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.LinkedList;
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37 import java.util.List;
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38 import java.util.Locale;
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39 import java.util.NoSuchElementException;
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41 import javax.swing.Box;
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42 import javax.swing.JApplet;
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43 import javax.swing.JCheckBoxMenuItem;
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44 import javax.swing.JFrame;
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45 import javax.swing.JLabel;
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46 import javax.swing.JMenu;
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47 import javax.swing.JMenuBar;
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48 import javax.swing.JMenuItem;
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49 import javax.swing.JOptionPane;
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50 import javax.swing.JPanel;
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51 import javax.swing.JRadioButtonMenuItem;
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52 import javax.swing.JTextField;
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53 import javax.swing.SwingUtilities;
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55 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
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56 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
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57 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
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58 import org.forester.archaeopteryx.tools.InferenceManager;
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59 import org.forester.archaeopteryx.tools.ProcessPool;
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60 import org.forester.archaeopteryx.tools.ProcessRunning;
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61 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
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62 import org.forester.phylogeny.Phylogeny;
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63 import org.forester.phylogeny.PhylogenyMethods;
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64 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
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65 import org.forester.phylogeny.PhylogenyNode;
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66 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
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67 import org.forester.phylogeny.data.Annotation;
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68 import org.forester.phylogeny.data.NodeDataField;
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69 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
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70 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
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71 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
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72 import org.forester.sdi.GSDI;
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73 import org.forester.sdi.GSDIR;
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74 import org.forester.sdi.SDIException;
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75 import org.forester.util.ForesterConstants;
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76 import org.forester.util.ForesterUtil;
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78 public abstract class MainFrame extends JFrame implements ActionListener {
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80 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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81 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
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82 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
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83 private static final long serialVersionUID = 3655000897845508358L;
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84 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
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87 static final String TYPE_MENU_HEADER = "Type";
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88 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
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89 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
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90 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
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91 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
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92 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
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93 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
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94 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
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95 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
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96 static final String OPTIONS_HEADER = "Options";
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97 static final String SEARCH_SUBHEADER = "Search:";
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98 static final String DISPLAY_SUBHEADER = "Display:";
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99 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
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100 static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions";
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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 COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";
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104 static final String DISPLAY_SCALE_LABEL = "Scale";
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105 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
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106 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
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107 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
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108 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
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109 static final String SEARCH_WITH_REGEX_TIP = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits.";
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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 = "Shapes for External Nodes";
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114 static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";
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115 static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";
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116 static final String SHOW_OVERVIEW_LABEL = "Overview";
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117 static final String FONT_SIZE_MENU_LABEL = "Font Size";
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118 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
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119 static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";
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120 static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";
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121 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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122 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
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123 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
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124 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
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125 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
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126 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
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127 static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";
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128 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
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129 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
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130 static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";
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131 static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";
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132 static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";
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133 JMenuBar _jmenubar;
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137 JMenu _options_jmenu;
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138 JMenu _font_size_menu;
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140 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
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142 JMenu _analysis_menu;
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143 JMenuItem _load_species_tree_item;
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144 JMenuItem _gsdi_item;
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145 JMenuItem _gsdir_item;
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146 JMenuItem _lineage_inference;
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148 JMenuItem _open_item;
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149 JMenuItem _open_url_item;
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150 JMenuItem _save_item;
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151 JMenuItem _save_all_item;
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152 JMenuItem _close_item;
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153 JMenuItem _exit_item;
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154 JMenuItem _new_item;
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156 JMenuItem _midpoint_root_item;
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157 JMenuItem _taxcolor_item;
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158 JMenuItem _confcolor_item;
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159 JMenuItem _color_rank_jmi;
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160 JMenuItem _collapse_species_specific_subtrees;
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161 JMenuItem _obtain_detailed_taxonomic_information_jmi;
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162 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
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163 JMenuItem _obtain_seq_information_jmi;
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164 JMenuItem _move_node_names_to_tax_sn_jmi;
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165 JMenuItem _move_node_names_to_seq_names_jmi;
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166 JMenuItem _extract_tax_code_from_node_names_jmi;
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167 JMenuItem _annotate_item;
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168 JMenuItem _remove_branch_color_item;
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169 JMenuItem _remove_visual_styles_item;
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170 JMenuItem _delete_selected_nodes_item;
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171 JMenuItem _delete_not_selected_nodes_item;
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173 JMenuItem _super_tiny_fonts_item;
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174 JMenuItem _tiny_fonts_item;
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175 JMenuItem _small_fonts_item;
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176 JMenuItem _medium_fonts_item;
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177 JMenuItem _large_fonts_item;
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179 // _ screen and print
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180 JMenuItem _choose_font_mi;
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181 JMenuItem _switch_colors_mi;
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182 JCheckBoxMenuItem _label_direction_cbmi;
