type_cbmi.setSelected( true );
\r
1303 throw new IllegalArgumentException( "unknown type: " + type );
\r
1307 final void setSpeciesTree( final Phylogeny species_tree ) {
\r
1308 _species_tree = species_tree;
\r
1311 void setTypeMenuToAllUnselected() {
\r
1312 _convex_type_cbmi.setSelected( false );
\r
1313 _curved_type_cbmi.setSelected( false );
\r
1314 _euro_type_cbmi.setSelected( false );
\r
1315 _rounded_type_cbmi.setSelected( false );
\r
1316 _triangular_type_cbmi.setSelected( false );
\r
1317 _rectangular_type_cbmi.setSelected( false );
\r
1318 _unrooted_type_cbmi.setSelected( false );
\r
1319 _circular_type_cbmi.setSelected( false );
\r
1322 void switchColors() {
\r
1323 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
\r
1324 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
\r
1325 csc.setVisible( true );
\r
1329 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1330 _mainpanel.getCurrentTreePanel().taxColor();
\r
1334 void typeChanged( final Object o ) {
\r
1335 updateTypeCheckboxes( getOptions(), o );
\r
1336 updateOptions( getOptions() );
\r
1337 if ( getCurrentTreePanel() != null ) {
\r
1338 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
\r
1339 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
\r
1340 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1341 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
\r
1342 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1343 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
\r
1344 getCurrentTreePanel().getControlPanel().showWhole();
\r
1346 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
\r
1347 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
\r
1350 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
\r
1352 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
\r
1353 updateScreenTextAntialias( getMainPanel().getTreePanels() );
\r
1354 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
\r
1355 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
\r
1356 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
\r
1359 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
\r
1365 void updateOptions( final Options options ) {
\r
1366 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
\r
1367 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
\r
1368 && _background_gradient_cbmi.isSelected() );
\r
1369 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
\r
1370 options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
\r
1371 && _show_annotation_ref_source.isSelected() );
\r
1372 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
\r
1373 && _abbreviate_scientific_names.isSelected() );
\r
1374 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
\r
1375 && _color_labels_same_as_parent_branch.isSelected() );
\r
1376 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
\r
1377 && _show_default_node_shapes_internal_cbmi.isSelected() );
\r
1378 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
\r
1379 && _show_default_node_shapes_external_cbmi.isSelected() );
\r
1380 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
\r
1381 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
\r
1383 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
\r
1384 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
\r
1386 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
\r
1387 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
\r
1389 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
\r
1390 && _search_case_senstive_cbmi.isSelected() );
\r
1391 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
\r
1392 options.setShowScale( _show_scale_cbmi.isSelected() );
\r
1394 if ( _label_direction_cbmi != null ) {
\r
1395 if ( _label_direction_cbmi.isSelected() ) {
\r
1396 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
\r
1399 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
\r
1402 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
\r
1403 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
\r
1404 && _show_confidence_stddev_cbmi.isSelected() );
\r
1405 if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
\r
1406 options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
\r
1408 if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
\r
1409 options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
\r
1411 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
\r
1412 && ( _print_using_actual_size_cbmi.isSelected() ) );
\r
1413 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
\r
1414 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
\r
1415 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
\r
1416 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
\r
1417 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1418 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
\r
1420 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
\r
1421 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1422 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
\r
1425 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
\r
1427 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
\r
1428 && _print_black_and_white_cbmi.isSelected() );
\r
1429 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
\r
1430 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
\r
1431 if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
\r
1432 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
\r
1434 else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
\r
1435 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
\r
1437 else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
\r
1438 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1440 else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
