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.
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18 // You should have received a copy of the GNU Lesser General Public
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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.JFileChooser;
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45 import javax.swing.JFrame;
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46 import javax.swing.JLabel;
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47 import javax.swing.JMenu;
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48 import javax.swing.JMenuBar;
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49 import javax.swing.JMenuItem;
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50 import javax.swing.JOptionPane;
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51 import javax.swing.JPanel;
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52 import javax.swing.JRadioButtonMenuItem;
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53 import javax.swing.JTextField;
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54 import javax.swing.SwingUtilities;
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55 import javax.swing.filechooser.FileFilter;
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57 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
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58 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
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59 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
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60 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
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61 import org.forester.archaeopteryx.tools.InferenceManager;
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62 import org.forester.archaeopteryx.tools.ProcessPool;
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63 import org.forester.archaeopteryx.tools.ProcessRunning;
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64 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
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65 import org.forester.io.writers.PhylogenyWriter;
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66 import org.forester.phylogeny.Phylogeny;
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67 import org.forester.phylogeny.PhylogenyMethods;
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68 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
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69 import org.forester.phylogeny.PhylogenyNode;
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70 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
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71 import org.forester.phylogeny.data.Annotation;
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72 import org.forester.phylogeny.data.NodeDataField;
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73 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
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74 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
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75 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
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76 import org.forester.sdi.GSDI;
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77 import org.forester.sdi.GSDIR;
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78 import org.forester.sdi.SDIException;
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79 import org.forester.util.ForesterConstants;
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80 import org.forester.util.ForesterUtil;
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81 import org.forester.util.WindowsUtils;
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83 public abstract class MainFrame extends JFrame implements ActionListener {
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85 final static NHFilter nhfilter = new NHFilter();
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86 final static NHXFilter nhxfilter = new NHXFilter();
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87 final static XMLFilter xmlfilter = new XMLFilter();
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88 final static TolFilter tolfilter = new TolFilter();
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89 final static NexusFilter nexusfilter = new NexusFilter();
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90 final static PdfFilter pdffilter = new PdfFilter();
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91 final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
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92 final static MsaFileFilter msafilter = new MsaFileFilter();
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93 final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
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94 final static DefaultFilter defaultfilter = new DefaultFilter();
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95 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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96 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
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97 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
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98 private static final long serialVersionUID = 3655000897845508358L;
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99 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
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102 static final String TYPE_MENU_HEADER = "Type";
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103 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
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104 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
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105 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
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106 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
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107 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
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108 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
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109 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
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110 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
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111 static final String OPTIONS_HEADER = "Options";
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112 static final String SEARCH_SUBHEADER = "Search:";
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113 static final String DISPLAY_SUBHEADER = "Display:";
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114 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
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115 static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions";
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116 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
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117 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
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118 static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";
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119 static final String DISPLAY_SCALE_LABEL = "Scale";
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120 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
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121 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
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122 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
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123 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
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124 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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125 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
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126 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
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127 static final String BG_GRAD_LABEL = "Background Color Gradient";
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128 static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";
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129 static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";
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130 static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";
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131 static final String SHOW_OVERVIEW_LABEL = "Overview";
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132 static final String FONT_SIZE_MENU_LABEL = "Font Size";
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133 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
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134 static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";
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135 static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";
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136 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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137 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
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138 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
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139 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
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140 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
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141 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
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142 static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";
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143 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
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144 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
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145 static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";
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146 static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";
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147 static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";
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148 JMenuBar _jmenubar;
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152 JMenu _options_jmenu;
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153 JMenu _font_size_menu;
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155 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
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157 JMenu _analysis_menu;
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158 JMenuItem _load_species_tree_item;
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159 JMenuItem _gsdi_item;
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160 JMenuItem _gsdir_item;
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161 JMenuItem _lineage_inference;
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163 JMenuItem _open_item;
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164 JMenuItem _open_url_item;
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165 JMenuItem _save_item;
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166 JMenuItem _save_all_item;
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167 JMenuItem _close_item;
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168 JMenuItem _exit_item;
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169 JMenuItem _new_item;
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170 JMenuItem _print_item;
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171 JMenuItem _write_to_pdf_item;
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172 JMenuItem _write_to_jpg_item;
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173 JMenuItem _write_to_gif_item;
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174 JMenuItem _write_to_tif_item;
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175 JMenuItem _write_to_png_item;
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176 JMenuItem _write_to_bmp_item;
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178 JMenuItem _midpoint_root_item;
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179 JMenuItem _taxcolor_item;
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180 JMenuItem _confcolor_item;
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181 JMenuItem _color_rank_jmi;
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182 JMenuItem _collapse_species_specific_subtrees;
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183 JMenuItem _obtain_detailed_taxonomic_information_jmi;
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184 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
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185 JMenuItem _obtain_seq_information_jmi;
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186 JMenuItem _move_node_names_to_tax_sn_jmi;
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187 JMenuItem _move_node_names_to_seq_names_jmi;
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188 JMenuItem _extract_tax_code_from_node_names_jmi;
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189 JMenuItem _annotate_item;
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190 JMenuItem _remove_branch_color_item;
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191 JMenuItem _remove_visual_styles_item;
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192 JMenuItem _delete_selected_nodes_item;
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193 JMenuItem _delete_not_selected_nodes_item;
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195 JMenuItem _super_tiny_fonts_item;
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196 JMenuItem _tiny_fonts_item;
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197 JMenuItem _small_fonts_item;
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198 JMenuItem _medium_fonts_item;
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199 JMenuItem _large_fonts_item;
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201 // _ screen and print
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202 JMenuItem _choose_font_mi;
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203 JMenuItem _switch_colors_mi;
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204 JCheckBoxMenuItem _label_direction_cbmi;
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205 // _ screen display
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206 JCheckBoxMenuItem _screen_antialias_cbmi;
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207 JCheckBoxMenuItem _background_gradient_cbmi;
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208 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
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209 JRadioButtonMenuItem _uniform_cladograms_rbmi;
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210 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
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211 JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
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212 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
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213 JCheckBoxMenuItem _show_overview_cbmi;
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214 JCheckBoxMenuItem _show_domain_labels;
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215 JCheckBoxMenuItem _show_annotation_ref_source;
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216 JCheckBoxMenuItem _abbreviate_scientific_names;
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217 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
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218 JMenuItem _overview_placment_mi;
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219 JMenuItem _choose_minimal_confidence_mi;
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220 JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
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221 JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
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222 JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
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223 JMenuItem _cycle_node_shape_mi;
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224 JMenuItem _cycle_node_fill_mi;
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225 JMenuItem _choose_node_size_mi;
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226 JMenuItem _cycle_data_return;
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227 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
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228 JCheckBoxMenuItem _right_line_up_domains_cbmi;
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229 JCheckBoxMenuItem _line_up_renderable_data_cbmi;
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231 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
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232 JCheckBoxMenuItem _antialias_print_cbmi;
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233 JCheckBoxMenuItem _print_black_and_white_cbmi;
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234 JCheckBoxMenuItem _print_using_actual_size_cbmi;
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235 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
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236 JMenuItem _print_size_mi;
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237 JMenuItem _choose_pdf_width_mi;
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239 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
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240 JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
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241 JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
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242 JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
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243 JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
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244 JCheckBoxMenuItem _replace_underscores_cbmi;
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245 JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
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246 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
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247 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
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249 JCheckBoxMenuItem _search_case_senstive_cbmi;
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250 JCheckBoxMenuItem _search_whole_words_only_cbmi;
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251 JCheckBoxMenuItem _inverse_search_result_cbmi;
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252 JCheckBoxMenuItem _search_with_regex_cbmi;
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255 JCheckBoxMenuItem _rectangular_type_cbmi;
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256 JCheckBoxMenuItem _triangular_type_cbmi;
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257 JCheckBoxMenuItem _curved_type_cbmi;
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258 JCheckBoxMenuItem _convex_type_cbmi;
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259 JCheckBoxMenuItem _euro_type_cbmi;
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260 JCheckBoxMenuItem _rounded_type_cbmi;
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261 JCheckBoxMenuItem _unrooted_type_cbmi;
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262 JCheckBoxMenuItem _circular_type_cbmi;
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263 // view as text menu:
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264 JMenuItem _view_as_NH_item;
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265 JMenuItem _view_as_XML_item;
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266 JMenuItem _view_as_nexus_item;
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267 JMenuItem _display_basic_information_item;
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269 JMenuItem _about_item;
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270 JMenuItem _help_item;
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271 JMenuItem _website_item;
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272 JMenuItem _phyloxml_website_item;
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273 JMenuItem _phyloxml_ref_item;
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274 JMenuItem _aptx_ref_item;
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276 JFileChooser _writetopdf_filechooser;
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278 JFileChooser _save_filechooser;
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279 JFileChooser _writetographics_filechooser;
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281 JMenu _process_menu;
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282 // Handy pointers to child components:
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283 MainPanel _mainpanel;
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284 Container _contentpane;
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285 final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
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286 Configuration _configuration;
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288 private Phylogeny _species_tree;
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289 InferenceManager _inference_manager;
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290 final ProcessPool _process_pool;
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291 private String _previous_node_annotation_ref;
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294 _process_pool = ProcessPool.createInstance();
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295 _writetopdf_filechooser = new JFileChooser();
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296 _save_filechooser = new JFileChooser();
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297 _save_filechooser.setCurrentDirectory( new File( "." ) );
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298 _save_filechooser.setMultiSelectionEnabled( false );
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299 _save_filechooser.setFileFilter( MainFrame.xmlfilter );
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300 _save_filechooser.addChoosableFileFilter( nhfilter );
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301 _save_filechooser.addChoosableFileFilter( nexusfilter );
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302 _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
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303 _writetographics_filechooser = new JFileChooser();
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304 _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter );
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308 * Action performed.