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183 // _ screen display
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184 JCheckBoxMenuItem _screen_antialias_cbmi;
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185 JCheckBoxMenuItem _background_gradient_cbmi;
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186 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
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187 JRadioButtonMenuItem _uniform_cladograms_rbmi;
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188 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
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189 JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
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190 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
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191 JCheckBoxMenuItem _show_overview_cbmi;
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192 JCheckBoxMenuItem _show_domain_labels;
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193 JCheckBoxMenuItem _show_annotation_ref_source;
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194 JCheckBoxMenuItem _abbreviate_scientific_names;
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195 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
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196 JMenuItem _overview_placment_mi;
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197 JMenuItem _choose_minimal_confidence_mi;
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198 JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
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199 JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
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200 JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
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201 JMenuItem _cycle_node_shape_mi;
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202 JMenuItem _cycle_node_fill_mi;
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203 JMenuItem _choose_node_size_mi;
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204 JMenuItem _cycle_data_return;
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205 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
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206 JCheckBoxMenuItem _right_line_up_domains_cbmi;
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207 JCheckBoxMenuItem _line_up_renderable_data_cbmi;
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209 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
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210 JCheckBoxMenuItem _antialias_print_cbmi;
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211 JCheckBoxMenuItem _print_black_and_white_cbmi;
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212 JCheckBoxMenuItem _print_using_actual_size_cbmi;
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213 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
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214 JMenuItem _print_size_mi;
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215 JMenuItem _choose_pdf_width_mi;
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217 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
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218 JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
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219 JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
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220 JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
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221 JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
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222 JCheckBoxMenuItem _replace_underscores_cbmi;
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223 JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
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224 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
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225 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
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227 JCheckBoxMenuItem _search_case_senstive_cbmi;
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228 JCheckBoxMenuItem _search_whole_words_only_cbmi;
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229 JCheckBoxMenuItem _inverse_search_result_cbmi;
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230 JCheckBoxMenuItem _search_with_regex_cbmi;
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233 JCheckBoxMenuItem _rectangular_type_cbmi;
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234 JCheckBoxMenuItem _triangular_type_cbmi;
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235 JCheckBoxMenuItem _curved_type_cbmi;
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236 JCheckBoxMenuItem _convex_type_cbmi;
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237 JCheckBoxMenuItem _euro_type_cbmi;
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238 JCheckBoxMenuItem _rounded_type_cbmi;
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239 JCheckBoxMenuItem _unrooted_type_cbmi;
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240 JCheckBoxMenuItem _circular_type_cbmi;
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241 // view as text menu:
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242 JMenuItem _view_as_NH_item;
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243 JMenuItem _view_as_XML_item;
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244 JMenuItem _view_as_nexus_item;
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245 JMenuItem _display_basic_information_item;
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247 JMenuItem _about_item;
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248 JMenuItem _help_item;
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249 JMenuItem _website_item;
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250 JMenuItem _phyloxml_website_item;
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251 JMenuItem _phyloxml_ref_item;
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252 JMenuItem _aptx_ref_item;
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254 JMenu _process_menu;
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255 // Handy pointers to child components:
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256 MainPanel _mainpanel;
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257 Container _contentpane;
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258 final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
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259 Configuration _configuration;
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261 private Phylogeny _species_tree;
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262 InferenceManager _inference_manager;
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263 final ProcessPool _process_pool;
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264 private String _previous_node_annotation_ref;
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267 _process_pool = ProcessPool.createInstance();
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271 * Action performed.
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274 public void actionPerformed( final ActionEvent e ) {
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275 final Object o = e.getSource();
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276 boolean is_applet = false;
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277 JApplet applet = null;
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278 if ( getCurrentTreePanel() != null ) {
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279 is_applet = getCurrentTreePanel().isApplet();
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281 applet = getCurrentTreePanel().obtainApplet();
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284 if ( o == _exit_item ) {
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287 else if ( o == _gsdi_item ) {
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288 if ( isSubtreeDisplayed() ) {
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293 else if ( o == _gsdir_item ) {
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294 if ( isSubtreeDisplayed() ) {
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299 else if ( o == _taxcolor_item ) {
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302 else if ( o == _confcolor_item ) {
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305 else if ( o == _color_rank_jmi ) {
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308 else if ( o == _collapse_species_specific_subtrees ) {
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309 if ( isSubtreeDisplayed() ) {
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312 if ( getCurrentTreePanel() != null ) {
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313 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
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316 else if ( o == _remove_branch_color_item ) {
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317 if ( isSubtreeDisplayed() ) {
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320 removeBranchColors();
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322 else if ( o == _remove_visual_styles_item ) {
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323 if ( isSubtreeDisplayed() ) {
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326 removeVisualStyles();
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328 else if ( o == _midpoint_root_item ) {
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329 if ( isSubtreeDisplayed() ) {
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334 else if ( o == _delete_selected_nodes_item ) {
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335 if ( isSubtreeDisplayed() ) {
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338 deleteSelectedNodes( true );
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340 else if ( o == _delete_not_selected_nodes_item ) {
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341 if ( isSubtreeDisplayed() ) {
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344 deleteSelectedNodes( false );
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346 else if ( o == _annotate_item ) {
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347 annotateSequences();
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349 else if ( o == _switch_colors_mi ) {
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352 else if ( o == _display_basic_information_item ) {
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353 if ( getCurrentTreePanel() != null ) {
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354 displayBasicInformation( getCurrentTreePanel().getTreeFile() );
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357 else if ( o == _view_as_NH_item ) {
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360 else if ( o == _view_as_XML_item ) {
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363 else if ( o == _view_as_nexus_item ) {
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366 else if ( o == _super_tiny_fonts_item ) {
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367 if ( getCurrentTreePanel() != null ) {
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368 getCurrentTreePanel().setSuperTinyFonts();
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369 getCurrentTreePanel().repaint();
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372 else if ( o == _tiny_fonts_item ) {
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373 if ( getCurrentTreePanel() != null ) {
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374 getCurrentTreePanel().setTinyFonts();
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375 getCurrentTreePanel().repaint();
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378 else if ( o == _small_fonts_item ) {
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379 if ( getCurrentTreePanel() != null ) {
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380 getCurrentTreePanel().setSmallFonts();
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381 getCurrentTreePanel().repaint();
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384 else if ( o == _medium_fonts_item ) {
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385 if ( getCurrentTreePanel() != null ) {
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386 getCurrentTreePanel().setMediumFonts();
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387 getCurrentTreePanel().repaint();