\r
1441 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
\r
1443 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
\r
1444 && _replace_underscores_cbmi.isSelected() );
\r
1445 options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
\r
1446 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
\r
1447 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
\r
1448 && _search_whole_words_only_cbmi.isSelected() );
\r
1449 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
\r
1450 && _inverse_search_result_cbmi.isSelected() );
\r
1451 if ( _graphics_export_visible_only_cbmi != null ) {
\r
1452 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
\r
1453 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
\r
1454 _graphics_export_using_actual_size_cbmi.setSelected( true );
\r
1455 _graphics_export_using_actual_size_cbmi.setEnabled( false );
\r
1458 _graphics_export_using_actual_size_cbmi.setEnabled( true );
\r
1461 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
\r
1462 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1464 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
\r
1465 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
\r
1467 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
\r
1468 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
\r
1470 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
\r
1471 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
\r
1473 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
\r
1474 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
\r
1476 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
\r
1477 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
\r
1479 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
\r
1480 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
\r
1482 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
\r
1483 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
\r
1487 void updateTypeCheckboxes( final Options options, final Object o ) {
\r
1488 setTypeMenuToAllUnselected();
\r
1489 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
\r
1492 void viewAsNexus() {
\r
1493 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1494 String title = "Nexus";
\r
1495 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1496 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1498 showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
\r
1504 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1505 String title = "New Hampshire";
\r
1506 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1507 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1509 showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
\r
1510 .getNhConversionSupportValueStyle() ),
\r
1515 void viewAsXML() {
\r
1516 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1517 String title = "phyloXML";
\r
1518 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1519 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1521 showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
\r
1525 private void annotateSequences() {
\r
1526 if ( getCurrentTreePanel() != null ) {
\r
1527 List<PhylogenyNode> nodes = null;
\r
1528 if ( ( getCurrentTreePanel().getFoundNodes0() != null )
\r
1529 || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
1530 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
1532 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
1534 .showMessageDialog( this,
\r
1535 "Need to select nodes, either via direct selection or via the \"Search\" function",
\r
1536 "No nodes selected for annotation",
\r
1537 JOptionPane.ERROR_MESSAGE );
\r
1540 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
1541 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1542 final JTextField ref_field = new JTextField( 10 );
\r
1543 final JTextField desc_filed = new JTextField( 20 );
\r
1544 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
\r
1545 : getPreviousNodeAnnotationReference() );
\r
1546 final JPanel my_panel = new JPanel();
\r
1547 my_panel.add( new JLabel( "Reference " ) );
\r
1548 my_panel.add( ref_field );
\r
1549 my_panel.add( Box.createHorizontalStrut( 15 ) );
\r
1550 my_panel.add( new JLabel( "Description " ) );
\r
1551 my_panel.add( desc_filed );
\r
1552 final int result = JOptionPane.showConfirmDialog( null,
\r
1554 "Enter the sequence annotation(s) for the "
\r
1555 + nodes.size() + " selected nodes",
\r
1556 JOptionPane.OK_CANCEL_OPTION );
\r
1557 if ( result == JOptionPane.OK_OPTION ) {
\r
1558 String ref = ref_field.getText();
\r
1559 String desc = desc_filed.getText();
\r
1560 if ( !ForesterUtil.isEmpty( ref ) ) {
\r
1562 ref = ref.replaceAll( "\\s+", " " );
\r
1563 if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )
\r
1564 || ( ref.length() < 3 ) ) {
\r
1565 JOptionPane.showMessageDialog( this,
\r
1566 "Reference needs to be in the form of \"GO:1234567\"",
\r
1567 "Illegal Format for Annotation Reference",
\r
1568 JOptionPane.ERROR_MESSAGE );
\r
1572 if ( ref != null ) {
\r
1573 setPreviousNodeAnnotationReference( ref );
\r
1575 if ( desc != null ) {
\r
1576 desc = desc.trim();
\r
1577 desc = desc.replaceAll( "\\s+", " " );
\r
1579 if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
\r
1580 for( final PhylogenyNode n : nodes ) {
\r
1581 ForesterUtil.ensurePresenceOfSequence( n );
\r
1582 final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
\r
1583 : new Annotation( ref );
\r
1584 if ( !ForesterUtil.isEmpty( desc ) ) {
\r
1585 ann.setDesc( desc );
\r
1587 n.getNodeData().getSequence().addAnnotation( ann );
\r
1590 getMainPanel().getControlPanel().showAnnotations();
\r
1596 private void chooseFont() {
\r
1597 final FontChooser fc = new FontChooser();
\r