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311 public void actionPerformed( final ActionEvent e ) {
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312 final Object o = e.getSource();
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313 boolean is_applet = false;
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314 JApplet applet = null;
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315 if ( getCurrentTreePanel() != null ) {
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316 is_applet = getCurrentTreePanel().isApplet();
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318 applet = getCurrentTreePanel().obtainApplet();
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321 if ( o == _exit_item ) {
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324 else if ( o == _gsdi_item ) {
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325 if ( isSubtreeDisplayed() ) {
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330 else if ( o == _gsdir_item ) {
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331 if ( isSubtreeDisplayed() ) {
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336 else if ( o == _taxcolor_item ) {
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339 else if ( o == _confcolor_item ) {
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342 else if ( o == _color_rank_jmi ) {
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345 else if ( o == _collapse_species_specific_subtrees ) {
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346 if ( isSubtreeDisplayed() ) {
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349 if ( getCurrentTreePanel() != null ) {
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350 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
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353 else if ( o == _remove_branch_color_item ) {
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354 if ( isSubtreeDisplayed() ) {
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357 removeBranchColors();
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359 else if ( o == _remove_visual_styles_item ) {
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360 if ( isSubtreeDisplayed() ) {
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363 removeVisualStyles();
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365 else if ( o == _midpoint_root_item ) {
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366 if ( isSubtreeDisplayed() ) {
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371 else if ( o == _delete_selected_nodes_item ) {
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372 if ( isSubtreeDisplayed() ) {
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375 deleteSelectedNodes( true );
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377 else if ( o == _delete_not_selected_nodes_item ) {
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378 if ( isSubtreeDisplayed() ) {
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381 deleteSelectedNodes( false );
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383 else if ( o == _annotate_item ) {
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384 annotateSequences();
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386 else if ( o == _switch_colors_mi ) {
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389 else if ( o == _display_basic_information_item ) {
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390 if ( getCurrentTreePanel() != null ) {
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391 displayBasicInformation( getCurrentTreePanel().getTreeFile() );
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394 else if ( o == _view_as_NH_item ) {
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397 else if ( o == _view_as_XML_item ) {
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400 else if ( o == _view_as_nexus_item ) {
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403 else if ( o == _super_tiny_fonts_item ) {
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404 if ( getCurrentTreePanel() != null ) {
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405 getCurrentTreePanel().setSuperTinyFonts();
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406 getCurrentTreePanel().repaint();
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409 else if ( o == _tiny_fonts_item ) {
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410 if ( getCurrentTreePanel() != null ) {
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411 getCurrentTreePanel().setTinyFonts();
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412 getCurrentTreePanel().repaint();
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415 else if ( o == _small_fonts_item ) {
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416 if ( getCurrentTreePanel() != null ) {
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417 getCurrentTreePanel().setSmallFonts();
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418 getCurrentTreePanel().repaint();
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421 else if ( o == _medium_fonts_item ) {
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422 if ( getCurrentTreePanel() != null ) {
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423 getCurrentTreePanel().setMediumFonts();
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424 getCurrentTreePanel().repaint();
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427 else if ( o == _large_fonts_item ) {
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428 if ( getCurrentTreePanel() != null ) {
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429 getCurrentTreePanel().setLargeFonts();
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430 getCurrentTreePanel().repaint();
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433 else if ( o == _choose_font_mi ) {
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436 else if ( o == _choose_minimal_confidence_mi ) {
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437 chooseMinimalConfidence();
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439 else if ( o == _choose_node_size_mi ) {
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440 chooseNodeSize( getOptions(), this );
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442 else if ( o == _overview_placment_mi ) {
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443 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
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445 else if ( o == _cycle_node_fill_mi ) {
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446 MainFrame.cycleNodeFill( getOptions() );
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448 else if ( o == _cycle_node_shape_mi ) {
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449 MainFrame.cycleNodeShape( getOptions() );
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451 else if ( o == _cycle_data_return ) {
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452 MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );
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454 else if ( o == _screen_antialias_cbmi ) {
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455 updateOptions( getOptions() );
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456 updateScreenTextAntialias( getMainPanel().getTreePanels() );
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458 else if ( o == _background_gradient_cbmi ) {
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459 updateOptions( getOptions() );
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461 else if ( o == _show_domain_labels ) {
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462 updateOptions( getOptions() );
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464 else if ( o == _show_annotation_ref_source ) {
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465 updateOptions( getOptions() );
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467 else if ( o == _abbreviate_scientific_names ) {
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468 updateOptions( getOptions() );
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470 else if ( o == _color_labels_same_as_parent_branch ) {
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471 updateOptions( getOptions() );
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473 else if ( o == _show_default_node_shapes_internal_cbmi ) {
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474 updateOptions( getOptions() );
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476 else if ( o == _show_default_node_shapes_external_cbmi ) {
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477 updateOptions( getOptions() );
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479 else if ( o == _show_default_node_shapes_for_marked_cbmi ) {
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480 updateOptions( getOptions() );
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482 else if ( o == _non_lined_up_cladograms_rbmi ) {
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483 updateOptions( getOptions() );
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486 else if ( o == _uniform_cladograms_rbmi ) {
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487 updateOptions( getOptions() );
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490 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
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491 updateOptions( getOptions() );
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494 else if ( o == _search_case_senstive_cbmi ) {
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495 updateOptions( getOptions() );
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496 getMainPanel().getControlPanel().search0();
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497 getMainPanel().getControlPanel().search1();
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499 else if ( o == _search_whole_words_only_cbmi ) {
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500 if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
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501 _search_with_regex_cbmi.setSelected( false );
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503 updateOptions( getOptions() );
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504 getMainPanel().getControlPanel().search0();
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505 getMainPanel().getControlPanel().search1();
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507 else if ( o == _inverse_search_result_cbmi ) {
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508 updateOptions( getOptions() );
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509 getMainPanel().getControlPanel().search0();
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510 getMainPanel().getControlPanel().search1();
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512 else if ( o == _search_with_regex_cbmi ) {
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513 if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
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514 _search_whole_words_only_cbmi.setSelected( false );
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516 if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
\r
517 _search_case_senstive_cbmi.setSelected( true );
\r
519 updateOptions( getOptions() );
\r
520 getMainPanel().getControlPanel().search0();
\r
521 getMainPanel().getControlPanel().search1();
\r
523 else if ( o == _show_scale_cbmi ) {
\r
524 updateOptions( getOptions() );
\r
526 else if ( o == _color_by_taxonomic_group_cbmi ) {
\r
527 updateOptions( getOptions() );
\r
529 else if ( o == _show_confidence_stddev_cbmi ) {
\r
530 updateOptions( getOptions() );
\r
532 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
\r
533 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
534 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
\r
536 updateOptions( getOptions() );
\r
538 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
\r
539 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
540 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
\r
542 updateOptions( getOptions() );
\r
544 else if ( o == _label_direction_cbmi ) {
\r
545 updateOptions( getOptions() );
\r
547 else if ( o == _show_overview_cbmi ) {
\r
548 updateOptions( getOptions() );
\r
549 if ( getCurrentTreePanel() != null ) {
\r
550 getCurrentTreePanel().updateOvSizes();
\r
553 else if ( o == _line_up_renderable_data_cbmi ) {
\r
554 if ( !_line_up_renderable_data_cbmi.isSelected() ) {
\r
555 _right_line_up_domains_cbmi.setSelected( false );
\r
557 updateOptions( getOptions() );
\r
559 else if ( o == _right_line_up_domains_cbmi ) {
\r
560 if ( _right_line_up_domains_cbmi.isSelected() ) {
\r
561 _line_up_renderable_data_cbmi.setSelected( true );
\r
563 updateOptions( getOptions() );
\r
565 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
\r
566 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
\r
567 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
\r
570 else if ( o == _about_item ) {
\r
573 else if ( o == _help_item ) {
\r
575 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );
\r
577 catch ( final IOException e1 ) {
\r
578 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
581 else if ( o == _website_item ) {
\r
583 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
\r
585 catch ( final IOException e1 ) {
\r
586 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
589 else if ( o == _phyloxml_website_item ) {
\r
591 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
\r
593 catch ( final IOException e1 ) {
\r
594 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
597 else if ( o == _aptx_ref_item ) {
\r
599 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
\r
601 catch ( final IOException e1 ) {
\r
602 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
605 else if ( o == _phyloxml_ref_item ) {
\r
607 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
\r
609 catch ( final IOException e1 ) {
\r
610 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
613 else if ( o == _write_to_pdf_item ) {
\r
614 final File curr_dir = writeToPdf( _mainpanel.getCurrentPhylogeny(),
\r
616 _writetopdf_filechooser,
\r
620 if ( curr_dir != null ) {
\r
621 setCurrentDir( curr_dir );
\r
624 else if ( o == _save_all_item ) {
\r
627 else if ( o == _write_to_jpg_item ) {
\r
628 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
629 GraphicsExportType.JPG,
\r
631 _writetographics_filechooser,
\r
635 if ( new_dir != null ) {
\r
636 setCurrentDir( new_dir );
\r
639 else if ( o == _write_to_gif_item ) {
\r
640 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
641 GraphicsExportType.GIF,
\r
643 _writetographics_filechooser,
\r
647 if ( new_dir != null ) {
\r
648 setCurrentDir( new_dir );
\r
652 else if ( o == _write_to_tif_item ) {
\r
653 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
654 GraphicsExportType.TIFF,
\r
656 _writetographics_filechooser,
\r
660 if ( new_dir != null ) {
\r
661 setCurrentDir( new_dir );
\r
665 else if ( o == _write_to_bmp_item ) {
\r
666 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
667 GraphicsExportType.BMP,
\r
669 _writetographics_filechooser,
\r
673 if ( new_dir != null ) {
\r
674 setCurrentDir( new_dir );
\r
678 else if ( o == _write_to_png_item ) {
\r
679 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
680 GraphicsExportType.PNG,
\r
682 _writetographics_filechooser,
\r
686 if ( new_dir != null ) {
\r
687 setCurrentDir( new_dir );
\r
690 else if ( o == _print_item ) {
\r
691 print( getCurrentTreePanel(), getOptions(), this );
\r
693 else if ( o == _save_item ) {
\r
694 writeToFile( _mainpanel.getCurrentPhylogeny() );
\r
697 else if ( o == _graphics_export_visible_only_cbmi ) {
\r
698 updateOptions( getOptions() );
\r
700 else if ( o == _antialias_print_cbmi ) {
\r
701 updateOptions( getOptions() );
\r
703 else if ( o == _print_black_and_white_cbmi ) {
\r
704 updateOptions( getOptions() );
\r
706 else if ( o == _print_using_actual_size_cbmi ) {
\r
707 updateOptions( getOptions() );
\r
709 else if ( o == _graphics_export_using_actual_size_cbmi ) {
\r
710 updateOptions( getOptions() );
\r
712 else if ( o == _print_size_mi ) {
\r
715 else if ( o == _choose_pdf_width_mi ) {
\r
719 if ( _load_phylogeny_from_webservice_menu_items != null ) {
\r
720 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
\r
721 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
\r
722 readPhylogeniesFromWebservice( i );
\r
727 _contentpane.repaint();
\r
730 public Configuration getConfiguration() {
\r
731 return _configuration;
\r
735 * This method returns the current external node data which
\r
736 * has been selected by the user by clicking the "Return ..."