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390 else if ( o == _large_fonts_item ) {
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391 if ( getCurrentTreePanel() != null ) {
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392 getCurrentTreePanel().setLargeFonts();
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393 getCurrentTreePanel().repaint();
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396 else if ( o == _choose_font_mi ) {
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399 else if ( o == _choose_minimal_confidence_mi ) {
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400 chooseMinimalConfidence();
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402 else if ( o == _choose_node_size_mi ) {
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403 chooseNodeSize( getOptions(), this );
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405 else if ( o == _overview_placment_mi ) {
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406 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
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408 else if ( o == _cycle_node_fill_mi ) {
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409 MainFrame.cycleNodeFill( getOptions() );
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411 else if ( o == _cycle_node_shape_mi ) {
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412 MainFrame.cycleNodeShape( getOptions() );
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414 else if ( o == _cycle_data_return ) {
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415 MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );
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417 else if ( o == _screen_antialias_cbmi ) {
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418 updateOptions( getOptions() );
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419 updateScreenTextAntialias( getMainPanel().getTreePanels() );
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421 else if ( o == _background_gradient_cbmi ) {
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422 updateOptions( getOptions() );
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424 else if ( o == _show_domain_labels ) {
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425 updateOptions( getOptions() );
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427 else if ( o == _show_annotation_ref_source ) {
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428 updateOptions( getOptions() );
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430 else if ( o == _abbreviate_scientific_names ) {
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431 updateOptions( getOptions() );
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433 else if ( o == _color_labels_same_as_parent_branch ) {
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434 updateOptions( getOptions() );
\r
436 else if ( o == _show_default_node_shapes_internal_cbmi ) {
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437 updateOptions( getOptions() );
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439 else if ( o == _show_default_node_shapes_external_cbmi ) {
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440 updateOptions( getOptions() );
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442 else if ( o == _show_default_node_shapes_for_marked_cbmi ) {
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443 updateOptions( getOptions() );
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445 else if ( o == _non_lined_up_cladograms_rbmi ) {
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446 updateOptions( getOptions() );
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449 else if ( o == _uniform_cladograms_rbmi ) {
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450 updateOptions( getOptions() );
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453 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
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454 updateOptions( getOptions() );
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457 else if ( o == _search_case_senstive_cbmi ) {
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458 updateOptions( getOptions() );
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459 getMainPanel().getControlPanel().search0();
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460 getMainPanel().getControlPanel().search1();
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462 else if ( o == _search_whole_words_only_cbmi ) {
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463 if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
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464 _search_with_regex_cbmi.setSelected( false );
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466 updateOptions( getOptions() );
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467 getMainPanel().getControlPanel().search0();
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468 getMainPanel().getControlPanel().search1();
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470 else if ( o == _inverse_search_result_cbmi ) {
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471 updateOptions( getOptions() );
\r
472 getMainPanel().getControlPanel().search0();
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473 getMainPanel().getControlPanel().search1();
\r
475 else if ( o == _search_with_regex_cbmi ) {
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476 if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
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477 _search_whole_words_only_cbmi.setSelected( false );
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479 if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
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480 _search_case_senstive_cbmi.setSelected( true );
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482 updateOptions( getOptions() );
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483 getMainPanel().getControlPanel().search0();
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484 getMainPanel().getControlPanel().search1();
\r
486 else if ( o == _show_scale_cbmi ) {
\r
487 updateOptions( getOptions() );
\r
489 else if ( o == _color_by_taxonomic_group_cbmi ) {
\r
490 updateOptions( getOptions() );
\r
492 else if ( o == _show_confidence_stddev_cbmi ) {
\r
493 updateOptions( getOptions() );
\r
495 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
\r
496 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
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497 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
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499 updateOptions( getOptions() );
\r
501 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
\r
502 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
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503 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
\r
505 updateOptions( getOptions() );
\r
507 else if ( o == _label_direction_cbmi ) {
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508 updateOptions( getOptions() );
\r
510 else if ( o == _show_overview_cbmi ) {
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511 updateOptions( getOptions() );
\r
512 if ( getCurrentTreePanel() != null ) {
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513 getCurrentTreePanel().updateOvSizes();
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516 else if ( o == _line_up_renderable_data_cbmi ) {
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517 if ( !_line_up_renderable_data_cbmi.isSelected() ) {
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518 _right_line_up_domains_cbmi.setSelected( false );
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520 updateOptions( getOptions() );
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522 else if ( o == _right_line_up_domains_cbmi ) {
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523 if ( _right_line_up_domains_cbmi.isSelected() ) {
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524 _line_up_renderable_data_cbmi.setSelected( true );
\r
526 updateOptions( getOptions() );
\r
528 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
\r
529 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
\r
530 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
\r
533 else if ( o == _about_item ) {
\r
536 else if ( o == _help_item ) {
\r
538 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );
\r
540 catch ( final IOException e1 ) {
\r
541 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
544 else if ( o == _website_item ) {
\r
546 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
\r
548 catch ( final IOException e1 ) {
\r
549 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
552 else if ( o == _phyloxml_website_item ) {
\r
554 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
\r
556 catch ( final IOException e1 ) {
\r
557 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
560 else if ( o == _aptx_ref_item ) {
\r
562 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
\r
564 catch ( final IOException e1 ) {
\r
565 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
568 else if ( o == _phyloxml_ref_item ) {
\r
570 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
\r
572 catch ( final IOException e1 ) {
\r
573 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
577 if ( _load_phylogeny_from_webservice_menu_items != null ) {
\r
578 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
\r
579 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
\r
580 readPhylogeniesFromWebservice( i );
\r
585 _contentpane.repaint();
\r
588 private void deleteSelectedNodes( final boolean delete ) {
\r
589 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
590 if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {
\r
593 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
594 if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
595 final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
596 for( final PhylogenyNode n : all_selected_nodes ) {
\r
597 if ( n.isExternal() ) {
\r
602 String function = "Retain";
\r
604 function = "Delete";
\r
606 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
608 .showMessageDialog( this,
\r
609 "Need to select external nodes, either via direct selection or via the \"Search\" function",
\r
610 "No external nodes selected to " + function.toLowerCase(),
\r
611 JOptionPane.ERROR_MESSAGE );
\r
614 final int todo = nodes.size();
\r
615 final int ext = phy.getNumberOfExternalNodes();
\r
621 JOptionPane.showMessageDialog( this,
\r
622 "Cannot delete all nodes",
\r
623 "Attempt to delete all nodes ",
\r
624 JOptionPane.ERROR_MESSAGE );
\r
627 final int result = JOptionPane.showConfirmDialog( null, function + " " + todo
\r
628 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res
\r
629 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );
\r
630 if ( result == JOptionPane.OK_OPTION ) {
\r
632 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
\r
633 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
\r
634 final PhylogenyNode n = it.next();
\r
635 if ( !nodes.contains( n ) ) {
\r
636 to_delete.add( n );
\r
639 for( final PhylogenyNode n : to_delete ) {
\r
640 phy.deleteSubtree( n, true );
\r
644 for( final PhylogenyNode n : nodes ) {
\r
645 phy.deleteSubtree( n, true );
\r
649 getCurrentTreePanel().setNodeInPreorderToNull();
\r
650 phy.externalNodesHaveChanged();
\r
651 phy.clearHashIdToNodeMap();
\r
652 phy.recalculateNumberOfExternalDescendants( true );
\r
653 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
654 getCurrentTreePanel().setEdited( true );
\r
659 void resetSearch() {
\r
660 getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
\r
661 getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
\r
662 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );
\r
663 getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );
\r
664 getMainPanel().getControlPanel().getSearchTextField0().setText( "" );
\r
665 getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );
\r
666 getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );
\r
667 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );
\r
668 getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );
\r
669 getMainPanel().getControlPanel().getSearchTextField1().setText( "" );
\r
670 getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );
\r
671 getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );
\r
674 public Configuration getConfiguration() {
\r
675 return _configuration;
\r
679 * This method returns the current external node data which
\r
680 * has been selected by the user by clicking the "Return ..."
