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.AncestralTaxonomyInferrer;
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62 import org.forester.archaeopteryx.tools.InferenceManager;
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63 import org.forester.archaeopteryx.tools.ProcessPool;
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64 import org.forester.archaeopteryx.tools.ProcessRunning;
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65 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
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66 import org.forester.io.writers.PhylogenyWriter;
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67 import org.forester.phylogeny.Phylogeny;
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68 import org.forester.phylogeny.PhylogenyMethods;
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69 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
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70 import org.forester.phylogeny.PhylogenyNode;
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71 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
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72 import org.forester.phylogeny.data.Annotation;
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73 import org.forester.phylogeny.data.NodeDataField;
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74 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
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75 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
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76 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
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77 import org.forester.sdi.GSDI;
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78 import org.forester.sdi.GSDIR;
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79 import org.forester.sdi.SDIException;
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80 import org.forester.util.ForesterConstants;
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81 import org.forester.util.ForesterUtil;
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82 import org.forester.util.WindowsUtils;
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84 public abstract class MainFrame extends JFrame implements ActionListener {
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86 final static NHFilter nhfilter = new NHFilter();
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87 final static NHXFilter nhxfilter = new NHXFilter();
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88 final static XMLFilter xmlfilter = new XMLFilter();
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89 final static TolFilter tolfilter = new TolFilter();
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90 final static NexusFilter nexusfilter = new NexusFilter();
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91 final static PdfFilter pdffilter = new PdfFilter();
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92 final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
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93 final static MsaFileFilter msafilter = new MsaFileFilter();
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94 final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
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95 final static DefaultFilter defaultfilter = new DefaultFilter();
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96 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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97 static final String PHYLOXML_REF_TOOL_TIP = AptxConstants.PHYLOXML_REFERENCE; //TODO //FIXME
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98 static final String APTX_REF_TOOL_TIP = AptxConstants.APTX_REFERENCE;
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99 private static final long serialVersionUID = 3655000897845508358L;
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100 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
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103 static final String TYPE_MENU_HEADER = "Type";
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104 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
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105 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
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106 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
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107 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
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108 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
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109 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
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110 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
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111 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
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112 static final String OPTIONS_HEADER = "Options";
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113 static final String SEARCH_SUBHEADER = "Search:";
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114 static final String DISPLAY_SUBHEADER = "Display:";
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115 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
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116 static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions";
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117 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
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118 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
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119 static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";
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120 static final String DISPLAY_SCALE_LABEL = "Scale";
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121 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
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122 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
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123 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
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124 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
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125 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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126 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
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127 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
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128 static final String BG_GRAD_LABEL = "Background Color Gradient";
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129 static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";
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130 static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";
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131 static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";
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132 static final String SHOW_OVERVIEW_LABEL = "Overview";
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133 static final String FONT_SIZE_MENU_LABEL = "Font Size";
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134 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
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135 static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";
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136 static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";
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137 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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138 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
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139 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
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140 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
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141 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
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142 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
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143 static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";
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144 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
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145 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
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146 static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";
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147 static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";
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148 static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";
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149 static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
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150 static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
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151 JMenuBar _jmenubar;
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155 JMenu _options_jmenu;
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156 JMenu _font_size_menu;
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158 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
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160 JMenu _analysis_menu;
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161 JMenuItem _load_species_tree_item;
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162 JMenuItem _gsdi_item;
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163 JMenuItem _gsdir_item;
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164 JMenuItem _lineage_inference;
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166 JMenuItem _open_item;
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167 JMenuItem _open_url_item;
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168 JMenuItem _save_item;
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169 JMenuItem _save_all_item;
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170 JMenuItem _close_item;
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171 JMenuItem _exit_item;
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172 JMenuItem _new_item;
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173 JMenuItem _print_item;
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174 JMenuItem _write_to_pdf_item;
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175 JMenuItem _write_to_jpg_item;
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176 JMenuItem _write_to_gif_item;
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177 JMenuItem _write_to_tif_item;
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178 JMenuItem _write_to_png_item;
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179 JMenuItem _write_to_bmp_item;
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181 JMenuItem _midpoint_root_item;
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182 JMenuItem _taxcolor_item;
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183 JMenuItem _confcolor_item;
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184 JMenuItem _color_rank_jmi;
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185 JMenuItem _collapse_species_specific_subtrees;
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186 JMenuItem _obtain_detailed_taxonomic_information_jmi;
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187 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
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188 JMenuItem _obtain_seq_information_jmi;
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189 JMenuItem _move_node_names_to_tax_sn_jmi;
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190 JMenuItem _move_node_names_to_seq_names_jmi;
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191 JMenuItem _extract_tax_code_from_node_names_jmi;
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192 JMenuItem _annotate_item;
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193 JMenuItem _remove_branch_color_item;
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194 JMenuItem _remove_visual_styles_item;
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195 JMenuItem _delete_selected_nodes_item;
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196 JMenuItem _delete_not_selected_nodes_item;
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198 JMenuItem _super_tiny_fonts_item;
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199 JMenuItem _tiny_fonts_item;
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200 JMenuItem _small_fonts_item;