\r
737 * menu item. This method is expected to be called from Javascript or
\r
738 * something like it.
\r
740 * @return current external node data as String
\r
742 public String getCurrentExternalNodesDataBuffer() {
\r
743 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
\r
746 public int getCurrentExternalNodesDataBufferChangeCounter() {
\r
747 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
\r
750 public int getCurrentExternalNodesDataBufferLength() {
\r
751 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
\r
754 public InferenceManager getInferenceManager() {
\r
755 return _inference_manager;
\r
758 public MainPanel getMainPanel() {
\r
762 public Options getOptions() {
\r
766 public ProcessPool getProcessPool() {
\r
767 return _process_pool;
\r
770 public void showTextFrame( final String s, final String title ) {
\r
772 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
\r
775 public void showWhole() {
\r
776 _mainpanel.getControlPanel().showWhole();
\r
779 public void updateProcessMenu() {
\r
780 // In general Swing is not thread safe.
\r
781 // See "Swing's Threading Policy".
\r
782 SwingUtilities.invokeLater( new Runnable() {
\r
785 public void run() {
\r
786 doUpdateProcessMenu();
\r
791 void activateSaveAllIfNeeded() {
\r
792 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
\r
793 _save_all_item.setEnabled( true );
\r
796 _save_all_item.setEnabled( false );
\r
800 void buildFileMenu() {
\r
801 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
\r
802 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
\r
803 _file_jmenu.addSeparator();
\r
804 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
\r
805 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
\r
806 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
\r
808 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
\r
809 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
\r
810 if ( AptxUtil.canWriteFormat( "gif" ) ) {
\r
811 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
\r
813 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
\r
814 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
\r
816 _file_jmenu.addSeparator();
\r
817 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
\r
818 _file_jmenu.addSeparator();
\r
819 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
\r
820 customizeJMenuItem( _save_item );
\r
821 customizeJMenuItem( _write_to_pdf_item );
\r
822 customizeJMenuItem( _write_to_png_item );
\r
823 customizeJMenuItem( _write_to_jpg_item );
\r
824 customizeJMenuItem( _write_to_gif_item );
\r
825 customizeJMenuItem( _write_to_tif_item );
\r
826 customizeJMenuItem( _write_to_bmp_item );
\r
827 customizeJMenuItem( _print_item );
\r
828 customizeJMenuItem( _exit_item );
\r
829 _jmenubar.add( _file_jmenu );
\r
832 void buildFontSizeMenu() {
\r
833 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
\r
834 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
\r
835 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
\r
836 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
\r
837 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
\r
838 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
\r
839 customizeJMenuItem( _super_tiny_fonts_item );
\r
840 customizeJMenuItem( _tiny_fonts_item );
\r
841 customizeJMenuItem( _small_fonts_item );
\r
842 customizeJMenuItem( _medium_fonts_item );
\r
843 customizeJMenuItem( _large_fonts_item );
\r
844 _jmenubar.add( _font_size_menu );
\r
847 void buildHelpMenu() {
\r
848 _help_jmenu = createMenu( "Help", getConfiguration() );
\r
849 _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
\r
850 _help_jmenu.addSeparator();
\r
851 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
\r
852 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...
\r
853 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
\r
854 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
\r
855 _help_jmenu.addSeparator();
\r
856 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
\r
857 customizeJMenuItem( _help_item );
\r
858 customizeJMenuItem( _website_item );
\r
859 customizeJMenuItem( _phyloxml_website_item );
\r
860 customizeJMenuItem( _aptx_ref_item );
\r
861 customizeJMenuItem( _phyloxml_ref_item );
\r
862 customizeJMenuItem( _about_item );
\r
863 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
\r
864 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
\r
865 _jmenubar.add( _help_jmenu );
\r
868 void buildTypeMenu() {
\r
869 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
\r
870 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
\r
871 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
\r
872 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
\r
873 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
\r
874 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
\r
875 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
\r
876 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
\r
877 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
\r
878 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
\r
879 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
\r
880 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
\r
881 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
\r
882 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
\r
883 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
\r
884 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
\r
885 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
\r
886 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
887 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
888 initializeTypeMenu( getOptions() );
\r
889 _jmenubar.add( _type_menu );
\r
892 void buildViewMenu() {
\r
893 _view_jmenu = createMenu( "View", getConfiguration() );
\r
894 _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
\r
895 _view_jmenu.addSeparator();
\r
896 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
\r
897 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
\r
898 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
\r
899 customizeJMenuItem( _display_basic_information_item );
\r
900 customizeJMenuItem( _view_as_NH_item );
\r
901 customizeJMenuItem( _view_as_XML_item );
\r
902 customizeJMenuItem( _view_as_nexus_item );
\r
903 _jmenubar.add( _view_jmenu );
\r
906 void checkTextFrames() {
\r
907 if ( _textframes.size() > 5 ) {
\r
909 if ( _textframes.getFirst() != null ) {
\r
910 _textframes.getFirst().removeMe();
\r
913 _textframes.removeFirst();
\r
916 catch ( final NoSuchElementException e ) {
\r
922 void choosePdfWidth() {
\r
923 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
924 "Please enter the default line width for PDF export.\n"
\r
925 + "[current value: "
\r
926 + getOptions().getPrintLineWidth() + "]\n",
\r
927 "Line Width for PDF Export",
\r
928 JOptionPane.QUESTION_MESSAGE,
\r
931 getOptions().getPrintLineWidth() );
\r
932 if ( !ForesterUtil.isEmpty( s ) ) {
\r
933 boolean success = true;
\r
935 final String m_str = s.trim();
\r
936 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
938 f = Float.parseFloat( m_str );
\r
940 catch ( final Exception ex ) {
\r
947 if ( success && ( f > 0.0 ) ) {
\r
948 getOptions().setPrintLineWidth( f );
\r
953 void choosePrintSize() {
\r
954 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
955 "Please enter values for width and height,\nseparated by a comma.\n"
\r
956 + "[current values: "
\r
957 + getOptions().getPrintSizeX() + ", "
\r
958 + getOptions().getPrintSizeY() + "]\n"
\r
959 + "[A4: " + Constants.A4_SIZE_X + ", "
\r
960 + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
\r
961 + Constants.US_LETTER_SIZE_X + ", "
\r
962 + Constants.US_LETTER_SIZE_Y + "]",
\r
963 "Default Size for Graphics Export",
\r
964 JOptionPane.QUESTION_MESSAGE,
\r
967 getOptions().getPrintSizeX() + ", "
\r
968 + getOptions().getPrintSizeY() );
\r
969 if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
\r
970 boolean success = true;
\r
973 final String[] str_ary = s.split( "," );
\r
974 if ( str_ary.length == 2 ) {
\r
975 final String x_str = str_ary[ 0 ].trim();
\r
976 final String y_str = str_ary[ 1 ].trim();
\r
977 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
\r
979 x = Integer.parseInt( x_str );
\r
980 y = Integer.parseInt( y_str );
\r
982 catch ( final Exception ex ) {
\r
993 if ( success && ( x > 1 ) && ( y > 1 ) ) {
\r
994 getOptions().setPrintSizeX( x );
\r
995 getOptions().setPrintSizeY( y );
\r
1001 removeAllTextFrames();
\r
1002 if ( _mainpanel != null ) {
\r
1003 _mainpanel.terminate();
\r
1005 if ( _contentpane != null ) {
\r
1006 _contentpane.removeAll();
\r
1008 setVisible( false );
\r
1012 void colorRank() {
\r
1013 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1014 final String[] ranks = AptxUtil.getAllPossibleRanks();
\r
1015 final String rank = ( String ) JOptionPane
\r
1016 .showInputDialog( this,
\r
1017 "What rank should the colorization be based on",
\r
1019 JOptionPane.QUESTION_MESSAGE,
\r
1023 if ( !ForesterUtil.isEmpty( rank ) ) {
\r
1024 _mainpanel.getCurrentTreePanel().colorRank( rank );
\r
1029 void confColor() {
\r
1030 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1031 _mainpanel.getCurrentTreePanel().confColor();
\r
1035 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
\r
1036 if ( item != null ) {
\r
1037 item.setFont( MainFrame.menu_font );
\r
1038 if ( !getConfiguration().isUseNativeUI() ) {
\r
1039 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
1040 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
1042 item.setSelected( is_selected );
\r
1043 item.addActionListener( this );
\r
1047 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
\r
1048 if ( jmi != null ) {
\r
1049 jmi.setFont( MainFrame.menu_font );
\r
1050 if ( !getConfiguration().isUseNativeUI() ) {
\r
1051 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
1052 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
1054 jmi.addActionListener( this );
\r
1059 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
\r
1060 if ( item != null ) {