\r
681 * menu item. This method is expected to be called from Javascript or
\r
682 * something like it.
\r
684 * @return current external node data as String
\r
686 public String getCurrentExternalNodesDataBuffer() {
\r
687 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
\r
690 public int getCurrentExternalNodesDataBufferChangeCounter() {
\r
691 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
\r
694 public int getCurrentExternalNodesDataBufferLength() {
\r
695 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
\r
698 public InferenceManager getInferenceManager() {
\r
699 return _inference_manager;
\r
702 public MainPanel getMainPanel() {
\r
706 public Options getOptions() {
\r
710 public ProcessPool getProcessPool() {
\r
711 return _process_pool;
\r
714 public void showTextFrame( final String s, final String title ) {
\r
716 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
\r
719 public void showWhole() {
\r
720 _mainpanel.getControlPanel().showWhole();
\r
723 public void updateProcessMenu() {
\r
724 // In general Swing is not thread safe.
\r
725 // See "Swing's Threading Policy".
\r
726 SwingUtilities.invokeLater( new Runnable() {
\r
729 public void run() {
\r
730 doUpdateProcessMenu();
\r
735 void activateSaveAllIfNeeded() {
\r
736 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
\r
737 _save_all_item.setEnabled( true );
\r
740 _save_all_item.setEnabled( false );
\r
744 void buildFileMenu() {
\r
745 _file_jmenu = createMenu( "File", getConfiguration() );
\r
746 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
\r
747 customizeJMenuItem( _exit_item );
\r
748 _jmenubar.add( _file_jmenu );
\r
751 void buildFontSizeMenu() {
\r
752 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
\r
753 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
\r
754 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
\r
755 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
\r
756 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
\r
757 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
\r
758 customizeJMenuItem( _super_tiny_fonts_item );
\r
759 customizeJMenuItem( _tiny_fonts_item );
\r
760 customizeJMenuItem( _small_fonts_item );
\r
761 customizeJMenuItem( _medium_fonts_item );
\r
762 customizeJMenuItem( _large_fonts_item );
\r
763 _jmenubar.add( _font_size_menu );
\r
766 void buildHelpMenu() {
\r
767 _help_jmenu = createMenu( "Help", getConfiguration() );
\r
768 _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
\r
769 _help_jmenu.addSeparator();
\r
770 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
\r
771 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...
\r
772 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
\r
773 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
\r
774 _help_jmenu.addSeparator();
\r
775 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
\r
776 customizeJMenuItem( _help_item );
\r
777 customizeJMenuItem( _website_item );
\r
778 customizeJMenuItem( _phyloxml_website_item );
\r
779 customizeJMenuItem( _aptx_ref_item );
\r
780 customizeJMenuItem( _phyloxml_ref_item );
\r
781 customizeJMenuItem( _about_item );
\r
782 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
\r
783 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
\r
784 _jmenubar.add( _help_jmenu );
\r
787 void buildTypeMenu() {
\r
788 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
\r
789 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
\r
790 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
\r
791 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
\r
792 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
\r
793 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
\r
794 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
\r
795 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
\r
796 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
\r
797 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
\r
798 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
\r
799 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
\r
800 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
\r
801 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
\r
802 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
\r
803 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
\r
804 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
\r
805 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
806 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
807 initializeTypeMenu( getOptions() );
\r
808 _jmenubar.add( _type_menu );
\r
811 void buildViewMenu() {
\r
812 _view_jmenu = createMenu( "View", getConfiguration() );
\r
813 _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
\r
814 _view_jmenu.addSeparator();
\r
815 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
\r
816 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
\r
817 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
\r
818 customizeJMenuItem( _display_basic_information_item );
\r
819 customizeJMenuItem( _view_as_NH_item );
\r
820 customizeJMenuItem( _view_as_XML_item );
\r
821 customizeJMenuItem( _view_as_nexus_item );
\r
822 _jmenubar.add( _view_jmenu );
\r
825 void checkTextFrames() {
\r
826 if ( _textframes.size() > 5 ) {
\r
828 if ( _textframes.getFirst() != null ) {
\r
829 _textframes.getFirst().removeMe();
\r
832 _textframes.removeFirst();
\r
835 catch ( final NoSuchElementException e ) {
\r
842 removeAllTextFrames();
\r
843 if ( _mainpanel != null ) {
\r
844 _mainpanel.terminate();
\r
846 if ( _contentpane != null ) {
\r
847 _contentpane.removeAll();
\r
849 setVisible( false );
\r
854 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
855 final String[] ranks = AptxUtil.getAllPossibleRanks();
\r
856 final String rank = ( String ) JOptionPane
\r
857 .showInputDialog( this,
\r
858 "What rank should the colorization be based on",
\r
860 JOptionPane.QUESTION_MESSAGE,
\r
864 if ( !ForesterUtil.isEmpty( rank ) ) {
\r
865 _mainpanel.getCurrentTreePanel().colorRank( rank );
\r
871 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
872 _mainpanel.getCurrentTreePanel().confColor();
\r
876 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
\r
877 if ( item != null ) {
\r
878 item.setFont( MainFrame.menu_font );
\r
879 if ( !getConfiguration().isUseNativeUI() ) {
\r
880 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
881 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
883 item.setSelected( is_selected );
\r
884 item.addActionListener( this );
\r
888 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
\r
889 if ( jmi != null ) {
\r
890 jmi.setFont( MainFrame.menu_font );
\r
891 if ( !getConfiguration().isUseNativeUI() ) {
\r
892 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
893 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
895 jmi.addActionListener( this );
\r
900 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
\r
901 if ( item != null ) {
\r
902 item.setFont( MainFrame.menu_font );
\r
903 if ( !getConfiguration().isUseNativeUI() ) {
\r
904 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
905 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
907 item.setSelected( is_selected );
\r
908 item.addActionListener( this );
\r
912 void displayBasicInformation( final File treefile ) {
\r
913 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
914 String title = "Basic Information";
\r
915 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
916 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
\r
918 showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
\r
922 void exceptionOccuredDuringOpenFile( final Exception e ) {
\r
924 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
926 catch ( final Exception ex ) {
\r
929 JOptionPane.showMessageDialog( this,
\r