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201 JMenuItem _medium_fonts_item;
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202 JMenuItem _large_fonts_item;
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204 // _ screen and print
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205 JMenuItem _choose_font_mi;
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206 JMenuItem _switch_colors_mi;
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207 JCheckBoxMenuItem _label_direction_cbmi;
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208 // _ screen display
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209 JCheckBoxMenuItem _screen_antialias_cbmi;
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210 JCheckBoxMenuItem _background_gradient_cbmi;
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211 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
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212 JRadioButtonMenuItem _uniform_cladograms_rbmi;
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213 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
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214 JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
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215 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
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216 JCheckBoxMenuItem _show_overview_cbmi;
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217 JCheckBoxMenuItem _show_domain_labels;
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218 JCheckBoxMenuItem _show_annotation_ref_source;
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219 JCheckBoxMenuItem _abbreviate_scientific_names;
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220 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
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221 JMenuItem _overview_placment_mi;
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222 JMenuItem _choose_minimal_confidence_mi;
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223 JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
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224 JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
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225 JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
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226 JMenuItem _cycle_node_shape_mi;
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227 JMenuItem _cycle_node_fill_mi;
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228 JMenuItem _choose_node_size_mi;
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229 JMenuItem _cycle_data_return;
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230 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
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231 JCheckBoxMenuItem _right_line_up_domains_cbmi;
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232 JCheckBoxMenuItem _line_up_renderable_data_cbmi;
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234 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
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235 JCheckBoxMenuItem _antialias_print_cbmi;
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236 JCheckBoxMenuItem _print_black_and_white_cbmi;
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237 //JMenuItem _print_size_mi;
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238 JMenuItem _choose_pdf_width_mi;
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240 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
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241 JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
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242 JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
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243 JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
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244 JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
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245 JCheckBoxMenuItem _replace_underscores_cbmi;
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246 JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
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247 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
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248 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
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250 JCheckBoxMenuItem _search_case_senstive_cbmi;
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251 JCheckBoxMenuItem _search_whole_words_only_cbmi;
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252 JCheckBoxMenuItem _inverse_search_result_cbmi;
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253 JCheckBoxMenuItem _search_with_regex_cbmi;
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254 JCheckBoxMenuItem _color_all_found_nodes_when_coloring_subtree_cbmi;
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257 JCheckBoxMenuItem _rectangular_type_cbmi;
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258 JCheckBoxMenuItem _triangular_type_cbmi;
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259 JCheckBoxMenuItem _curved_type_cbmi;
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260 JCheckBoxMenuItem _convex_type_cbmi;
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261 JCheckBoxMenuItem _euro_type_cbmi;
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262 JCheckBoxMenuItem _rounded_type_cbmi;
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263 JCheckBoxMenuItem _unrooted_type_cbmi;
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264 JCheckBoxMenuItem _circular_type_cbmi;
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265 // view as text menu:
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266 JMenuItem _view_as_NH_item;
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267 JMenuItem _view_as_XML_item;
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268 JMenuItem _view_as_nexus_item;
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269 JMenuItem _display_basic_information_item;
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271 JMenuItem _about_item;
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272 JMenuItem _help_item;
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273 JMenuItem _website_item;
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274 JMenuItem _phyloxml_website_item;
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275 JMenuItem _phyloxml_ref_item;
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276 JMenuItem _aptx_ref_item;
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279 JFileChooser _writetopdf_filechooser;
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280 JFileChooser _save_filechooser;
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281 JFileChooser _writetographics_filechooser;
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283 JMenu _process_menu;
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284 MainPanel _mainpanel;
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285 Container _contentpane;
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286 final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
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287 Configuration _configuration;
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289 private Phylogeny _species_tree;
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290 InferenceManager _inference_manager;
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291 final ProcessPool _process_pool;
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292 private String _previous_node_annotation_ref;
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295 _process_pool = ProcessPool.createInstance();
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296 _writetopdf_filechooser = new JFileChooser();
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297 _writetopdf_filechooser.setMultiSelectionEnabled( false );
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298 _writetopdf_filechooser.addChoosableFileFilter( pdffilter );
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299 _writetographics_filechooser = new JFileChooser();
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300 _writetographics_filechooser.setMultiSelectionEnabled( false );
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301 _writetographics_filechooser.addChoosableFileFilter( graphicsfilefilter );
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302 _save_filechooser = new JFileChooser();
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303 _save_filechooser.setMultiSelectionEnabled( false );
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304 _save_filechooser.setFileFilter( xmlfilter );
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305 _save_filechooser.addChoosableFileFilter( nhfilter );
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306 _save_filechooser.addChoosableFileFilter( nexusfilter );
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307 _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
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309 final String home_dir = System.getProperty( "user.home" );
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310 _save_filechooser.setCurrentDirectory( new File( home_dir ) );
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311 _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) );
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312 _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) );
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314 catch ( final Exception e ) {
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315 e.printStackTrace();
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316 // Do nothing. Not important.
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321 * Action performed.
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324 public void actionPerformed( final ActionEvent e ) {
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325 final Object o = e.getSource();
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326 boolean is_applet = false;
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327 JApplet applet = null;
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328 if ( getCurrentTreePanel() != null ) {
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329 is_applet = getCurrentTreePanel().isApplet();
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331 applet = getCurrentTreePanel().obtainApplet();
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334 if ( o == _exit_item ) {
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337 else if ( o == _gsdi_item ) {
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338 if ( isSubtreeDisplayed() ) {
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343 else if ( o == _gsdir_item ) {
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344 if ( isSubtreeDisplayed() ) {
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349 else if ( o == _taxcolor_item ) {
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352 else if ( o == _confcolor_item ) {
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355 else if ( o == _color_rank_jmi ) {
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358 else if ( o == _collapse_species_specific_subtrees ) {
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359 if ( isSubtreeDisplayed() ) {
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362 if ( getCurrentTreePanel() != null ) {
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363 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
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366 else if ( o == _remove_branch_color_item ) {
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367 if ( isSubtreeDisplayed() ) {
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370 removeBranchColors();
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372 else if ( o == _remove_visual_styles_item ) {
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373 if ( isSubtreeDisplayed() ) {
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376 removeVisualStyles();
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378 else if ( o == _midpoint_root_item ) {
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379 if ( isSubtreeDisplayed() ) {
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384 else if ( o == _delete_selected_nodes_item ) {
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385 if ( isSubtreeDisplayed() ) {
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388 deleteSelectedNodes( true );
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390 else if ( o == _delete_not_selected_nodes_item ) {
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391 if ( isSubtreeDisplayed() ) {
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394 deleteSelectedNodes( false );