\r
1061 item.setFont( MainFrame.menu_font );
\r
1062 if ( !getConfiguration().isUseNativeUI() ) {
\r
1063 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
1064 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
1066 item.setSelected( is_selected );
\r
1067 item.addActionListener( this );
\r
1071 void displayBasicInformation( final File treefile ) {
\r
1072 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1073 String title = "Basic Information";
\r
1074 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1075 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
\r
1077 showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
\r
1081 void exceptionOccuredDuringOpenFile( final Exception e ) {
\r
1083 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
1085 catch ( final Exception ex ) {
\r
1088 JOptionPane.showMessageDialog( this,
\r
1089 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
1090 "Error during File|Open",
\r
1091 JOptionPane.ERROR_MESSAGE );
\r
1094 void exceptionOccuredDuringSaveAs( final Exception e ) {
\r
1096 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
1098 catch ( final Exception ex ) {
\r
1101 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
\r
1104 void executeGSDI() {
\r
1105 if ( !isOKforSDI( false, true ) ) {
\r
1108 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
\r
1109 JOptionPane.showMessageDialog( this,
\r
1110 "Gene tree is not rooted.",
\r
1111 "Cannot execute GSDI",
\r
1112 JOptionPane.ERROR_MESSAGE );
\r
1115 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
1116 gene_tree.setAllNodesToNotCollapse();
\r
1117 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
1119 final Phylogeny species_tree = getSpeciesTree().copy();
\r
1121 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
\r
1123 catch ( final SDIException e ) {
\r
1124 JOptionPane.showMessageDialog( this,
\r
1125 e.getLocalizedMessage(),
\r
1126 "Error during GSDI",
\r
1127 JOptionPane.ERROR_MESSAGE );
\r
1130 catch ( final Exception e ) {
\r
1131 AptxUtil.unexpectedException( e );
\r
1134 gene_tree.setRerootable( false );
\r
1135 gene_tree.clearHashIdToNodeMap();
\r
1136 gene_tree.recalculateNumberOfExternalDescendants( true );
\r
1137 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
\r
1138 getMainPanel().getControlPanel().setShowEvents( true );
\r
1140 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
1141 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
1143 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
1145 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
1146 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
1147 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
1148 JOptionPane.showMessageDialog( this,
\r
1149 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
1150 + "Potential duplications: "
\r
1151 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
1152 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
1153 + "Stripped gene tree nodes: "
\r
1154 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1155 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
1156 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1157 "GSDI successfully completed",
\r
1158 JOptionPane.WARNING_MESSAGE );
\r
1161 JOptionPane.showMessageDialog( this,
\r
1162 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
1163 + "Potential duplications: "
\r
1164 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
1165 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
1166 + "Stripped gene tree nodes: "
\r
1167 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1168 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
1169 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1170 "GSDI successfully completed",
\r
1171 JOptionPane.INFORMATION_MESSAGE );
\r
1175 void executeGSDIR() {
\r
1176 if ( !isOKforSDI( false, false ) ) {
\r
1179 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
\r
1181 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
\r
1182 JOptionPane.showMessageDialog( this,
\r
1183 "Gene tree is not completely binary",
\r
1184 "Cannot execute GSDI",
\r
1185 JOptionPane.ERROR_MESSAGE );
\r
1188 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
1189 gene_tree.setAllNodesToNotCollapse();
\r
1190 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
1191 GSDIR gsdir = null;
\r
1192 final Phylogeny species_tree = getSpeciesTree().copy();
\r
1194 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
\r
1196 catch ( final SDIException e ) {
\r
1197 JOptionPane.showMessageDialog( this,
\r
1198 e.getLocalizedMessage(),
\r
1199 "Error during GSDIR",
\r
1200 JOptionPane.ERROR_MESSAGE );
\r
1203 catch ( final Exception e ) {
\r
1204 AptxUtil.unexpectedException( e );
\r
1207 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
\r
1208 result_gene_tree.setRerootable( false );
\r
1209 result_gene_tree.clearHashIdToNodeMap();
\r
1210 result_gene_tree.recalculateNumberOfExternalDescendants( true );
\r
1211 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
\r
1212 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
\r
1213 getMainPanel().getControlPanel().setShowEvents( true );
\r
1215 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
1216 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
1218 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
1220 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
1221 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
1222 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
1223 JOptionPane.showMessageDialog( this,
\r
1224 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1225 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1226 + "Stripped gene tree nodes: "
\r
1227 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1228 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1229 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1230 "GSDIR successfully completed",
\r
1231 JOptionPane.WARNING_MESSAGE );
\r
1234 JOptionPane.showMessageDialog( this,
\r
1235 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1236 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1237 + "Stripped gene tree nodes: "
\r
1238 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1239 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1240 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1241 "GSDIR successfully completed",
\r
1242 JOptionPane.INFORMATION_MESSAGE );
\r
1246 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
\r
1247 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
\r
1248 JOptionPane.showMessageDialog( this,
\r
1249 "Gene tree and species tree have no species in common.",
\r
1250 "Error during SDI",
\r
1251 JOptionPane.ERROR_MESSAGE );
\r
1254 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
\r
1255 JOptionPane.showMessageDialog( this,
\r
1256 "Gene tree and species tree have only one species in common.",
\r
1257 "Error during SDI",
\r
1258 JOptionPane.ERROR_MESSAGE );
\r
1266 ControlPanel getControlPanel() {
\r
1267 return getMainPanel().getControlPanel();
\r
1270 File getCurrentDir() {
\r
1271 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
\r
1272 if ( ForesterUtil.isWindows() ) {
\r
1274 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
\r
1276 catch ( final Exception e ) {
\r
1277 _current_dir = null;
\r
1281 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
\r
1282 if ( System.getProperty( "user.home" ) != null ) {
\r
1283 _current_dir = new File( System.getProperty( "user.home" ) );
\r
1285 else if ( System.getProperty( "user.dir" ) != null ) {
\r
1286 _current_dir = new File( System.getProperty( "user.dir" ) );
\r
1289 return _current_dir;
\r
1292 TreePanel getCurrentTreePanel() {
\r
1293 return getMainPanel().getCurrentTreePanel();
\r
1296 JMenu getHelpMenu() {
\r
1297 return _help_jmenu;
\r
1300 JCheckBoxMenuItem getlabelDirectionCbmi() {
\r
1301 return _label_direction_cbmi;
\r
1304 JMenuBar getMenuBarOfMainFrame() {
\r
1308 final Phylogeny getSpeciesTree() {
\r
1309 return _species_tree;
\r
1312 void initializeTypeMenu( final Options options ) {
\r
1313 setTypeMenuToAllUnselected();
\r
1314 switch ( options.getPhylogenyGraphicsType() ) {
\r
1316 _convex_type_cbmi.setSelected( true );
\r
1319 _curved_type_cbmi.setSelected( true );
\r
1322 _euro_type_cbmi.setSelected( true );
\r
1325 _rounded_type_cbmi.setSelected( true );
\r
1328 _triangular_type_cbmi.setSelected( true );
\r
1331 _unrooted_type_cbmi.setSelected( true );
\r
1334 _circular_type_cbmi.setSelected( true );
\r
1337 _rectangular_type_cbmi.setSelected( true );
\r
1342 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
\r
1343 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1346 else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
\r
1347 JOptionPane.showMessageDialog( this,
\r
1348 "No species tree loaded",
\r
1349 "Cannot execute GSDI",
\r
1350 JOptionPane.ERROR_MESSAGE );
\r
1353 else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
\r
1354 JOptionPane.showMessageDialog( this,
\r
1355 "Species tree is not completely binary",
\r
1356 "Cannot execute GSDI",
\r
1357 JOptionPane.ERROR_MESSAGE );
\r
1360 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
\r
1361 JOptionPane.showMessageDialog( this,
\r
1362 "Gene tree is not completely binary",
\r
1363 "Cannot execute GSDI",
\r
1364 JOptionPane.ERROR_MESSAGE );
\r
1372 boolean isSubtreeDisplayed() {
\r
1373 if ( getCurrentTreePanel() != null ) {
\r
1374 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
\r
1376 .showMessageDialog( this,
\r
1377 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
\r
1378 "Operation can not be exectuted on a sub-tree",
\r
1379 JOptionPane.WARNING_MESSAGE );
\r
1386 void midpointRoot() {
\r
1387 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1388 _mainpanel.getCurrentTreePanel().midpointRoot();
\r
1392 static void printPhylogenyToPdf( final String file_name,
\r
1393 final Options opts,
\r
1394 final TreePanel tp,
\r
1395 final Component comp ) {
\r
1396 if ( !opts.isPrintUsingActualSize() ) {
\r