930 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
931 "Error during File|Open",
\r
932 JOptionPane.ERROR_MESSAGE );
\r
935 void exceptionOccuredDuringSaveAs( final Exception e ) {
\r
937 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
939 catch ( final Exception ex ) {
\r
942 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
\r
945 void executeGSDI() {
\r
946 if ( !isOKforSDI( false, true ) ) {
\r
949 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
\r
950 JOptionPane.showMessageDialog( this,
\r
951 "Gene tree is not rooted.",
\r
952 "Cannot execute GSDI",
\r
953 JOptionPane.ERROR_MESSAGE );
\r
956 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
957 gene_tree.setAllNodesToNotCollapse();
\r
958 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
960 final Phylogeny species_tree = getSpeciesTree().copy();
\r
962 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
\r
964 catch ( final SDIException e ) {
\r
965 JOptionPane.showMessageDialog( this,
\r
966 e.getLocalizedMessage(),
\r
967 "Error during GSDI",
\r
968 JOptionPane.ERROR_MESSAGE );
\r
971 catch ( final Exception e ) {
\r
972 AptxUtil.unexpectedException( e );
\r
975 gene_tree.setRerootable( false );
\r
976 gene_tree.clearHashIdToNodeMap();
\r
977 gene_tree.recalculateNumberOfExternalDescendants( true );
\r
978 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
\r
979 getMainPanel().getControlPanel().setShowEvents( true );
\r
981 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
982 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
984 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
986 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
987 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
988 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
989 JOptionPane.showMessageDialog( this,
\r
990 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
991 + "Potential duplications: "
\r
992 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
993 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
994 + "Stripped gene tree nodes: "
\r
995 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
996 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
997 + "Number of polytomies in species tree used: " + poly + "\n",
\r
998 "GSDI successfully completed",
\r
999 JOptionPane.WARNING_MESSAGE );
\r
1002 JOptionPane.showMessageDialog( this,
\r
1003 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
1004 + "Potential duplications: "
\r
1005 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
1006 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
1007 + "Stripped gene tree nodes: "
\r
1008 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1009 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
1010 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1011 "GSDI successfully completed",
\r
1012 JOptionPane.INFORMATION_MESSAGE );
\r
1016 void executeGSDIR() {
\r
1017 if ( !isOKforSDI( false, false ) ) {
\r
1020 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
\r
1022 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
\r
1023 JOptionPane.showMessageDialog( this,
\r
1024 "Gene tree is not completely binary",
\r
1025 "Cannot execute GSDI",
\r
1026 JOptionPane.ERROR_MESSAGE );
\r
1029 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
1030 gene_tree.setAllNodesToNotCollapse();
\r
1031 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
1032 GSDIR gsdir = null;
\r
1033 final Phylogeny species_tree = getSpeciesTree().copy();
\r
1035 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
\r
1037 catch ( final SDIException e ) {
\r
1038 JOptionPane.showMessageDialog( this,
\r
1039 e.getLocalizedMessage(),
\r
1040 "Error during GSDIR",
\r
1041 JOptionPane.ERROR_MESSAGE );
\r
1044 catch ( final Exception e ) {
\r
1045 AptxUtil.unexpectedException( e );
\r
1048 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
\r
1049 result_gene_tree.setRerootable( false );
\r
1050 result_gene_tree.clearHashIdToNodeMap();
\r
1051 result_gene_tree.recalculateNumberOfExternalDescendants( true );
\r
1052 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
\r
1053 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
\r
1054 getMainPanel().getControlPanel().setShowEvents( true );
\r
1056 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
1057 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
1059 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
1061 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
1062 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
1063 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
1064 JOptionPane.showMessageDialog( this,
\r
1065 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1066 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1067 + "Stripped gene tree nodes: "
\r
1068 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1069 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1070 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1071 "GSDIR successfully completed",
\r
1072 JOptionPane.WARNING_MESSAGE );
\r
1075 JOptionPane.showMessageDialog( this,
\r
1076 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1077 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1078 + "Stripped gene tree nodes: "
\r
1079 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1080 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1081 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1082 "GSDIR successfully completed",
\r
1083 JOptionPane.INFORMATION_MESSAGE );
\r
1087 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
\r
1088 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
\r
1089 JOptionPane.showMessageDialog( this,
\r
1090 "Gene tree and species tree have no species in common.",
\r
1091 "Error during SDI",
\r
1092 JOptionPane.ERROR_MESSAGE );
\r
1095 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
\r
1096 JOptionPane.showMessageDialog( this,
\r
1097 "Gene tree and species tree have only one species in common.",
\r
1098 "Error during SDI",
\r
1099 JOptionPane.ERROR_MESSAGE );
\r
1107 TreePanel getCurrentTreePanel() {
\r
1108 return getMainPanel().getCurrentTreePanel();
\r
1111 JMenu getHelpMenu() {
\r
1112 return _help_jmenu;
\r
1115 JCheckBoxMenuItem getlabelDirectionCbmi() {
\r
1116 return _label_direction_cbmi;
\r
1119 JMenuBar getMenuBarOfMainFrame() {
\r
1123 final Phylogeny getSpeciesTree() {
\r
1124 return _species_tree;
\r
1127 void initializeTypeMenu( final Options options ) {
\r
1128 setTypeMenuToAllUnselected();
\r
1129 switch ( options.getPhylogenyGraphicsType() ) {
\r
1131 _convex_type_cbmi.setSelected( true );
\r
1134 _curved_type_cbmi.setSelected( true );
\r
1137 _euro_type_cbmi.setSelected( true );
\r
1140 _rounded_type_cbmi.setSelected( true );
\r
1143 _triangular_type_cbmi.setSelected( true );
\r
1146 _unrooted_type_cbmi.setSelected( true );
\r
1149 _circular_type_cbmi.setSelected( true );
\r
1152 _rectangular_type_cbmi.setSelected( true );
\r
1157 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
\r
1158 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1161 else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
\r
1162 JOptionPane.showMessageDialog( this,
\r
1163 "No species tree loaded",
\r
1164 "Cannot execute GSDI",
\r
1165 JOptionPane.ERROR_MESSAGE );
\r
1168 else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
\r
1169 JOptionPane.showMessageDialog( this,
\r
1170 "Species tree is not completely binary",
\r
1171 "Cannot execute GSDI",
\r
1172 JOptionPane.ERROR_MESSAGE );
\r
1175 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
\r
1176 JOptionPane.showMessageDialog( this,
\r
1177 "Gene tree is not completely binary",
\r
1178 "Cannot execute GSDI",
\r
1179 JOptionPane.ERROR_MESSAGE );
\r
1187 boolean isSubtreeDisplayed() {
\r