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396 else if ( o == _annotate_item ) {
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397 annotateSequences();
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399 else if ( o == _switch_colors_mi ) {
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402 else if ( o == _display_basic_information_item ) {
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403 if ( getCurrentTreePanel() != null ) {
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404 displayBasicInformation( getCurrentTreePanel().getTreeFile() );
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407 else if ( o == _view_as_NH_item ) {
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410 else if ( o == _view_as_XML_item ) {
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413 else if ( o == _view_as_nexus_item ) {
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416 else if ( o == _super_tiny_fonts_item ) {
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417 if ( getCurrentTreePanel() != null ) {
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418 getCurrentTreePanel().setSuperTinyFonts();
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419 getCurrentTreePanel().repaint();
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422 else if ( o == _tiny_fonts_item ) {
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423 if ( getCurrentTreePanel() != null ) {
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424 getCurrentTreePanel().setTinyFonts();
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425 getCurrentTreePanel().repaint();
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428 else if ( o == _small_fonts_item ) {
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429 if ( getCurrentTreePanel() != null ) {
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430 getCurrentTreePanel().setSmallFonts();
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431 getCurrentTreePanel().repaint();
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434 else if ( o == _medium_fonts_item ) {
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435 if ( getCurrentTreePanel() != null ) {
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436 getCurrentTreePanel().setMediumFonts();
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437 getCurrentTreePanel().repaint();
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440 else if ( o == _large_fonts_item ) {
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441 if ( getCurrentTreePanel() != null ) {
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442 getCurrentTreePanel().setLargeFonts();
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443 getCurrentTreePanel().repaint();
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446 else if ( o == _choose_font_mi ) {
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449 else if ( o == _choose_minimal_confidence_mi ) {
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450 chooseMinimalConfidence();
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452 else if ( o == _choose_node_size_mi ) {
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453 chooseNodeSize( getOptions(), this );
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455 else if ( o == _overview_placment_mi ) {
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456 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
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458 else if ( o == _cycle_node_fill_mi ) {
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459 MainFrame.cycleNodeFill( getOptions() );
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461 else if ( o == _cycle_node_shape_mi ) {
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462 MainFrame.cycleNodeShape( getOptions() );
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464 else if ( o == _cycle_data_return ) {
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465 MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );
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467 else if ( o == _screen_antialias_cbmi ) {
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468 updateOptions( getOptions() );
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469 updateScreenTextAntialias( getMainPanel().getTreePanels() );
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471 else if ( o == _background_gradient_cbmi ) {
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472 updateOptions( getOptions() );
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474 else if ( o == _show_domain_labels ) {
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475 updateOptions( getOptions() );
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477 else if ( o == _show_annotation_ref_source ) {
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478 updateOptions( getOptions() );
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480 else if ( o == _abbreviate_scientific_names ) {
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481 updateOptions( getOptions() );
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483 else if ( o == _color_labels_same_as_parent_branch ) {
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484 updateOptions( getOptions() );
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486 else if ( o == _show_default_node_shapes_internal_cbmi ) {
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487 updateOptions( getOptions() );
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489 else if ( o == _show_default_node_shapes_external_cbmi ) {
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490 updateOptions( getOptions() );
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492 else if ( o == _show_default_node_shapes_for_marked_cbmi ) {
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493 updateOptions( getOptions() );
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495 else if ( o == _non_lined_up_cladograms_rbmi ) {
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496 updateOptions( getOptions() );
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499 else if ( o == _uniform_cladograms_rbmi ) {
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500 updateOptions( getOptions() );
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503 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
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504 updateOptions( getOptions() );
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507 else if ( o == _search_case_senstive_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_whole_words_only_cbmi ) {
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513 if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
\r
514 _search_with_regex_cbmi.setSelected( false );
\r
516 updateOptions( getOptions() );
\r
517 getMainPanel().getControlPanel().search0();
\r
518 getMainPanel().getControlPanel().search1();
\r
520 else if ( o == _inverse_search_result_cbmi ) {
\r
521 updateOptions( getOptions() );
\r
522 getMainPanel().getControlPanel().search0();
\r
523 getMainPanel().getControlPanel().search1();
\r
525 else if ( o == _search_with_regex_cbmi ) {
\r
526 if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
\r
527 _search_whole_words_only_cbmi.setSelected( false );
\r
529 if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
\r
530 _search_case_senstive_cbmi.setSelected( true );
\r
532 updateOptions( getOptions() );
\r
533 getMainPanel().getControlPanel().search0();
\r
534 getMainPanel().getControlPanel().search1();
\r
536 else if ( o == _color_all_found_nodes_when_coloring_subtree_cbmi ) {
\r
537 updateOptions( getOptions() );
\r
539 else if ( o == _show_scale_cbmi ) {
\r
540 updateOptions( getOptions() );
\r
542 else if ( o == _color_by_taxonomic_group_cbmi ) {
\r
543 updateOptions( getOptions() );
\r
545 else if ( o == _show_confidence_stddev_cbmi ) {
\r
546 updateOptions( getOptions() );
\r
548 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
\r
549 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
550 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
\r
552 updateOptions( getOptions() );
\r
554 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
\r
555 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
556 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
\r
558 updateOptions( getOptions() );
\r
560 else if ( o == _label_direction_cbmi ) {
\r
561 updateOptions( getOptions() );
\r
563 else if ( o == _show_overview_cbmi ) {
\r
564 updateOptions( getOptions() );
\r
565 if ( getCurrentTreePanel() != null ) {
\r
566 getCurrentTreePanel().updateOvSizes();
\r
569 else if ( o == _line_up_renderable_data_cbmi ) {
\r
570 if ( !_line_up_renderable_data_cbmi.isSelected() ) {
\r
571 _right_line_up_domains_cbmi.setSelected( false );
\r
573 updateOptions( getOptions() );
\r
575 else if ( o == _right_line_up_domains_cbmi ) {
\r
576 if ( _right_line_up_domains_cbmi.isSelected() ) {
\r
577 _line_up_renderable_data_cbmi.setSelected( true );
\r
579 updateOptions( getOptions() );
\r
581 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
\r
582 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
\r
583 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
\r
586 else if ( o == _about_item ) {
\r
589 else if ( o == _help_item ) {
\r
591 AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE, is_applet, applet );
\r
593 catch ( final IOException e1 ) {
\r
594 ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
\r
597 else if ( o == _website_item ) {
\r
599 AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE, is_applet, applet );
\r
601 catch ( final IOException e1 ) {
\r
602 ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
\r
605 else if ( o == _phyloxml_website_item ) {
\r
607 AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, is_applet, applet );
\r
609 catch ( final IOException e1 ) {
\r
610 ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
\r
613 else if ( o == _aptx_ref_item ) {
\r
615 AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL, is_applet, applet );
\r
617 catch ( final IOException e1 ) {
\r
618 ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
\r
621 else if ( o == _phyloxml_ref_item ) {
\r
623 AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL, is_applet, applet );
\r
625 catch ( final IOException e1 ) {
\r
626 ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
\r
629 else if ( o == _write_to_pdf_item ) {
\r
630 final File curr_dir = writeToPdf( _mainpanel.getCurrentPhylogeny(),
\r
632 _writetopdf_filechooser,
\r
636 if ( curr_dir != null ) {
\r
637 setCurrentDir( curr_dir );
\r
640 else if ( o == _save_all_item ) {
\r
643 else if ( o == _write_to_jpg_item ) {
\r
644 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
645 GraphicsExportType.JPG,
\r
647 _writetographics_filechooser,
\r
651 if ( new_dir != null ) {
\r
652 setCurrentDir( new_dir );
\r
655 else if ( o == _write_to_gif_item ) {
\r
656 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
657 GraphicsExportType.GIF,
\r
659 _writetographics_filechooser,
\r
663 if ( new_dir != null ) {
\r
664 setCurrentDir( new_dir );
\r
667 else if ( o == _write_to_tif_item ) {
\r
668 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
669 GraphicsExportType.TIFF,
\r
671 _writetographics_filechooser,
\r
675 if ( new_dir != null ) {
\r
676 setCurrentDir( new_dir );
\r
679 else if ( o == _write_to_bmp_item ) {
\r
680 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
681 GraphicsExportType.BMP,
\r
683 _writetographics_filechooser,
\r
687 if ( new_dir != null ) {
\r
688 setCurrentDir( new_dir );
\r
691 else if ( o == _write_to_png_item ) {
\r
692 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
693 GraphicsExportType.PNG,
\r
695 _writetographics_filechooser,
\r
699 if ( new_dir != null ) {
\r
700 setCurrentDir( new_dir );
\r
703 else if ( o == _print_item ) {
\r
704 print( getCurrentTreePanel(), getOptions(), this );
\r
706 else if ( o == _save_item ) {
\r
707 final File new_dir = writeToFile( _mainpanel.getCurrentPhylogeny(),
\r
713 if ( new_dir != null ) {
\r
714 setCurrentDir( new_dir );
\r
717 else if ( o == _graphics_export_visible_only_cbmi ) {
\r
718 updateOptions( getOptions() );
\r
720 else if ( o == _antialias_print_cbmi ) {
\r
721 updateOptions( getOptions() );
\r
723 else if ( o == _print_black_and_white_cbmi ) {
\r
724 updateOptions( getOptions() );
\r
726 else if ( o == _choose_pdf_width_mi ) {
\r
729 else if ( o == _lineage_inference ) {
\r
730 if ( isSubtreeDisplayed() ) {
\r
731 JOptionPane.showMessageDialog( this,
\r
732 "Subtree is shown.",
\r
733 "Cannot infer ancestral taxonomies",
\r
734 JOptionPane.ERROR_MESSAGE );
\r
737 executeLineageInference();
\r
740 if ( _load_phylogeny_from_webservice_menu_items != null ) {
\r
741 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
\r
742 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
\r
743 readPhylogeniesFromWebservice( i );
\r
748 _contentpane.repaint();
\r
751 public Configuration getConfiguration() {
\r
752 return _configuration;
\r
756 * This method returns the current external node data which
\r
757 * has been selected by the user by clicking the "Return ..."