1397 tp.calcParametersForPainting( opts.getPrintSizeX(), opts.getPrintSizeY() );
\r
1398 tp.resetPreferredSize();
\r
1401 String pdf_written_to = "";
\r
1402 boolean error = false;
\r
1404 if ( opts.isPrintUsingActualSize() ) {
\r
1405 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth(), tp.getHeight() );
\r
1408 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
\r
1410 opts.getPrintSizeX(),
\r
1411 opts.getPrintSizeY() );
\r
1414 catch ( final IOException e ) {
\r
1416 JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
\r
1419 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
\r
1420 JOptionPane.showMessageDialog( comp,
\r
1421 "Wrote PDF to: " + pdf_written_to,
\r
1423 JOptionPane.INFORMATION_MESSAGE );
\r
1426 JOptionPane.showMessageDialog( comp,
\r
1427 "There was an unknown problem when attempting to write to PDF file: \""
\r
1428 + file_name + "\"",
\r
1430 JOptionPane.ERROR_MESSAGE );
\r
1433 if ( !opts.isPrintUsingActualSize() ) {
\r
1434 tp.getControlPanel().showWhole();
\r
1438 void readPhylogeniesFromWebservice( final int i ) {
\r
1439 final UrlTreeReader reader = new UrlTreeReader( this, i );
\r
1440 new Thread( reader ).start();
\r
1443 void removeAllTextFrames() {
\r
1444 for( final TextFrame tf : _textframes ) {
\r
1445 if ( tf != null ) {
\r
1449 _textframes.clear();
\r
1452 void resetSearch() {
\r
1453 getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
\r
1454 getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
\r
1455 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );
\r
1456 getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );
\r
1457 getMainPanel().getControlPanel().getSearchTextField0().setText( "" );
\r
1458 getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );
\r
1459 getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );
\r
1460 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );
\r
1461 getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );
\r
1462 getMainPanel().getControlPanel().getSearchTextField1().setText( "" );
\r
1463 getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );
\r
1464 getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );
\r
1467 void setConfiguration( final Configuration configuration ) {
\r
1468 _configuration = configuration;
\r
1471 void setCurrentDir( final File current_dir ) {
\r
1472 _current_dir = current_dir;
\r
1475 void setInferenceManager( final InferenceManager i ) {
\r
1476 _inference_manager = i;
\r
1479 void setOptions( final Options options ) {
\r
1480 _options = options;
\r
1483 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
\r
1484 setTypeMenuToAllUnselected();
\r
1487 _circular_type_cbmi.setSelected( true );
\r
1490 _convex_type_cbmi.setSelected( true );
\r
1493 _curved_type_cbmi.setSelected( true );
\r
1496 _euro_type_cbmi.setSelected( true );
\r
1499 _rounded_type_cbmi.setSelected( true );
\r
1502 _rectangular_type_cbmi.setSelected( true );
\r
1505 _triangular_type_cbmi.setSelected( true );
\r
1508 _unrooted_type_cbmi.setSelected( true );
\r
1511 throw new IllegalArgumentException( "unknown type: " + type );
\r
1515 final void setSpeciesTree( final Phylogeny species_tree ) {
\r
1516 _species_tree = species_tree;
\r
1519 void setTypeMenuToAllUnselected() {
\r
1520 _convex_type_cbmi.setSelected( false );
\r
1521 _curved_type_cbmi.setSelected( false );
\r
1522 _euro_type_cbmi.setSelected( false );
\r
1523 _rounded_type_cbmi.setSelected( false );
\r
1524 _triangular_type_cbmi.setSelected( false );
\r
1525 _rectangular_type_cbmi.setSelected( false );
\r
1526 _unrooted_type_cbmi.setSelected( false );
\r
1527 _circular_type_cbmi.setSelected( false );
\r
1530 void switchColors() {
\r
1531 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
\r
1532 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
\r
1533 csc.setVisible( true );
\r
1537 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1538 _mainpanel.getCurrentTreePanel().taxColor();
\r
1542 void typeChanged( final Object o ) {
\r
1543 updateTypeCheckboxes( getOptions(), o );
\r
1544 updateOptions( getOptions() );
\r
1545 if ( getCurrentTreePanel() != null ) {
\r
1546 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
\r
1547 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
\r
1548 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1549 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
\r
1550 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1551 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
\r
1552 getCurrentTreePanel().getControlPanel().showWhole();
\r
1554 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
\r
1555 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
\r
1558 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
\r
1560 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
\r
1561 updateScreenTextAntialias( getMainPanel().getTreePanels() );
\r
1562 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
\r
1563 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
\r
1564 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
\r
1567 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
\r
1573 void updateOptions( final Options options ) {
\r
1574 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
\r
1575 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
\r
1576 && _background_gradient_cbmi.isSelected() );
\r
1577 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
\r
1578 options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
\r
1579 && _show_annotation_ref_source.isSelected() );
\r
1580 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
\r
1581 && _abbreviate_scientific_names.isSelected() );
\r
1582 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
\r
1583 && _color_labels_same_as_parent_branch.isSelected() );
\r
1584 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
\r
1585 && _show_default_node_shapes_internal_cbmi.isSelected() );
\r
1586 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
\r
1587 && _show_default_node_shapes_external_cbmi.isSelected() );
\r
1588 options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
\r
1589 && _show_default_node_shapes_for_marked_cbmi.isSelected() );
\r
1590 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
\r
1591 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
\r
1593 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
\r
1594 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
\r
1596 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
\r
1597 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
\r
1599 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
\r
1600 && _search_case_senstive_cbmi.isSelected() );
\r
1601 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
\r
1602 options.setShowScale( _show_scale_cbmi.isSelected() );
\r
1604 if ( _label_direction_cbmi != null ) {
\r
1605 if ( _label_direction_cbmi.isSelected() ) {
\r
1606 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
\r
1609 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
\r
1612 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
\r
1613 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
\r
1614 && _show_confidence_stddev_cbmi.isSelected() );
\r
1615 if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
\r
1616 options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
\r
1618 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
\r
1619 && ( _print_using_actual_size_cbmi.isSelected() ) );
\r
1620 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
\r
1621 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
\r
1622 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
\r
1623 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
\r
1624 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1625 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
\r
1627 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
\r
1628 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1629 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
\r
1632 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
\r
1634 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
\r
1635 && _print_black_and_white_cbmi.isSelected() );
\r
1636 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
\r
1637 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
\r
1638 if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
\r
1639 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
\r
1641 else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
\r
1642 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
\r
1644 else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
\r
1645 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1647 else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
\r
1648 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
\r
1650 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
\r
1651 && _replace_underscores_cbmi.isSelected() );
\r
1652 options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
\r
1653 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
\r
1654 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
\r
1655 && _search_whole_words_only_cbmi.isSelected() );
\r
1656 options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
\r
1657 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
\r
1658 && _inverse_search_result_cbmi.isSelected() );
\r
1659 if ( _graphics_export_visible_only_cbmi != null ) {
\r
1660 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
\r
1661 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
\r
1662 _graphics_export_using_actual_size_cbmi.setSelected( true );
\r
1663 _graphics_export_using_actual_size_cbmi.setEnabled( false );
\r
1666 _graphics_export_using_actual_size_cbmi.setEnabled( true );
\r
1669 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
\r
1670 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1672 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
\r
1673 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
\r
1675 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
\r