1188 if ( getCurrentTreePanel() != null ) {
\r
1189 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
\r
1191 .showMessageDialog( this,
\r
1192 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
\r
1193 "Operation can not be exectuted on a sub-tree",
\r
1194 JOptionPane.WARNING_MESSAGE );
\r
1201 void midpointRoot() {
\r
1202 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1203 _mainpanel.getCurrentTreePanel().midpointRoot();
\r
1207 void readPhylogeniesFromWebservice( final int i ) {
\r
1208 final UrlTreeReader reader = new UrlTreeReader( this, i );
\r
1209 new Thread( reader ).start();
\r
1212 void removeAllTextFrames() {
\r
1213 for( final TextFrame tf : _textframes ) {
\r
1214 if ( tf != null ) {
\r
1218 _textframes.clear();
\r
1221 void setConfiguration( final Configuration configuration ) {
\r
1222 _configuration = configuration;
\r
1225 void setInferenceManager( final InferenceManager i ) {
\r
1226 _inference_manager = i;
\r
1229 void setOptions( final Options options ) {
\r
1230 _options = options;
\r
1233 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
\r
1234 setTypeMenuToAllUnselected();
\r
1237 _circular_type_cbmi.setSelected( true );
\r
1240 _convex_type_cbmi.setSelected( true );
\r
1243 _curved_type_cbmi.setSelected( true );
\r
1246 _euro_type_cbmi.setSelected( true );
\r
1249 _rounded_type_cbmi.setSelected( true );
\r
1252 _rectangular_type_cbmi.setSelected( true );
\r
1255 _triangular_type_cbmi.setSelected( true );
\r
1258 _unrooted_type_cbmi.setSelected( true );
\r
1261 throw new IllegalArgumentException( "unknown type: " + type );
\r
1265 final void setSpeciesTree( final Phylogeny species_tree ) {
\r
1266 _species_tree = species_tree;
\r
1269 void setTypeMenuToAllUnselected() {
\r
1270 _convex_type_cbmi.setSelected( false );
\r
1271 _curved_type_cbmi.setSelected( false );
\r
1272 _euro_type_cbmi.setSelected( false );
\r
1273 _rounded_type_cbmi.setSelected( false );
\r
1274 _triangular_type_cbmi.setSelected( false );
\r
1275 _rectangular_type_cbmi.setSelected( false );
\r
1276 _unrooted_type_cbmi.setSelected( false );
\r
1277 _circular_type_cbmi.setSelected( false );
\r
1280 void switchColors() {
\r
1281 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
\r
1282 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
\r
1283 csc.setVisible( true );
\r
1287 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1288 _mainpanel.getCurrentTreePanel().taxColor();
\r
1292 void typeChanged( final Object o ) {
\r
1293 updateTypeCheckboxes( getOptions(), o );
\r
1294 updateOptions( getOptions() );
\r
1295 if ( getCurrentTreePanel() != null ) {
\r
1296 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
\r
1297 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
\r
1298 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1299 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
\r
1300 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1301 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
\r
1302 getCurrentTreePanel().getControlPanel().showWhole();
\r
1304 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
\r
1305 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
\r
1308 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
\r
1310 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
\r
1311 updateScreenTextAntialias( getMainPanel().getTreePanels() );
\r
1312 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
\r
1313 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
\r
1314 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
\r
1317 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
\r
1323 void updateOptions( final Options options ) {
\r
1324 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
\r
1325 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
\r
1326 && _background_gradient_cbmi.isSelected() );
\r
1327 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
\r
1328 options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
\r
1329 && _show_annotation_ref_source.isSelected() );
\r
1330 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
\r
1331 && _abbreviate_scientific_names.isSelected() );
\r
1332 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
\r
1333 && _color_labels_same_as_parent_branch.isSelected() );
\r
1334 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
\r
1335 && _show_default_node_shapes_internal_cbmi.isSelected() );
\r
1336 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
\r
1337 && _show_default_node_shapes_external_cbmi.isSelected() );
\r
1338 options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
\r
1339 && _show_default_node_shapes_for_marked_cbmi.isSelected() );
\r
1340 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
\r
1341 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
\r
1343 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
\r
1344 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
\r
1346 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
\r
1347 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
\r
1349 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
\r
1350 && _search_case_senstive_cbmi.isSelected() );
\r
1351 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
\r
1352 options.setShowScale( _show_scale_cbmi.isSelected() );
\r
1354 if ( _label_direction_cbmi != null ) {
\r
1355 if ( _label_direction_cbmi.isSelected() ) {
\r
1356 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
\r
1359 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
\r
1362 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
\r
1363 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
\r
1364 && _show_confidence_stddev_cbmi.isSelected() );
\r
1365 if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
\r
1366 options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
\r
1368 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
\r
1369 && ( _print_using_actual_size_cbmi.isSelected() ) );
\r
1370 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
\r
1371 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
\r
1372 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
\r
1373 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
\r
1374 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1375 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
\r
1377 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
\r
1378 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1379 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
\r
1382 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
\r
1384 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
\r
1385 && _print_black_and_white_cbmi.isSelected() );
\r
1386 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
\r
1387 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
\r
1388 if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
\r
1389 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
\r
1391 else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
\r
1392 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
\r
1394 else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
\r
1395 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1397 else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
\r
1398 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
\r
1400 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
\r
1401 && _replace_underscores_cbmi.isSelected() );
\r
1402 options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
\r
1403 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
\r
1404 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
\r
1405 && _search_whole_words_only_cbmi.isSelected() );
\r
1406 options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
\r
1407 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
\r