\r
758 * menu item. This method is expected to be called from Javascript or
\r
759 * something like it.
\r
761 * @return current external node data as String
\r
763 public String getCurrentExternalNodesDataBuffer() {
\r
764 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
\r
767 public int getCurrentExternalNodesDataBufferChangeCounter() {
\r
768 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
\r
771 public int getCurrentExternalNodesDataBufferLength() {
\r
772 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
\r
775 public InferenceManager getInferenceManager() {
\r
776 return _inference_manager;
\r
779 public MainPanel getMainPanel() {
\r
783 public Options getOptions() {
\r
787 public ProcessPool getProcessPool() {
\r
788 return _process_pool;
\r
791 public void showTextFrame( final String s, final String title ) {
\r
793 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
\r
796 public void showWhole() {
\r
797 _mainpanel.getControlPanel().showWhole();
\r
800 public void updateProcessMenu() {
\r
801 // In general Swing is not thread safe.
\r
802 // See "Swing's Threading Policy".
\r
803 SwingUtilities.invokeLater( new Runnable() {
\r
806 public void run() {
\r
807 doUpdateProcessMenu();
\r
812 private void annotateSequences() {
\r
813 if ( getCurrentTreePanel() != null ) {
\r
814 List<PhylogenyNode> nodes = null;
\r
815 if ( ( getCurrentTreePanel().getFoundNodes0() != null )
\r
816 || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
817 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
819 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
821 .showMessageDialog( this,
\r
822 "Need to select nodes, either via direct selection or via the \"Search\" function",
\r
823 "No nodes selected for annotation",
\r
824 JOptionPane.ERROR_MESSAGE );
\r
827 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
828 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
829 final JTextField ref_field = new JTextField( 10 );
\r
830 final JTextField desc_filed = new JTextField( 20 );
\r
831 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
\r
832 : getPreviousNodeAnnotationReference() );
\r
833 final JPanel my_panel = new JPanel();
\r
834 my_panel.add( new JLabel( "Reference " ) );
\r
835 my_panel.add( ref_field );
\r
836 my_panel.add( Box.createHorizontalStrut( 15 ) );
\r
837 my_panel.add( new JLabel( "Description " ) );
\r
838 my_panel.add( desc_filed );
\r
839 final int result = JOptionPane.showConfirmDialog( null,
\r
841 "Enter the sequence annotation(s) for the "
\r
842 + nodes.size() + " selected nodes",
\r
843 JOptionPane.OK_CANCEL_OPTION );
\r
844 if ( result == JOptionPane.OK_OPTION ) {
\r
845 String ref = ref_field.getText();
\r
846 String desc = desc_filed.getText();
\r
847 if ( !ForesterUtil.isEmpty( ref ) ) {
\r
849 ref = ref.replaceAll( "\\s+", " " );
\r
850 if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )
\r
851 || ( ref.length() < 3 ) ) {
\r
852 JOptionPane.showMessageDialog( this,
\r
853 "Reference needs to be in the form of \"GO:1234567\"",
\r
854 "Illegal Format for Annotation Reference",
\r
855 JOptionPane.ERROR_MESSAGE );
\r
859 if ( ref != null ) {
\r
860 setPreviousNodeAnnotationReference( ref );
\r
862 if ( desc != null ) {
\r
863 desc = desc.trim();
\r
864 desc = desc.replaceAll( "\\s+", " " );
\r
866 if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
\r
867 for( final PhylogenyNode n : nodes ) {
\r
868 ForesterUtil.ensurePresenceOfSequence( n );
\r
869 final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
\r
870 : new Annotation( ref );
\r
871 if ( !ForesterUtil.isEmpty( desc ) ) {
\r
872 ann.setDesc( desc );
\r
874 n.getNodeData().getSequence().addAnnotation( ann );
\r
877 getMainPanel().getControlPanel().showAnnotations();
\r
883 private void chooseFont() {
\r
884 final FontChooser fc = new FontChooser();
\r
885 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
\r
886 fc.showDialog( this, "Select the Base Font" );
\r
887 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
\r
888 getControlPanel().displayedPhylogenyMightHaveChanged( true );
\r
889 getMainPanel().getCurrentTreePanel().resetPreferredSize();
\r
890 getMainPanel().getCurrentTreePanel().updateOvSizes();
\r
895 private void chooseMinimalConfidence() {
\r
896 final String s = ( String ) JOptionPane
\r
897 .showInputDialog( this,
\r
898 "Please enter the minimum for confidence values to be displayed.\n"
\r
899 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
\r
900 "Minimal Confidence Value",
\r
901 JOptionPane.QUESTION_MESSAGE,
\r
904 getOptions().getMinConfidenceValue() );
\r
905 if ( !ForesterUtil.isEmpty( s ) ) {
\r
906 boolean success = true;
\r
908 final String m_str = s.trim();
\r
909 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
911 m = Double.parseDouble( m_str );
\r
913 catch ( final Exception ex ) {
\r
920 if ( success && ( m >= 0.0 ) ) {
\r
921 getOptions().setMinConfidenceValue( m );
\r
926 private void deleteSelectedNodes( final boolean delete ) {
\r
927 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
928 if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {
\r
931 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
932 if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
933 final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
934 for( final PhylogenyNode n : all_selected_nodes ) {
\r
935 if ( n.isExternal() ) {
\r
940 String function = "Retain";
\r
942 function = "Delete";
\r
944 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
946 .showMessageDialog( this,
\r
947 "Need to select external nodes, either via direct selection or via the \"Search\" function",
\r
948 "No external nodes selected to " + function.toLowerCase(),
\r
949 JOptionPane.ERROR_MESSAGE );
\r
952 final int todo = nodes.size();
\r
953 final int ext = phy.getNumberOfExternalNodes();
\r
959 JOptionPane.showMessageDialog( this,
\r
960 "Cannot delete all nodes",
\r
961 "Attempt to delete all nodes ",
\r
962 JOptionPane.ERROR_MESSAGE );
\r
965 final int result = JOptionPane.showConfirmDialog( null, function + " " + todo
\r
966 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res
\r
967 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );
\r
968 if ( result == JOptionPane.OK_OPTION ) {
\r
970 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
\r