1598 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
\r
1599 fc.showDialog( this, "Select the Base Font" );
\r
1600 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
\r
1603 private void chooseMinimalConfidence() {
\r
1604 final String s = ( String ) JOptionPane
\r
1605 .showInputDialog( this,
\r
1606 "Please enter the minimum for confidence values to be displayed.\n"
\r
1607 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
\r
1608 "Minimal Confidence Value",
\r
1609 JOptionPane.QUESTION_MESSAGE,
\r
1612 getOptions().getMinConfidenceValue() );
\r
1613 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1614 boolean success = true;
\r
1616 final String m_str = s.trim();
\r
1617 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1619 m = Double.parseDouble( m_str );
\r
1621 catch ( final Exception ex ) {
\r
1628 if ( success && ( m >= 0.0 ) ) {
\r
1629 getOptions().setMinConfidenceValue( m );
\r
1634 private void doUpdateProcessMenu() {
\r
1635 if ( _process_pool.size() > 0 ) {
\r
1636 if ( _process_menu == null ) {
\r
1637 _process_menu = createMenu( "", getConfiguration() );
\r
1638 _process_menu.setForeground( Color.RED );
\r
1640 _process_menu.removeAll();
\r
1641 final String text = "processes running: " + _process_pool.size();
\r
1642 _process_menu.setText( text );
\r
1643 _jmenubar.add( _process_menu );
\r
1644 for( int i = 0; i < _process_pool.size(); ++i ) {
\r
1645 final ProcessRunning p = _process_pool.getProcessByIndex( i );
\r
1646 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
\r
1650 if ( _process_menu != null ) {
\r
1651 _process_menu.removeAll();
\r
1652 _jmenubar.remove( _process_menu );
\r
1655 _jmenubar.validate();
\r
1656 _jmenubar.repaint();
\r
1660 private String getPreviousNodeAnnotationReference() {
\r
1661 return _previous_node_annotation_ref;
\r
1664 private void removeBranchColors() {
\r
1665 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1666 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
\r
1670 private void removeVisualStyles() {
\r
1671 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1672 AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
\r
1676 private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
\r
1677 _previous_node_annotation_ref = previous_node_annotation_ref;
\r
1681 * Display the about box.
\r
1683 static void about() {
\r
1684 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
\r
1685 about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );
\r
1686 about.append( "All Rights Reserved\n" );
\r
1687 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
\r
1688 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
\r
1689 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
\r
1690 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
\r
1691 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
\r
1692 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
\r
1693 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
\r
1695 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
\r
1696 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
\r
1697 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
\r
1698 + ForesterUtil.OS_VERSION + "]\n" );
\r
1700 final Runtime rt = java.lang.Runtime.getRuntime();
\r
1701 final long free_memory = rt.freeMemory() / 1000000;
\r
1702 final long total_memory = rt.totalMemory() / 1000000;
\r
1703 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
\r
1704 about.append( "[locale: " + Locale.getDefault() + "]\n" );
\r
1705 about.append( "References:\n" );
\r
1706 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
\r
1707 about.append( "For more information & download:\n" );
\r
1708 about.append( Constants.APTX_WEB_SITE + "\n" );
\r
1709 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
\r
1710 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
\r
1713 static void chooseNodeSize( final Options options, final Component parent ) {
\r
1714 final String s = ( String ) JOptionPane.showInputDialog( parent,
\r
1715 "Please enter the default size for node shapes.\n"
\r
1716 + "[current value: "
\r
1717 + options.getDefaultNodeShapeSize() + "]\n",
\r
1718 "Node Shape Size",
\r
1719 JOptionPane.QUESTION_MESSAGE,
\r
1722 options.getDefaultNodeShapeSize() );
\r
1723 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1724 boolean success = true;
\r
1726 final String m_str = s.trim();
\r
1727 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1729 m = Double.parseDouble( m_str );
\r
1731 catch ( final Exception ex ) {
\r
1738 if ( success && ( m >= 0.0 ) ) {
\r
1739 final short size = ForesterUtil.roundToShort( m );
\r
1740 if ( size >= 0.0 ) {
\r
1741 options.setDefaultNodeShapeSize( size );
\r
1747 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
\r
1748 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
\r
1751 static JMenu createMenu( final String title, final Configuration conf ) {
\r
1752 final JMenu jmenu = new JMenu( title );
\r
1753 if ( !conf.isUseNativeUI() ) {
\r
1754 jmenu.setFont( MainFrame.menu_font );
\r
1755 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
\r
1756 jmenu.setForeground( conf.getGuiMenuTextColor() );
\r
1761 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
\r
1762 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
\r
1763 if ( !configuration.isUseNativeUI() ) {
\r
1764 label.setBackground( configuration.getGuiMenuBackgroundColor() );
\r
1765 label.setForeground( configuration.getGuiMenuTextColor() );
\r
1766 label.setOpaque( true );
\r
1768 label.setSelected( false );
\r
1769 label.setEnabled( false );
\r
1773 static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
\r
1774 switch ( op.getDefaultNodeFill() ) {
\r