1408 && _inverse_search_result_cbmi.isSelected() );
\r
1409 if ( _graphics_export_visible_only_cbmi != null ) {
\r
1410 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
\r
1411 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
\r
1412 _graphics_export_using_actual_size_cbmi.setSelected( true );
\r
1413 _graphics_export_using_actual_size_cbmi.setEnabled( false );
\r
1416 _graphics_export_using_actual_size_cbmi.setEnabled( true );
\r
1419 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
\r
1420 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1422 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
\r
1423 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
\r
1425 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
\r
1426 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
\r
1428 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
\r
1429 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
\r
1431 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
\r
1432 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
\r
1434 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
\r
1435 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
\r
1437 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
\r
1438 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
\r
1440 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
\r
1441 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
\r
1443 if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
\r
1444 options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
\r
1446 if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
\r
1447 options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
\r
1451 void updateTypeCheckboxes( final Options options, final Object o ) {
\r
1452 setTypeMenuToAllUnselected();
\r
1453 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
\r
1456 void viewAsNexus() {
\r
1457 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1458 String title = "Nexus";
\r
1459 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1460 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1462 showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
\r
1468 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1469 String title = "New Hampshire";
\r
1470 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1471 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1473 showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
\r
1474 .getNhConversionSupportValueStyle() ),
\r
1479 void viewAsXML() {
\r
1480 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1481 String title = "phyloXML";
\r
1482 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1483 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1485 showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
\r
1489 private void annotateSequences() {
\r
1490 if ( getCurrentTreePanel() != null ) {
\r
1491 List<PhylogenyNode> nodes = null;
\r
1492 if ( ( getCurrentTreePanel().getFoundNodes0() != null )
\r
1493 || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
1494 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
1496 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
1498 .showMessageDialog( this,
\r
1499 "Need to select nodes, either via direct selection or via the \"Search\" function",
\r
1500 "No nodes selected for annotation",
\r
1501 JOptionPane.ERROR_MESSAGE );
\r
1504 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
1505 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1506 final JTextField ref_field = new JTextField( 10 );
\r
1507 final JTextField desc_filed = new JTextField( 20 );
\r
1508 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
\r
1509 : getPreviousNodeAnnotationReference() );
\r
1510 final JPanel my_panel = new JPanel();
\r
1511 my_panel.add( new JLabel( "Reference " ) );
\r
1512 my_panel.add( ref_field );
\r
1513 my_panel.add( Box.createHorizontalStrut( 15 ) );
\r
1514 my_panel.add( new JLabel( "Description " ) );
\r
1515 my_panel.add( desc_filed );
\r
1516 final int result = JOptionPane.showConfirmDialog( null,
\r
1518 "Enter the sequence annotation(s) for the "
\r
1519 + nodes.size() + " selected nodes",
\r
1520 JOptionPane.OK_CANCEL_OPTION );
\r
1521 if ( result == JOptionPane.OK_OPTION ) {
\r
1522 String ref = ref_field.getText();
\r
1523 String desc = desc_filed.getText();
\r
1524 if ( !ForesterUtil.isEmpty( ref ) ) {
\r
1526 ref = ref.replaceAll( "\\s+", " " );
\r
1527 if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )
\r
1528 || ( ref.length() < 3 ) ) {
\r
1529 JOptionPane.showMessageDialog( this,
\r
1530 "Reference needs to be in the form of \"GO:1234567\"",
\r
1531 "Illegal Format for Annotation Reference",
\r
1532 JOptionPane.ERROR_MESSAGE );
\r
1536 if ( ref != null ) {
\r
1537 setPreviousNodeAnnotationReference( ref );
\r
1539 if ( desc != null ) {
\r
1540 desc = desc.trim();
\r
1541 desc = desc.replaceAll( "\\s+", " " );
\r
1543 if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
\r
1544 for( final PhylogenyNode n : nodes ) {
\r
1545 ForesterUtil.ensurePresenceOfSequence( n );
\r
1546 final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
\r
1547 : new Annotation( ref );
\r
1548 if ( !ForesterUtil.isEmpty( desc ) ) {
\r
1549 ann.setDesc( desc );
\r
1551 n.getNodeData().getSequence().addAnnotation( ann );
\r
1554 getMainPanel().getControlPanel().showAnnotations();
\r
1560 private void chooseFont() {
\r
1561 final FontChooser fc = new FontChooser();
\r
1562 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
\r
1563 fc.showDialog( this, "Select the Base Font" );
\r
1564 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
\r
1567 private void chooseMinimalConfidence() {
\r
1568 final String s = ( String ) JOptionPane
\r
1569 .showInputDialog( this,
\r
1570 "Please enter the minimum for confidence values to be displayed.\n"
\r
1571 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
\r
1572 "Minimal Confidence Value",
\r
1573 JOptionPane.QUESTION_MESSAGE,
\r
1576 getOptions().getMinConfidenceValue() );
\r
1577 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1578 boolean success = true;
\r
1580 final String m_str = s.trim();
\r
1581 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1583 m = Double.parseDouble( m_str );
\r
1585 catch ( final Exception ex ) {
\r
1592 if ( success && ( m >= 0.0 ) ) {
\r
1593 getOptions().setMinConfidenceValue( m );
\r
1598 private void doUpdateProcessMenu() {
\r
1599 if ( _process_pool.size() > 0 ) {
\r
1600 if ( _process_menu == null ) {
\r
1601 _process_menu = createMenu( "", getConfiguration() );
\r
1602 _process_menu.setForeground( Color.RED );
\r
1604 _process_menu.removeAll();
\r
1605 final String text = "processes running: " + _process_pool.size();
\r
1606 _process_menu.setText( text );
\r
1607 _jmenubar.add( _process_menu );
\r
1608 for( int i = 0; i < _process_pool.size(); ++i ) {
\r
1609 final ProcessRunning p = _process_pool.getProcessByIndex( i );
\r
1610 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
\r
1614 if ( _process_menu != null ) {
\r
1615 _process_menu.removeAll();
\r
1616 _jmenubar.remove( _process_menu );
\r
1619 _jmenubar.validate();
\r
1620 _jmenubar.repaint();
\r
1624 private String getPreviousNodeAnnotationReference() {
\r
1625 return _previous_node_annotation_ref;
\r
1628 private void removeBranchColors() {
\r
1629 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1630 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
\r
1634 private void removeVisualStyles() {
\r
1635 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1636 AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
\r
1640 private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
\r
1641 _previous_node_annotation_ref = previous_node_annotation_ref;
\r
1645 * Display the about box.