971 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
\r
972 final PhylogenyNode n = it.next();
\r
973 if ( !nodes.contains( n ) ) {
\r
974 to_delete.add( n );
\r
977 for( final PhylogenyNode n : to_delete ) {
\r
978 phy.deleteSubtree( n, true );
\r
982 for( final PhylogenyNode n : nodes ) {
\r
983 phy.deleteSubtree( n, true );
\r
987 getCurrentTreePanel().setNodeInPreorderToNull();
\r
988 phy.externalNodesHaveChanged();
\r
989 phy.clearHashIdToNodeMap();
\r
990 phy.recalculateNumberOfExternalDescendants( true );
\r
991 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
992 getCurrentTreePanel().setEdited( true );
\r
997 private void doUpdateProcessMenu() {
\r
998 if ( _process_pool.size() > 0 ) {
\r
999 if ( _process_menu == null ) {
\r
1000 _process_menu = createMenu( "", getConfiguration() );
\r
1001 _process_menu.setForeground( Color.RED );
\r
1003 _process_menu.removeAll();
\r
1004 final String text = "processes running: " + _process_pool.size();
\r
1005 _process_menu.setText( text );
\r
1006 _jmenubar.add( _process_menu );
\r
1007 for( int i = 0; i < _process_pool.size(); ++i ) {
\r
1008 final ProcessRunning p = _process_pool.getProcessByIndex( i );
\r
1009 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
\r
1013 if ( _process_menu != null ) {
\r
1014 _process_menu.removeAll();
\r
1015 _jmenubar.remove( _process_menu );
\r
1018 _jmenubar.validate();
\r
1019 _jmenubar.repaint();
\r
1023 private String getPreviousNodeAnnotationReference() {
\r
1024 return _previous_node_annotation_ref;
\r
1027 private void removeBranchColors() {
\r
1028 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1029 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
\r
1033 private void removeVisualStyles() {
\r
1034 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1035 AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
\r
1039 private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
\r
1040 _previous_node_annotation_ref = previous_node_annotation_ref;
\r
1043 private void writeAllToFile() {
\r
1044 if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
\r
1047 final File my_dir = getCurrentDir();
\r
1048 if ( my_dir != null ) {
\r
1049 _save_filechooser.setCurrentDirectory( my_dir );
\r
1051 _save_filechooser.setSelectedFile( new File( "" ) );
\r
1052 final int result = _save_filechooser.showSaveDialog( _contentpane );
\r
1053 final File file = _save_filechooser.getSelectedFile();
\r
1054 setCurrentDir( _save_filechooser.getCurrentDirectory() );
\r
1055 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
1056 if ( file.exists() ) {
\r
1057 final int i = JOptionPane.showConfirmDialog( this,
\r
1058 file + " already exists. Overwrite?",
\r
1060 JOptionPane.OK_CANCEL_OPTION,
\r
1061 JOptionPane.WARNING_MESSAGE );
\r
1062 if ( i != JOptionPane.OK_OPTION ) {
\r
1069 catch ( final Exception e ) {
\r
1070 JOptionPane.showMessageDialog( this,
\r
1071 "Failed to delete: " + file,
\r
1073 JOptionPane.WARNING_MESSAGE );
\r
1077 final int count = getMainPanel().getTabbedPane().getTabCount();
\r
1078 final List<Phylogeny> trees = new ArrayList<Phylogeny>();
\r
1079 for( int i = 0; i < count; ++i ) {
\r
1080 final Phylogeny phy = getMainPanel().getPhylogeny( i );
\r
1081 if ( ForesterUtil.isEmpty( phy.getName() )
\r
1082 && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
\r
1083 phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
\r
1086 getMainPanel().getTreePanels().get( i ).setEdited( false );
\r
1088 final PhylogenyWriter writer = new PhylogenyWriter();
\r
1090 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
\r
1092 catch ( final IOException e ) {
\r
1093 JOptionPane.showMessageDialog( this,
\r
1094 "Failed to write to: " + file,
\r
1096 JOptionPane.WARNING_MESSAGE );
\r
1101 void activateSaveAllIfNeeded() {
\r
1102 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
\r
1103 _save_all_item.setEnabled( true );
\r
1106 _save_all_item.setEnabled( false );
\r
1110 void buildFileMenu() {
\r
1111 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
\r
1112 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
\r
1113 _file_jmenu.addSeparator();
\r
1114 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
\r
1115 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
\r
1116 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
\r
1118 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
\r
1119 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
\r
1120 if ( AptxUtil.canWriteFormat( "gif" ) ) {
\r
1121 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
\r
1123 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
\r
1124 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
\r
1126 _file_jmenu.addSeparator();
\r
1127 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
\r
1128 _file_jmenu.addSeparator();
\r
1129 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
\r
1130 customizeJMenuItem( _save_item );
\r
1131 customizeJMenuItem( _write_to_pdf_item );
\r
1132 customizeJMenuItem( _write_to_png_item );
\r
1133 customizeJMenuItem( _write_to_jpg_item );
\r
1134 customizeJMenuItem( _write_to_gif_item );
\r
1135 customizeJMenuItem( _write_to_tif_item );
\r
1136 customizeJMenuItem( _write_to_bmp_item );
\r
1137 customizeJMenuItem( _print_item );
\r
1138 customizeJMenuItem( _exit_item );
\r
1139 _jmenubar.add( _file_jmenu );
\r
1142 void buildFontSizeMenu() {
\r
1143 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
\r
1144 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
\r
1145 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
\r
1146 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
\r
1147 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
\r
1148 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
\r
1149 customizeJMenuItem( _super_tiny_fonts_item );
\r
1150 customizeJMenuItem( _tiny_fonts_item );
\r
1151 customizeJMenuItem( _small_fonts_item );
\r
1152 customizeJMenuItem( _medium_fonts_item );
\r
1153 customizeJMenuItem( _large_fonts_item );
\r
1154 _jmenubar.add( _font_size_menu );
\r
1157 void buildHelpMenu() {
\r
1158 _help_jmenu = createMenu( "Help", getConfiguration() );
\r
1159 _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
\r
1160 _help_jmenu.addSeparator();
\r
1161 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
\r
1162 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...