1676 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
\r
1678 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
\r
1679 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
\r
1681 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
\r
1682 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
\r
1684 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
\r
1685 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
\r
1687 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
\r
1688 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
\r
1690 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
\r
1691 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
\r
1693 if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
\r
1694 options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
\r
1696 if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
\r
1697 options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
\r
1701 void updateTypeCheckboxes( final Options options, final Object o ) {
\r
1702 setTypeMenuToAllUnselected();
\r
1703 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
\r
1706 void viewAsNexus() {
\r
1707 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1708 String title = "Nexus";
\r
1709 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1710 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1712 showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
\r
1718 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1719 String title = "New Hampshire";
\r
1720 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1721 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1723 showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
\r
1724 .getNhConversionSupportValueStyle() ),
\r
1729 void viewAsXML() {
\r
1730 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1731 String title = "phyloXML";
\r
1732 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1733 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1735 showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
\r
1739 boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
\r
1741 final PhylogenyWriter writer = new PhylogenyWriter();
\r
1742 writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );
\r
1744 catch ( final Exception e ) {
\r
1746 exceptionOccuredDuringSaveAs( e );
\r
1751 boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
\r
1753 final PhylogenyWriter writer = new PhylogenyWriter();
\r
1754 writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
\r
1756 catch ( final Exception e ) {
\r
1758 exceptionOccuredDuringSaveAs( e );
\r
1763 boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
\r
1765 final PhylogenyWriter writer = new PhylogenyWriter();
\r
1766 writer.toPhyloXML( file, t, 0 );
\r
1768 catch ( final Exception e ) {
\r
1770 exceptionOccuredDuringSaveAs( e );
\r
1775 static void writePhylogenyToGraphicsFile( final String file_name,
\r
1776 final GraphicsExportType type,
\r
1777 final MainPanel mp,
\r
1778 final Component comp,
\r
1779 final Container contentpane ) {
\r
1780 mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(),
\r
1781 mp.getCurrentTreePanel().getHeight() );
\r
1782 String file_written_to = "";
\r
1783 boolean error = false;
\r
1785 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
\r
1786 mp.getCurrentTreePanel().getWidth(),
\r
1787 mp.getCurrentTreePanel().getHeight(),
\r
1788 mp.getCurrentTreePanel(),
\r
1789 mp.getControlPanel(),
\r
1791 mp.getOptions() );
\r
1793 catch ( final IOException e ) {
\r
1795 JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
\r
1798 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
\r
1799 JOptionPane.showMessageDialog( comp,
\r
1800 "Wrote image to: " + file_written_to,
\r
1801 "Graphics Export",
\r
1802 JOptionPane.INFORMATION_MESSAGE );
\r
1805 JOptionPane.showMessageDialog( comp,
\r
1806 "There was an unknown problem when attempting to write to an image file: \""
\r
1807 + file_name + "\"",
\r
1809 JOptionPane.ERROR_MESSAGE );
\r
1812 contentpane.repaint();
\r
1815 void writeToFile( final Phylogeny t ) {
\r
1816 if ( t == null ) {
\r
1819 String initial_filename = null;
\r
1820 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
\r
1822 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
\r
1824 catch ( final IOException e ) {
\r
1825 initial_filename = null;
\r
1828 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
\r
1829 _save_filechooser.setSelectedFile( new File( initial_filename ) );
\r
1832 _save_filechooser.setSelectedFile( new File( "" ) );
\r
1834 final File my_dir = getCurrentDir();
\r
1835 if ( my_dir != null ) {
\r
1836 _save_filechooser.setCurrentDirectory( my_dir );
\r
1838 final int result = _save_filechooser.showSaveDialog( _contentpane );
\r
1839 final File file = _save_filechooser.getSelectedFile();
\r
1840 setCurrentDir( _save_filechooser.getCurrentDirectory() );
\r
1841 boolean exception = false;
\r
1842 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
1843 if ( file.exists() ) {
\r
1844 final int i = JOptionPane.showConfirmDialog( this,
\r
1845 file + " already exists.\nOverwrite?",
\r
1847 JOptionPane.OK_CANCEL_OPTION,
\r
1848 JOptionPane.QUESTION_MESSAGE );
\r
1849 if ( i != JOptionPane.OK_OPTION ) {
\r
1853 final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
\r
1855 ForesterUtil.copyFile( file, to );
\r
1857 catch ( final Exception e ) {
\r
1858 JOptionPane.showMessageDialog( this,
\r
1859 "Failed to create backup copy " + to,
\r
1860 "Failed to Create Backup Copy",
\r
1861 JOptionPane.WARNING_MESSAGE );
\r
1866 catch ( final Exception e ) {
\r
1867 JOptionPane.showMessageDialog( this,
\r
1868 "Failed to delete: " + file,
\r
1869 "Failed to Delete",
\r
1870 JOptionPane.WARNING_MESSAGE );
\r
1874 if ( _save_filechooser.getFileFilter() == MainFrame.nhfilter ) {
\r
1875 exception = writeAsNewHampshire( t, exception, file );
\r
1877 else if ( _save_filechooser.getFileFilter() == MainFrame.xmlfilter ) {
\r
1878 exception = writeAsPhyloXml( t, exception, file );
\r
1880 else if ( _save_filechooser.getFileFilter() == MainFrame.nexusfilter ) {
\r
1881 exception = writeAsNexus( t, exception, file );
\r
1885 final String file_name = file.getName().trim().toLowerCase();
\r
1886 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
1887 || file_name.endsWith( ".tree" ) ) {
\r
1888 exception = writeAsNewHampshire( t, exception, file );
\r
1890 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
\r
1891 exception = writeAsNexus( t, exception, file );
\r
1893 // XML is default:
\r
1895 exception = writeAsPhyloXml( t, exception, file );
\r
1898 if ( !exception ) {
\r
1899 getMainPanel().setTitleOfSelectedTab( file.getName() );
\r
1900 getMainPanel().getCurrentTreePanel().setTreeFile( file );
\r
1901 getMainPanel().getCurrentTreePanel().setEdited( false );
\r
1906 static File writeToGraphicsFile( final Phylogeny t,
\r
1907 final GraphicsExportType type,
\r
1908 final MainPanel mp,
\r
1909 final JFileChooser writetographics_filechooser,
\r
1910 final Component component,
\r
1911 final Container contentpane,
\r
1912 final File current_dir ) {
\r
1913 File new_dir = null;
\r
1914 if ( ( t == null ) || t.isEmpty() ) {
\r
1917 String initial_filename = "";
\r
1918 if ( mp.getCurrentTreePanel().getTreeFile() != null ) {
\r
1919 initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();
\r
1921 if ( initial_filename.indexOf( '.' ) > 0 ) {
\r
1922 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
\r
1924 initial_filename = initial_filename + "." + type;
\r
1925 writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
\r
1926 final File my_dir = current_dir;
\r
1927 if ( my_dir != null ) {
\r
1928 writetographics_filechooser.setCurrentDirectory( my_dir );
\r
1930 final int result = writetographics_filechooser.showSaveDialog( contentpane );
\r
1931 File file = writetographics_filechooser.getSelectedFile();
\r
1932 //setCurrentDir( writetographics_filechooser.getCurrentDirectory() );
\r
1933 new_dir = writetographics_filechooser.getCurrentDirectory();
\r
1934 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
1935 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
\r
1936 file = new File( file.toString() + "." + type );
\r
1938 if ( file.exists() ) {
\r
1939 final int i = JOptionPane.showConfirmDialog( component,
\r
1940 file + " already exists. Overwrite?",
\r
1942 JOptionPane.OK_CANCEL_OPTION,
\r
1943 JOptionPane.WARNING_MESSAGE );
\r
1944 if ( i != JOptionPane.OK_OPTION ) {
\r
1951 catch ( final Exception e ) {
\r
1952 JOptionPane.showMessageDialog( component,
\r
1953 "Failed to delete: " + file,
\r
1955 JOptionPane.WARNING_MESSAGE );
\r
1959 writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane );
\r
1964 static File writeToPdf( final Phylogeny t,
\r
1965 final MainPanel mp,
\r
1966 final JFileChooser writetopdf_filechooser,
\r
1967 final File curr_dir,
\r
1968 final Container contentpane,
\r
1969 final Component component ) {
\r
1970 if ( ( t == null ) || t.isEmpty() ) {
\r
1973 String initial_filename = "";
\r
1974 if ( mp.getCurrentTreePanel().getTreeFile() != null ) {
\r
1975 initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();
\r
1977 if ( initial_filename.indexOf( '.' ) > 0 ) {
\r
1978 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
\r
1980 initial_filename = initial_filename + ".pdf";
\r
1981 writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
\r
1982 final File my_dir = curr_dir;
\r
1983 if ( my_dir != null ) {
\r
1984 writetopdf_filechooser.setCurrentDirectory( my_dir );
\r
1986 final int result = writetopdf_filechooser.showSaveDialog( contentpane );
\r
1987 File file = writetopdf_filechooser.getSelectedFile();
\r
1988 // setCurrentDir( writetopdf_filechooser.getCurrentDirectory() );
\r
1989 final File new_current_dir = writetopdf_filechooser.getCurrentDirectory();
\r
1990 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
1991 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
\r
1992 file = new File( file.toString() + ".pdf" );
\r
1994 if ( file.exists() ) {
\r
1995 final int i = JOptionPane.showConfirmDialog( component,