\r
1647 static void about() {
\r
1648 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
\r
1649 about.append( "Copyright (C) 2014 Christian M Zmasek\n" );
\r
1650 about.append( "All Rights Reserved\n" );
\r
1651 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
\r
1652 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
\r
1653 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
\r
1654 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
\r
1655 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
\r
1656 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
\r
1657 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
\r
1659 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
\r
1660 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
\r
1661 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
\r
1662 + ForesterUtil.OS_VERSION + "]\n" );
\r
1664 final Runtime rt = java.lang.Runtime.getRuntime();
\r
1665 final long free_memory = rt.freeMemory() / 1000000;
\r
1666 final long total_memory = rt.totalMemory() / 1000000;
\r
1667 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
\r
1668 about.append( "[locale: " + Locale.getDefault() + "]\n" );
\r
1669 about.append( "References:\n" );
\r
1670 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
\r
1671 about.append( "For more information & download:\n" );
\r
1672 about.append( Constants.APTX_WEB_SITE + "\n" );
\r
1673 about.append( "Documentation:\n" );
\r
1674 about.append( Constants.APTX_DOC_SITE + "\n" );
\r
1675 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
\r
1676 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
\r
1679 static void chooseNodeSize( final Options options, final Component parent ) {
\r
1680 final String s = ( String ) JOptionPane.showInputDialog( parent,
\r
1681 "Please enter the default size for node shapes.\n"
\r
1682 + "[current value: "
\r
1683 + options.getDefaultNodeShapeSize() + "]\n",
\r
1684 "Node Shape Size",
\r
1685 JOptionPane.QUESTION_MESSAGE,
\r
1688 options.getDefaultNodeShapeSize() );
\r
1689 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1690 boolean success = true;
\r
1692 final String m_str = s.trim();
\r
1693 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1695 m = Double.parseDouble( m_str );
\r
1697 catch ( final Exception ex ) {
\r
1704 if ( success && ( m >= 0.0 ) ) {
\r
1705 final short size = ForesterUtil.roundToShort( m );
\r
1706 if ( size >= 0.0 ) {
\r
1707 options.setDefaultNodeShapeSize( size );
\r
1713 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
\r
1714 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
\r
1717 static JMenu createMenu( final String title, final Configuration conf ) {
\r
1718 final JMenu jmenu = new JMenu( title );
\r
1719 if ( !conf.isUseNativeUI() ) {
\r
1720 jmenu.setFont( MainFrame.menu_font );
\r
1721 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
\r
1722 jmenu.setForeground( conf.getGuiMenuTextColor() );
\r
1727 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
\r
1728 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
\r
1729 if ( !configuration.isUseNativeUI() ) {
\r
1730 label.setBackground( configuration.getGuiMenuBackgroundColor() );
\r
1731 label.setForeground( configuration.getGuiMenuTextColor() );
\r
1732 label.setOpaque( true );
\r
1734 label.setSelected( false );
\r
1735 label.setEnabled( false );
\r
1739 static void cycleNodeFill( final Options op ) {
\r
1740 switch ( op.getDefaultNodeFill() ) {
\r
1742 op.setDefaultNodeFill( NodeFill.SOLID );
\r
1745 op.setDefaultNodeFill( NodeFill.GRADIENT );
\r
1748 op.setDefaultNodeFill( NodeFill.NONE );
\r
1751 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
\r
1755 static void cycleNodeShape( final Options op ) {
\r
1756 switch ( op.getDefaultNodeShape() ) {
\r
1758 op.setDefaultNodeShape( NodeShape.RECTANGLE );
\r
1761 op.setDefaultNodeShape( NodeShape.CIRCLE );
\r
1764 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
\r
1768 private static void cycleNodeDataReturn( final Options op, Configuration conf ) {
\r
1769 switch ( op.getExtDescNodeDataToReturn() ) {
\r
1771 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
\r
1774 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
\r
1776 case DOMAINS_COLLAPSED_PER_PROTEIN:
\r
1777 op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
\r
1779 case SEQ_ANNOTATIONS:
\r
1780 op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
\r
1783 op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
\r
1785 case SEQUENCE_MOL_SEQ_FASTA:
\r
1786 if ( conf != null && conf.getExtDescNodeDataToReturn() != null
\r
1787 && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL
\r
1788 && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN
\r
1789 && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS
\r
1790 && conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS
\r
1791 && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA
\r
1793 op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );
\r
1796 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
\r
1800 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
\r
1804 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
\r
1805 switch ( op.getOvPlacement() ) {
\r
1807 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
\r
1810 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
\r
1813 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
\r
1816 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
\r
1819 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
\r
1821 if ( tree_panel != null ) {
\r
1822 tree_panel.updateOvSettings();
\r
1826 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
\r
1827 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
\r
1828 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
1829 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
\r
1832 mi.setText( "Cycle Node Shape Fill Type..." );
\r
1836 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
\r
1837 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
\r
1838 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
1839 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
\r
1842 mi.setText( "Cycle Node Shape Fill Type..." );
\r
1846 static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {
\r
1847 if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {
\r
1848 mi.setText( "Cycle Node Return Data... (current: "
\r
1849 + options.getExtDescNodeDataToReturn().toString() + ")" );
\r
1852 mi.setText( "Cycle Node Return Data..." );
\r
1856 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
\r
1857 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
\r
1858 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
\r
1861 mi.setText( "Cycle Overview Placement..." );
\r
1865 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
\r
1866 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
\r
1867 mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
\r
1871 mi.setText( "Select Color Scheme..." );
\r
1875 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
\r
1876 mi.setText( "Select Default Font... (current: " + font_desc + ")" );
\r
1879 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
\r
1880 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
\r
1881 mi.setEnabled( true );
\r
1883 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
\r
1884 mi.setEnabled( true );
\r
1887 mi.setEnabled( false );
\r
1889 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
\r
1892 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
\r
1893 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
\r
1896 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
\r
1897 for( final TreePanel tree_panel : treepanels ) {
\r
1898 tree_panel.setTextAntialias();
\r