\r
1163 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
\r
1164 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
\r
1165 _help_jmenu.addSeparator();
\r
1166 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
\r
1167 customizeJMenuItem( _help_item );
\r
1168 customizeJMenuItem( _website_item );
\r
1169 customizeJMenuItem( _phyloxml_website_item );
\r
1170 customizeJMenuItem( _aptx_ref_item );
\r
1171 customizeJMenuItem( _phyloxml_ref_item );
\r
1172 customizeJMenuItem( _about_item );
\r
1173 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
\r
1174 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
\r
1175 _jmenubar.add( _help_jmenu );
\r
1178 void buildTypeMenu() {
\r
1179 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
\r
1180 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
\r
1181 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
\r
1182 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
\r
1183 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
\r
1184 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
\r
1185 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
\r
1186 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
\r
1187 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
\r
1188 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
\r
1189 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
\r
1190 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
\r
1191 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
\r
1192 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
\r
1193 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
\r
1194 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
\r
1195 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
\r
1196 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
1197 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
1198 initializeTypeMenu( getOptions() );
\r
1199 _jmenubar.add( _type_menu );
\r
1202 void buildViewMenu() {
\r
1203 _view_jmenu = createMenu( "View", getConfiguration() );
\r
1204 _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
\r
1205 _view_jmenu.addSeparator();
\r
1206 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
\r
1207 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
\r
1208 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
\r
1209 customizeJMenuItem( _display_basic_information_item );
\r
1210 customizeJMenuItem( _view_as_NH_item );
\r
1211 customizeJMenuItem( _view_as_XML_item );
\r
1212 customizeJMenuItem( _view_as_nexus_item );
\r
1213 _jmenubar.add( _view_jmenu );
\r
1216 void checkTextFrames() {
\r
1217 if ( _textframes.size() > 5 ) {
\r
1219 if ( _textframes.getFirst() != null ) {
\r
1220 _textframes.getFirst().removeMe();
\r
1223 _textframes.removeFirst();
\r
1226 catch ( final NoSuchElementException e ) {
\r
1232 void choosePdfWidth() {
\r
1233 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
1234 "Please enter the default line width for PDF export.\n"
\r
1235 + "[current value: "
\r
1236 + getOptions().getPrintLineWidth() + "]\n",
\r
1237 "Line Width for PDF Export",
\r
1238 JOptionPane.QUESTION_MESSAGE,
\r
1241 getOptions().getPrintLineWidth() );
\r
1242 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1243 boolean success = true;
\r
1245 final String m_str = s.trim();
\r
1246 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1248 f = Float.parseFloat( m_str );
\r
1250 catch ( final Exception ex ) {
\r
1257 if ( success && ( f > 0.0 ) ) {
\r
1258 getOptions().setPrintLineWidth( f );
\r
1264 removeAllTextFrames();
\r
1265 if ( _mainpanel != null ) {
\r
1266 _mainpanel.terminate();
\r
1268 if ( _contentpane != null ) {
\r
1269 _contentpane.removeAll();
\r
1271 setVisible( false );
\r
1275 void colorRank() {
\r
1276 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1277 final String[] ranks = AptxUtil.getAllPossibleRanks();
\r
1278 final String rank = ( String ) JOptionPane
\r
1279 .showInputDialog( this,
\r
1280 "What rank should the colorization be based on",
\r
1282 JOptionPane.QUESTION_MESSAGE,
\r
1286 if ( !ForesterUtil.isEmpty( rank ) ) {
\r
1287 _mainpanel.getCurrentTreePanel().colorRank( rank );
\r
1292 void confColor() {
\r
1293 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1294 _mainpanel.getCurrentTreePanel().confColor();
\r
1298 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
\r
1299 if ( item != null ) {
\r
1300 item.setFont( MainFrame.menu_font );
\r
1301 if ( !getConfiguration().isUseNativeUI() ) {
\r
1302 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
1303 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
1305 item.setSelected( is_selected );
\r
1306 item.addActionListener( this );
\r
1310 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
\r
1311 if ( jmi != null ) {
\r
1312 jmi.setFont( MainFrame.menu_font );
\r
1313 if ( !getConfiguration().isUseNativeUI() ) {
\r
1314 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
1315 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
1317 jmi.addActionListener( this );
\r
1322 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
\r
1323 if ( item != null ) {
\r
1324 item.setFont( MainFrame.menu_font );
\r
1325 if ( !getConfiguration().isUseNativeUI() ) {
\r
1326 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
1327 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
1329 item.setSelected( is_selected );
\r
1330 item.addActionListener( this );
\r
1334 void displayBasicInformation( final File treefile ) {
\r
1335 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1336 String title = "Basic Information";
\r
1337 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1338 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
\r
1340 showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
\r
1344 void exceptionOccuredDuringOpenFile( final Exception e ) {
\r
1346 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
1348 catch ( final Exception ex ) {
\r
1351 JOptionPane.showMessageDialog( this,
\r
1352 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
1353 "Error during File|Open",
\r
1354 JOptionPane.ERROR_MESSAGE );
\r
1357 void executeGSDI() {
\r
1358 if ( !isOKforSDI( false, true ) ) {
\r
1361 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
\r
1362 JOptionPane.showMessageDialog( this,
\r
1363 "Gene tree is not rooted.",
\r
1364 "Cannot execute GSDI",
\r
1365 JOptionPane.ERROR_MESSAGE );
\r
1368 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
1369 gene_tree.setAllNodesToNotCollapse();
\r
1370 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
1372 final Phylogeny species_tree = getSpeciesTree().copy();
\r
1374 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
\r
1376 catch ( final SDIException e ) {
\r
1377 JOptionPane.showMessageDialog( this,
\r
1378 e.getLocalizedMessage(),
\r
1379 "Error during GSDI",
\r
1380 JOptionPane.ERROR_MESSAGE );
\r
1383 catch ( final Exception e ) {
\r
1384 AptxUtil.unexpectedException( e );
\r
1387 gene_tree.setRerootable( false );
\r
1388 gene_tree.clearHashIdToNodeMap();
\r
1389 gene_tree.recalculateNumberOfExternalDescendants( true );
\r
1390 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
\r
1391 getMainPanel().getControlPanel().setShowEvents( true );
\r
1393 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
1394 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
1396 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
1398 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
1399 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
1400 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
1401 JOptionPane.showMessageDialog( this,
\r
1402 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
1403 + "Potential duplications: "
\r
1404 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
1405 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
1406 + "Stripped gene tree nodes: "
\r
1407 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1408 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
1409 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1410 "GSDI successfully completed",
\r
1411 JOptionPane.WARNING_MESSAGE );
\r
1414 JOptionPane.showMessageDialog( this,
\r
1415 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
1416 + "Potential duplications: "
\r
1417 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
1418 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
1419 + "Stripped gene tree nodes: "
\r
1420 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1421 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
1422 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1423 "GSDI successfully completed",
\r
1424 JOptionPane.INFORMATION_MESSAGE );
\r
1428 void executeGSDIR() {
\r
1429 if ( !isOKforSDI( false, false ) ) {
\r
1432 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
\r
1434 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
\r
1435 JOptionPane.showMessageDialog( this,
\r
1436 "Gene tree is not completely binary",
\r
1437 "Cannot execute GSDI",
\r
1438 JOptionPane.ERROR_MESSAGE );
\r
1441 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
1442 gene_tree.setAllNodesToNotCollapse();
\r
1443 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
1444 GSDIR gsdir = null;
\r
1445 final Phylogeny species_tree = getSpeciesTree().copy();
\r
1447 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
\r
1449 catch ( final SDIException e ) {
\r