\r
1996 file + " already exists. Overwrite?",
\r
1998 JOptionPane.OK_CANCEL_OPTION,
\r
1999 JOptionPane.WARNING_MESSAGE );
\r
2000 if ( i != JOptionPane.OK_OPTION ) {
\r
2004 printPhylogenyToPdf( file.toString(), mp.getOptions(), mp.getCurrentTreePanel(), component );
\r
2006 return new_current_dir;
\r
2009 private void annotateSequences() {
\r
2010 if ( getCurrentTreePanel() != null ) {
\r
2011 List<PhylogenyNode> nodes = null;
\r
2012 if ( ( getCurrentTreePanel().getFoundNodes0() != null )
\r
2013 || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
2014 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
2016 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
2018 .showMessageDialog( this,
\r
2019 "Need to select nodes, either via direct selection or via the \"Search\" function",
\r
2020 "No nodes selected for annotation",
\r
2021 JOptionPane.ERROR_MESSAGE );
\r
2024 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
2025 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
2026 final JTextField ref_field = new JTextField( 10 );
\r
2027 final JTextField desc_filed = new JTextField( 20 );
\r
2028 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
\r
2029 : getPreviousNodeAnnotationReference() );
\r
2030 final JPanel my_panel = new JPanel();
\r
2031 my_panel.add( new JLabel( "Reference " ) );
\r
2032 my_panel.add( ref_field );
\r
2033 my_panel.add( Box.createHorizontalStrut( 15 ) );
\r
2034 my_panel.add( new JLabel( "Description " ) );
\r
2035 my_panel.add( desc_filed );
\r
2036 final int result = JOptionPane.showConfirmDialog( null,
\r
2038 "Enter the sequence annotation(s) for the "
\r
2039 + nodes.size() + " selected nodes",
\r
2040 JOptionPane.OK_CANCEL_OPTION );
\r
2041 if ( result == JOptionPane.OK_OPTION ) {
\r
2042 String ref = ref_field.getText();
\r
2043 String desc = desc_filed.getText();
\r
2044 if ( !ForesterUtil.isEmpty( ref ) ) {
\r
2046 ref = ref.replaceAll( "\\s+", " " );
\r
2047 if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )
\r
2048 || ( ref.length() < 3 ) ) {
\r
2049 JOptionPane.showMessageDialog( this,
\r
2050 "Reference needs to be in the form of \"GO:1234567\"",
\r
2051 "Illegal Format for Annotation Reference",
\r
2052 JOptionPane.ERROR_MESSAGE );
\r
2056 if ( ref != null ) {
\r
2057 setPreviousNodeAnnotationReference( ref );
\r
2059 if ( desc != null ) {
\r
2060 desc = desc.trim();
\r
2061 desc = desc.replaceAll( "\\s+", " " );
\r
2063 if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
\r
2064 for( final PhylogenyNode n : nodes ) {
\r
2065 ForesterUtil.ensurePresenceOfSequence( n );
\r
2066 final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
\r
2067 : new Annotation( ref );
\r
2068 if ( !ForesterUtil.isEmpty( desc ) ) {
\r
2069 ann.setDesc( desc );
\r
2071 n.getNodeData().getSequence().addAnnotation( ann );
\r
2074 getMainPanel().getControlPanel().showAnnotations();
\r
2080 private void chooseFont() {
\r
2081 final FontChooser fc = new FontChooser();
\r
2082 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
\r
2083 fc.showDialog( this, "Select the Base Font" );
\r
2084 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
\r
2087 private void chooseMinimalConfidence() {
\r
2088 final String s = ( String ) JOptionPane
\r
2089 .showInputDialog( this,
\r
2090 "Please enter the minimum for confidence values to be displayed.\n"
\r
2091 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
\r
2092 "Minimal Confidence Value",
\r
2093 JOptionPane.QUESTION_MESSAGE,
\r
2096 getOptions().getMinConfidenceValue() );
\r
2097 if ( !ForesterUtil.isEmpty( s ) ) {
\r
2098 boolean success = true;
\r
2100 final String m_str = s.trim();
\r
2101 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
2103 m = Double.parseDouble( m_str );
\r
2105 catch ( final Exception ex ) {
\r
2112 if ( success && ( m >= 0.0 ) ) {
\r
2113 getOptions().setMinConfidenceValue( m );
\r
2118 private void deleteSelectedNodes( final boolean delete ) {
\r
2119 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
2120 if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {
\r
2123 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
2124 if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
2125 final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
2126 for( final PhylogenyNode n : all_selected_nodes ) {
\r
2127 if ( n.isExternal() ) {
\r
2132 String function = "Retain";
\r
2134 function = "Delete";
\r
2136 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
2138 .showMessageDialog( this,
\r
2139 "Need to select external nodes, either via direct selection or via the \"Search\" function",
\r
2140 "No external nodes selected to " + function.toLowerCase(),
\r
2141 JOptionPane.ERROR_MESSAGE );
\r
2144 final int todo = nodes.size();
\r
2145 final int ext = phy.getNumberOfExternalNodes();
\r
2151 JOptionPane.showMessageDialog( this,
\r
2152 "Cannot delete all nodes",
\r
2153 "Attempt to delete all nodes ",
\r
2154 JOptionPane.ERROR_MESSAGE );
\r
2157 final int result = JOptionPane.showConfirmDialog( null, function + " " + todo
\r
2158 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res
\r
2159 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );
\r
2160 if ( result == JOptionPane.OK_OPTION ) {
\r
2162 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
\r
2163 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
\r
2164 final PhylogenyNode n = it.next();
\r
2165 if ( !nodes.contains( n ) ) {
\r
2166 to_delete.add( n );
\r
2169 for( final PhylogenyNode n : to_delete ) {
\r
2170 phy.deleteSubtree( n, true );
\r
2174 for( final PhylogenyNode n : nodes ) {
\r
2175 phy.deleteSubtree( n, true );
\r
2179 getCurrentTreePanel().setNodeInPreorderToNull();
\r
2180 phy.externalNodesHaveChanged();
\r
2181 phy.clearHashIdToNodeMap();
\r
2182 phy.recalculateNumberOfExternalDescendants( true );
\r
2183 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
2184 getCurrentTreePanel().setEdited( true );
\r
2189 private void doUpdateProcessMenu() {
\r
2190 if ( _process_pool.size() > 0 ) {
\r
2191 if ( _process_menu == null ) {
\r
2192 _process_menu = createMenu( "", getConfiguration() );
\r
2193 _process_menu.setForeground( Color.RED );
\r
2195 _process_menu.removeAll();
\r
2196 final String text = "processes running: " + _process_pool.size();
\r
2197 _process_menu.setText( text );
\r
2198 _jmenubar.add( _process_menu );
\r
2199 for( int i = 0; i < _process_pool.size(); ++i ) {
\r
2200 final ProcessRunning p = _process_pool.getProcessByIndex( i );
\r
2201 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
\r
2205 if ( _process_menu != null ) {
\r
2206 _process_menu.removeAll();
\r
2207 _jmenubar.remove( _process_menu );
\r
2210 _jmenubar.validate();
\r
2211 _jmenubar.repaint();
\r
2215 private String getPreviousNodeAnnotationReference() {
\r
2216 return _previous_node_annotation_ref;
\r
2219 static void print( final TreePanel tp, final Options op, final Component c ) {
\r
2220 if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) {
\r
2223 if ( !op.isPrintUsingActualSize() ) {
\r
2224 tp.calcParametersForPainting( op.getPrintSizeX() - 80, op.getPrintSizeY() - 140 );
\r
2225 tp.resetPreferredSize();
\r
2228 final String job_name = Constants.PRG_NAME;
\r
2229 boolean error = false;
\r
2230 String printer_name = null;
\r
2232 printer_name = Printer.print( tp, job_name );
\r
2234 catch ( final Exception e ) {
\r
2236 JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
\r
2238 if ( !error && ( printer_name != null ) ) {
\r
2239 String msg = "Printing data sent to printer";
\r
2240 if ( printer_name.length() > 1 ) {
\r
2241 msg += " [" + printer_name + "]";
\r
2243 JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
\r
2245 if ( !op.isPrintUsingActualSize() ) {
\r
2246 tp.getControlPanel().showWhole();
\r
2250 private void removeBranchColors() {
\r
2251 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
2252 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
\r
2256 private void removeVisualStyles() {
\r
2257 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
2258 AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
\r
2262 private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
\r
2263 _previous_node_annotation_ref = previous_node_annotation_ref;
\r
2266 private void writeAllToFile() {
\r
2267 if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
\r
2270 final File my_dir = getCurrentDir();
\r
2271 if ( my_dir != null ) {
\r
2272 _save_filechooser.setCurrentDirectory( my_dir );
\r
2274 _save_filechooser.setSelectedFile( new File( "" ) );
\r
2275 final int result = _save_filechooser.showSaveDialog( _contentpane );
\r
2276 final File file = _save_filechooser.getSelectedFile();
\r
2277 setCurrentDir( _save_filechooser.getCurrentDirectory() );
\r
2278 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2279 if ( file.exists() ) {
\r
2280 final int i = JOptionPane.showConfirmDialog( this,
\r
2281 file + " already exists. Overwrite?",
\r
2283 JOptionPane.OK_CANCEL_OPTION,
\r
2284 JOptionPane.WARNING_MESSAGE );
\r
2285 if ( i != JOptionPane.OK_OPTION ) {
\r
2292 catch ( final Exception e ) {
\r
2293 JOptionPane.showMessageDialog( this,
\r
2294 "Failed to delete: " + file,
\r
2296 JOptionPane.WARNING_MESSAGE );
\r
2300 final int count = getMainPanel().getTabbedPane().getTabCount();
\r
2301 final List<Phylogeny> trees = new ArrayList<Phylogeny>();
\r
2302 for( int i = 0; i < count; ++i ) {
\r
2303 final Phylogeny phy = getMainPanel().getPhylogeny( i );
\r
2304 if ( ForesterUtil.isEmpty( phy.getName() )
\r
2305 && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
\r
2306 phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
\r
2309 getMainPanel().getTreePanels().get( i ).setEdited( false );
\r
2311 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2313 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
\r
2315 catch ( final IOException e ) {
\r
2316 JOptionPane.showMessageDialog( this,
\r
2317 "Failed to write to: " + file,
\r
2319 JOptionPane.WARNING_MESSAGE );
\r
2325 * Display the about box.