1776 op.setDefaultNodeFill( NodeFill.SOLID );
\r
1779 op.setDefaultNodeFill( NodeFill.GRADIENT );
\r
1782 op.setDefaultNodeFill( NodeFill.NONE );
\r
1785 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
\r
1789 static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
\r
1790 switch ( op.getDefaultNodeShape() ) {
\r
1792 op.setDefaultNodeShape( NodeShape.RECTANGLE );
\r
1795 op.setDefaultNodeShape( NodeShape.CIRCLE );
\r
1798 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
\r
1802 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
\r
1803 switch ( op.getOvPlacement() ) {
\r
1805 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
\r
1808 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
\r
1811 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
\r
1814 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
\r
1817 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
\r
1819 if ( tree_panel != null ) {
\r
1820 tree_panel.updateOvSettings();
\r
1824 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
\r
1825 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
\r
1826 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
1827 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
\r
1830 mi.setText( "Cycle Node Shape Fill Type..." );
\r
1834 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
\r
1835 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
\r
1836 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
1837 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
\r
1840 mi.setText( "Cycle Node Shape Fill Type..." );
\r
1844 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
\r
1845 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
\r
1846 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
\r
1849 mi.setText( "Cycle Overview Placement..." );
\r
1853 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
\r
1854 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
\r
1855 mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
\r
1859 mi.setText( "Select Color Scheme..." );
\r
1863 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
\r
1864 mi.setText( "Select Default Font... (current: " + font_desc + ")" );
\r
1867 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
\r
1868 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
\r
1869 mi.setEnabled( true );
\r
1871 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
\r
1872 mi.setEnabled( true );
\r
1875 mi.setEnabled( false );
\r
1877 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
\r
1880 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
\r
1881 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
\r
1884 static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
\r
1885 final JCheckBoxMenuItem scale,
\r
1886 final JCheckBoxMenuItem branch_lengths,
\r
1887 final JRadioButtonMenuItem non_lined_up,
\r
1888 final JRadioButtonMenuItem uniform_clado,
\r
1889 final JRadioButtonMenuItem nonuniform_clado,
\r
1890 final JCheckBoxMenuItem label_direction_cbmi ) {
\r
1891 final TreePanel tree_panel = main_panel.getCurrentTreePanel();
\r
1892 final ControlPanel control = main_panel.getControlPanel();
\r
1893 final Options options = main_panel.getOptions();
\r
1894 scale.setSelected( options.isShowScale() );
\r
1895 branch_lengths.setSelected( options.isShowBranchLengthValues() );
\r
1896 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
\r
1897 if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
\r
1898 scale.setSelected( false );
\r
1899 scale.setEnabled( false );
\r
1900 branch_lengths.setSelected( false );
\r
1901 branch_lengths.setEnabled( false );
\r
1903 else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
\r
1904 scale.setSelected( false );
\r
1905 scale.setEnabled( false );
\r
1906 branch_lengths.setEnabled( true );
\r
1909 scale.setEnabled( true );
\r
1910 branch_lengths.setEnabled( true );
\r
1912 if ( ( tree_panel != null )
\r
1913 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
\r
1914 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
\r
1915 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
\r
1916 branch_lengths.setSelected( false );
\r
1917 branch_lengths.setEnabled( false );
\r
1919 if ( tree_panel != null ) {
\r
1920 if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
\r
1921 || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
\r
1922 non_lined_up.setEnabled( false );
\r
1923 uniform_clado.setEnabled( false );
\r
1924 nonuniform_clado.setEnabled( false );
\r
1927 non_lined_up.setEnabled( true );
\r
1928 uniform_clado.setEnabled( true );
\r
1929 nonuniform_clado.setEnabled( true );
\r
1933 if ( ( tree_panel != null )
\r
1934 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
\r
1935 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
\r
1936 branch_lengths.setSelected( false );
\r
1937 branch_lengths.setEnabled( false );
\r
1939 if ( ( tree_panel != null )
\r
1940 && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
\r
1941 .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
\r
1942 non_lined_up.setEnabled( false );
\r
1945 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
\r
1946 non_lined_up.setEnabled( true );
\r
1949 label_direction_cbmi.setEnabled( true );
\r
1950 if ( tree_panel != null ) {
\r
1951 if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
\r
1952 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
\r
1953 label_direction_cbmi.setEnabled( false );
\r
1955 if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
\r
1956 scale.setSelected( false );
\r
1957 scale.setEnabled( false );
\r
1962 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
\r
1963 for( final TreePanel tree_panel : treepanels ) {
\r
1964 tree_panel.setTextAntialias();
\r