1450 JOptionPane.showMessageDialog( this,
\r
1451 e.getLocalizedMessage(),
\r
1452 "Error during GSDIR",
\r
1453 JOptionPane.ERROR_MESSAGE );
\r
1456 catch ( final Exception e ) {
\r
1457 AptxUtil.unexpectedException( e );
\r
1460 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
\r
1461 result_gene_tree.setRerootable( false );
\r
1462 result_gene_tree.clearHashIdToNodeMap();
\r
1463 result_gene_tree.recalculateNumberOfExternalDescendants( true );
\r
1464 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
\r
1465 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
\r
1466 getMainPanel().getControlPanel().setShowEvents( true );
\r
1468 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
1469 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
1471 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
1473 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
1474 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
1475 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
1476 JOptionPane.showMessageDialog( this,
\r
1477 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1478 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1479 + "Stripped gene tree nodes: "
\r
1480 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1481 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1482 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1483 "GSDIR successfully completed",
\r
1484 JOptionPane.WARNING_MESSAGE );
\r
1487 JOptionPane.showMessageDialog( this,
\r
1488 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1489 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1490 + "Stripped gene tree nodes: "
\r
1491 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1492 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1493 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1494 "GSDIR successfully completed",
\r
1495 JOptionPane.INFORMATION_MESSAGE );
\r
1499 void executeLineageInference() {
\r
1500 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
\r
1503 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
\r
1504 JOptionPane.showMessageDialog( this,
\r
1505 "Phylogeny is not rooted.",
\r
1506 "Cannot infer ancestral taxonomies",
\r
1507 JOptionPane.ERROR_MESSAGE );
\r
1510 final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
\r
1511 _mainpanel.getCurrentTreePanel(),
\r
1512 _mainpanel.getCurrentPhylogeny()
\r
1514 new Thread( inferrer ).start();
\r
1517 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
\r
1518 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
\r
1519 JOptionPane.showMessageDialog( this,
\r
1520 "Gene tree and species tree have no species in common.",
\r
1521 "Error during SDI",
\r
1522 JOptionPane.ERROR_MESSAGE );
\r
1525 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
\r
1526 JOptionPane.showMessageDialog( this,
\r
1527 "Gene tree and species tree have only one species in common.",
\r
1528 "Error during SDI",
\r
1529 JOptionPane.ERROR_MESSAGE );
\r
1537 ControlPanel getControlPanel() {
\r
1538 return getMainPanel().getControlPanel();
\r
1541 File getCurrentDir() {
\r
1542 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
\r
1543 if ( ForesterUtil.isWindows() ) {
\r
1545 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
\r
1547 catch ( final Exception e ) {
\r
1548 _current_dir = null;
\r
1552 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
\r
1553 if ( System.getProperty( "user.home" ) != null ) {
\r
1554 _current_dir = new File( System.getProperty( "user.home" ) );
\r
1556 else if ( System.getProperty( "user.dir" ) != null ) {
\r
1557 _current_dir = new File( System.getProperty( "user.dir" ) );
\r
1560 return _current_dir;
\r
1563 TreePanel getCurrentTreePanel() {
\r
1564 return getMainPanel().getCurrentTreePanel();
\r
1567 JMenu getHelpMenu() {
\r
1568 return _help_jmenu;
\r
1571 JCheckBoxMenuItem getlabelDirectionCbmi() {
\r
1572 return _label_direction_cbmi;
\r
1575 JMenuBar getMenuBarOfMainFrame() {
\r
1579 final Phylogeny getSpeciesTree() {
\r
1580 return _species_tree;
\r
1583 void initializeTypeMenu( final Options options ) {
\r
1584 setTypeMenuToAllUnselected();
\r
1585 switch ( options.getPhylogenyGraphicsType() ) {
\r
1587 _convex_type_cbmi.setSelected( true );
\r
1590 _curved_type_cbmi.setSelected( true );
\r
1593 _euro_type_cbmi.setSelected( true );
\r
1596 _rounded_type_cbmi.setSelected( true );
\r
1599 _triangular_type_cbmi.setSelected( true );
\r
1602 _unrooted_type_cbmi.setSelected( true );
\r
1605 _circular_type_cbmi.setSelected( true );
\r
1608 _rectangular_type_cbmi.setSelected( true );
\r
1613 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
\r
1614 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1617 else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
\r
1618 JOptionPane.showMessageDialog( this,
\r
1619 "No species tree loaded",
\r
1620 "Cannot execute GSDI",
\r
1621 JOptionPane.ERROR_MESSAGE );
\r
1624 else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
\r
1625 JOptionPane.showMessageDialog( this,
\r
1626 "Species tree is not completely binary",
\r
1627 "Cannot execute GSDI",
\r
1628 JOptionPane.ERROR_MESSAGE );
\r
1631 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
\r
1632 JOptionPane.showMessageDialog( this,
\r
1633 "Gene tree is not completely binary",
\r
1634 "Cannot execute GSDI",
\r
1635 JOptionPane.ERROR_MESSAGE );
\r
1643 boolean isSubtreeDisplayed() {
\r
1644 if ( getCurrentTreePanel() != null ) {
\r
1645 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
\r
1647 .showMessageDialog( this,
\r
1648 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
\r
1649 "Operation can not be exectuted on a sub-tree",
\r
1650 JOptionPane.WARNING_MESSAGE );
\r
1657 void midpointRoot() {
\r
1658 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1659 _mainpanel.getCurrentTreePanel().midpointRoot();
\r
1663 void readPhylogeniesFromWebservice( final int i ) {
\r
1664 final UrlTreeReader reader = new UrlTreeReader( this, i );
\r
1665 new Thread( reader ).start();
\r
1668 void removeAllTextFrames() {
\r
1669 for( final TextFrame tf : _textframes ) {
\r
1670 if ( tf != null ) {
\r
1674 _textframes.clear();
\r
1677 void resetSearch() {
\r
1678 getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
\r
1679 getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
\r
1680 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );
\r
1681 getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );
\r
1682 getMainPanel().getControlPanel().getSearchTextField0().setText( "" );
\r
1683 getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );
\r
1684 getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );
\r
1685 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );
\r
1686 getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );
\r
1687 getMainPanel().getControlPanel().getSearchTextField1().setText( "" );
\r
1688 getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );
\r
1689 getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );
\r
1692 void setConfiguration( final Configuration configuration ) {
\r
1693 _configuration = configuration;
\r
1696 void setCurrentDir( final File current_dir ) {
\r
1697 _current_dir = current_dir;
\r
1700 void setInferenceManager( final InferenceManager i ) {
\r
1701 _inference_manager = i;
\r
1704 void setOptions( final Options options ) {
\r
1705 _options = options;
\r
1708 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
\r
1709 setTypeMenuToAllUnselected();
\r
1712 _circular_type_cbmi.setSelected( true );
\r
1715 _convex_type_cbmi.setSelected( true );
\r
1718 _curved_type_cbmi.setSelected( true );
\r
1721 _euro_type_cbmi.setSelected( true );
\r
1724 _rounded_type_cbmi.setSelected( true );
\r
1727 _rectangular_type_cbmi.setSelected( true );
\r
1730 _triangular_type_cbmi.setSelected( true );
\r
1733 _unrooted_type_cbmi.setSelected( true );
\r
1736 throw new IllegalArgumentException( "unknown type: " + type );
\r
1740 final void setSpeciesTree( final Phylogeny species_tree ) {
\r
1741 _species_tree = species_tree;
\r
1744 void setTypeMenuToAllUnselected() {
\r
1745 _convex_type_cbmi.setSelected( false );
\r
1746 _curved_type_cbmi.setSelected( false );
\r
1747 _euro_type_cbmi.setSelected( false );
\r
1748 _rounded_type_cbmi.setSelected( false );
\r
1749 _triangular_type_cbmi.setSelected( false );
\r
1750 _rectangular_type_cbmi.setSelected( false );
\r
1751 _unrooted_type_cbmi.setSelected( false );
\r
1752 _circular_type_cbmi.setSelected( false );
\r
1755 void switchColors() {
\r
1756 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
\r
1757 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
\r
1758 csc.setVisible( true );
\r
1762 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1763 _mainpanel.getCurrentTreePanel().taxColor();
\r
1767 void typeChanged( final Object o ) {
\r
1768 updateTypeCheckboxes( getOptions(), o );
\r
1769 updateOptions( getOptions() );
\r
1770 if ( getCurrentTreePanel() != null ) {
\r
1771 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
\r
1772 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
\r
1773 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1774 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
\r
1775 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1776 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
\r
1777 getCurrentTreePanel().getControlPanel().showWhole();
\r
1779 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
\r