\r
2327 static void about() {
\r
2328 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
\r
2329 about.append( "Copyright (C) 2014 Christian M Zmasek\n" );
\r
2330 about.append( "All Rights Reserved\n" );
\r
2331 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
\r
2332 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
\r
2333 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
\r
2334 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
\r
2335 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
\r
2336 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
\r
2337 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
\r
2339 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
\r
2340 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
\r
2341 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
\r
2342 + ForesterUtil.OS_VERSION + "]\n" );
\r
2344 final Runtime rt = java.lang.Runtime.getRuntime();
\r
2345 final long free_memory = rt.freeMemory() / 1000000;
\r
2346 final long total_memory = rt.totalMemory() / 1000000;
\r
2347 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
\r
2348 about.append( "[locale: " + Locale.getDefault() + "]\n" );
\r
2349 about.append( "References:\n" );
\r
2350 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
\r
2351 about.append( "For more information & download:\n" );
\r
2352 about.append( Constants.APTX_WEB_SITE + "\n" );
\r
2353 about.append( "Documentation:\n" );
\r
2354 about.append( Constants.APTX_DOC_SITE + "\n" );
\r
2355 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
\r
2356 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
\r
2359 static void chooseNodeSize( final Options options, final Component parent ) {
\r
2360 final String s = ( String ) JOptionPane.showInputDialog( parent,
\r
2361 "Please enter the default size for node shapes.\n"
\r
2362 + "[current value: "
\r
2363 + options.getDefaultNodeShapeSize() + "]\n",
\r
2364 "Node Shape Size",
\r
2365 JOptionPane.QUESTION_MESSAGE,
\r
2368 options.getDefaultNodeShapeSize() );
\r
2369 if ( !ForesterUtil.isEmpty( s ) ) {
\r
2370 boolean success = true;
\r
2372 final String m_str = s.trim();
\r
2373 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
2375 m = Double.parseDouble( m_str );
\r
2377 catch ( final Exception ex ) {
\r
2384 if ( success && ( m >= 0.0 ) ) {
\r
2385 final short size = ForesterUtil.roundToShort( m );
\r
2386 if ( size >= 0.0 ) {
\r
2387 options.setDefaultNodeShapeSize( size );
\r
2393 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
\r
2394 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
\r
2397 static JMenu createMenu( final String title, final Configuration conf ) {
\r
2398 final JMenu jmenu = new JMenu( title );
\r
2399 if ( !conf.isUseNativeUI() ) {
\r
2400 jmenu.setFont( MainFrame.menu_font );
\r
2401 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
\r
2402 jmenu.setForeground( conf.getGuiMenuTextColor() );
\r
2407 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
\r
2408 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
\r
2409 if ( !configuration.isUseNativeUI() ) {
\r
2410 label.setBackground( configuration.getGuiMenuBackgroundColor() );
\r
2411 label.setForeground( configuration.getGuiMenuTextColor() );
\r
2412 label.setOpaque( true );
\r
2414 label.setSelected( false );
\r
2415 label.setEnabled( false );
\r
2419 static void cycleNodeFill( final Options op ) {
\r
2420 switch ( op.getDefaultNodeFill() ) {
\r
2422 op.setDefaultNodeFill( NodeFill.SOLID );
\r
2425 op.setDefaultNodeFill( NodeFill.GRADIENT );
\r
2428 op.setDefaultNodeFill( NodeFill.NONE );
\r
2431 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
\r
2435 static void cycleNodeShape( final Options op ) {
\r
2436 switch ( op.getDefaultNodeShape() ) {
\r
2438 op.setDefaultNodeShape( NodeShape.RECTANGLE );
\r
2441 op.setDefaultNodeShape( NodeShape.CIRCLE );
\r
2444 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
\r
2448 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
\r
2449 switch ( op.getOvPlacement() ) {
\r
2451 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
\r
2454 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
\r
2457 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
\r
2460 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
\r
2463 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
\r
2465 if ( tree_panel != null ) {
\r
2466 tree_panel.updateOvSettings();
\r
2470 static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {
\r
2471 if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {
\r
2472 mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" );
\r
2475 mi.setText( "Cycle Node Return Data..." );
\r
2479 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
\r
2480 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
\r
2481 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
2482 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
\r
2485 mi.setText( "Cycle Node Shape Fill Type..." );
\r
2489 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
\r
2490 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
\r
2491 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
2492 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
\r
2495 mi.setText( "Cycle Node Shape Fill Type..." );
\r
2499 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
\r
2500 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
\r
2501 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
\r
2504 mi.setText( "Cycle Overview Placement..." );
\r
2508 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
\r
2509 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
\r
2510 mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
\r
2514 mi.setText( "Select Color Scheme..." );
\r
2518 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
\r
2519 mi.setText( "Select Default Font... (current: " + font_desc + ")" );
\r
2522 static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
\r
2523 mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
\r
2524 + o.getPrintSizeY() + ")" );
\r
2527 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
\r
2528 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
\r
2531 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
\r
2532 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
\r
2533 mi.setEnabled( true );
\r
2535 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
\r
2536 mi.setEnabled( true );
\r
2539 mi.setEnabled( false );
\r
2541 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
\r
2544 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
\r
2545 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
\r
2548 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
\r
2549 for( final TreePanel tree_panel : treepanels ) {
\r
2550 tree_panel.setTextAntialias();
\r
2554 private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {
\r
2555 switch ( op.getExtDescNodeDataToReturn() ) {
\r
2557 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
\r
2560 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
\r
2562 case DOMAINS_COLLAPSED_PER_PROTEIN:
\r
2563 op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
\r
2565 case SEQ_ANNOTATIONS:
\r
2566 op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
\r
2569 op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
\r
2571 case SEQUENCE_MOL_SEQ_FASTA:
\r
2572 if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )
\r
2573 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )
\r
2574 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )
\r
2575 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )
\r
2576 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )
\r
2577 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {
\r
2578 op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );
\r
2581 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
\r
2585 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
\r
2590 class DefaultFilter extends FileFilter {
\r
2593 public boolean accept( final File f ) {
\r
2594 final String file_name = f.getName().trim().toLowerCase();
\r
2595 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2596 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
\r
2597 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
\r
2598 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
\r
2599 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
\r
2600 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
\r
2601 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
\r
2602 || file_name.endsWith( ".con" ) || f.isDirectory();
\r
2606 public String getDescription() {
\r
2607 return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
\r
2611 class GraphicsFileFilter extends FileFilter {
\r
2614 public boolean accept( final File f ) {
\r
2615 final String file_name = f.getName().trim().toLowerCase();
\r
2616 return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
\r
2617 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
\r
2621 public String getDescription() {
\r
2622 return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
\r
2626 class MsaFileFilter extends FileFilter {
\r
2629 public boolean accept( final File f ) {
\r
2630 final String file_name = f.getName().trim().toLowerCase();
\r
2631 return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
\r
2632 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
\r
2636 public String getDescription() {
\r
2637 return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
\r
2641 class NexusFilter extends FileFilter {
\r
2644 public boolean accept( final File f ) {
\r
2645 final String file_name = f.getName().trim().toLowerCase();
\r
2646 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
\r
2647 || file_name.endsWith( ".tre" ) || f.isDirectory();
\r
2651 public String getDescription() {
\r
2652 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
\r
2656 class NHFilter extends FileFilter {
\r
2659 public boolean accept( final File f ) {
\r
2660 final String file_name = f.getName().trim().toLowerCase();
\r
2661 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2662 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
\r
2663 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
\r
2664 || f.isDirectory();
\r
2668 public String getDescription() {
\r
2669 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
\r
2673 class NHXFilter extends FileFilter {
\r
2676 public boolean accept( final File f ) {
\r
2677 final String file_name = f.getName().trim().toLowerCase();
\r
2678 return file_name.endsWith( ".nhx" ) || f.isDirectory();
\r
2682 public String getDescription() {
\r
2683 return "NHX files (*.nhx) [deprecated]";
\r
2687 class PdfFilter extends FileFilter {
\r
2690 public boolean accept( final File f ) {
\r
2691 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
\r
2695 public String getDescription() {
\r
2696 return "PDF files (*.pdf)";
\r
2700 class SequencesFileFilter extends FileFilter {
\r
2703 public boolean accept( final File f ) {
\r
2704 final String file_name = f.getName().trim().toLowerCase();
\r
2705 return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
\r
2706 || file_name.endsWith( ".seqs" ) || f.isDirectory();
\r
2710 public String getDescription() {
\r
2711 return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
\r
2715 class TolFilter extends FileFilter {
\r
2718 public boolean accept( final File f ) {
\r
2719 final String file_name = f.getName().trim().toLowerCase();
\r
2720 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
\r
2721 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
\r
2725 public String getDescription() {
\r
2726 return "Tree of Life files (*.tol, *.tolxml)";
\r
2730 class XMLFilter extends FileFilter {
\r
2733 public boolean accept( final File f ) {
\r
2734 final String file_name = f.getName().trim().toLowerCase();
\r
2735 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
\r
2736 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
\r
2740 public String getDescription() {
\r
2741 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";
\r
git://source.jalview.org / jalview.git / blob