1780 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
\r
1783 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
\r
1785 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
\r
1786 updateScreenTextAntialias( getMainPanel().getTreePanels() );
\r
1787 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
\r
1788 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
\r
1789 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
\r
1792 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
\r
1798 void updateOptions( final Options options ) {
\r
1799 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
\r
1800 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
\r
1801 && _background_gradient_cbmi.isSelected() );
\r
1802 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
\r
1803 options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
\r
1804 && _show_annotation_ref_source.isSelected() );
\r
1805 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
\r
1806 && _abbreviate_scientific_names.isSelected() );
\r
1807 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
\r
1808 && _color_labels_same_as_parent_branch.isSelected() );
\r
1809 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
\r
1810 && _show_default_node_shapes_internal_cbmi.isSelected() );
\r
1811 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
\r
1812 && _show_default_node_shapes_external_cbmi.isSelected() );
\r
1813 options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
\r
1814 && _show_default_node_shapes_for_marked_cbmi.isSelected() );
\r
1815 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
\r
1816 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
\r
1818 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
\r
1819 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
\r
1821 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
\r
1822 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
\r
1824 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
\r
1825 && _search_case_senstive_cbmi.isSelected() );
\r
1826 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
\r
1827 options.setShowScale( _show_scale_cbmi.isSelected() );
\r
1829 if ( _label_direction_cbmi != null ) {
\r
1830 if ( _label_direction_cbmi.isSelected() ) {
\r
1831 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
\r
1834 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
\r
1837 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
\r
1838 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
\r
1839 && _show_confidence_stddev_cbmi.isSelected() );
\r
1840 if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
\r
1841 options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
\r
1843 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
\r
1844 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
\r
1845 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1846 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
\r
1848 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
\r
1849 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1850 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
\r
1853 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
\r
1855 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
\r
1856 && _print_black_and_white_cbmi.isSelected() );
\r
1857 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
\r
1858 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
\r
1859 if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
\r
1860 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
\r
1862 else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
\r
1863 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
\r
1865 else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
\r
1866 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1868 else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
\r
1869 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
\r
1871 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
\r
1872 && _replace_underscores_cbmi.isSelected() );
\r
1873 options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
\r
1874 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
\r
1875 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
\r
1876 && _search_whole_words_only_cbmi.isSelected() );
\r
1877 options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
\r
1878 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
\r
1879 && _inverse_search_result_cbmi.isSelected() );
\r
1880 if ( _graphics_export_visible_only_cbmi != null ) {
\r
1881 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
\r
1883 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
\r
1884 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1886 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
\r
1887 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
\r
1889 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
\r
1890 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
\r
1892 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
\r
1893 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
\r
1895 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
\r
1896 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
\r
1898 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
\r
1899 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
\r
1901 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
\r
1902 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
\r
1904 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
\r
1905 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
\r
1907 if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
\r
1908 options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
\r
1910 if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
\r
1911 options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
\r
1913 if ( ( _color_all_found_nodes_when_coloring_subtree_cbmi != null ) && _color_all_found_nodes_when_coloring_subtree_cbmi.isEnabled() ) {
\r
1914 options.setColorAllFoundNodesWhenColoringSubtree( _color_all_found_nodes_when_coloring_subtree_cbmi.isSelected() );
\r
1918 void updateTypeCheckboxes( final Options options, final Object o ) {
\r
1919 setTypeMenuToAllUnselected();
\r
1920 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
\r
1923 void viewAsNexus() {
\r
1924 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1925 String title = "Nexus";
\r
1926 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1927 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1929 showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
\r
1935 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1936 String title = "New Hampshire";
\r
1937 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1938 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1940 showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
\r
1941 .getNhConversionSupportValueStyle() ),
\r
1946 void viewAsXML() {
\r
1947 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1948 String title = "phyloXML";
\r
1949 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1950 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1952 showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
\r
1956 private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {
\r
1957 switch ( op.getExtDescNodeDataToReturn() ) {
\r
1959 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
\r
1962 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
\r
1964 case DOMAINS_COLLAPSED_PER_PROTEIN:
\r
1965 op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
\r
1967 case SEQ_ANNOTATIONS:
\r
1968 op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
\r
1971 op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
\r
1973 case SEQUENCE_MOL_SEQ_FASTA:
\r
1974 if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )
\r
1975 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )
\r
1976 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )
\r
1977 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )
\r
1978 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )
\r
1979 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {
\r
1980 op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );
\r
1983 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
\r
1987 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
\r
1992 * Display the about box.
\r
1994 static void about() {
\r
1995 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + AptxConstants.VERSION + "\n" );
\r
1996 about.append( "Copyright (C) 2016 Christian M Zmasek\n" );
\r
1997 about.append( "All Rights Reserved\n" );
\r
1998 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
\r
1999 about.append( "Last modified: " + AptxConstants.PRG_DATE + "\n" );
\r
2000 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
\r
2001 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
\r
2002 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
\r
2003 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
\r
2004 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
\r
2006 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
\r
2007 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
\r
2008 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
\r
2009 + ForesterUtil.OS_VERSION + "]\n" );
\r
2011 final Runtime rt = java.lang.Runtime.getRuntime();
\r
2012 final long free_memory = rt.freeMemory() / 1000000;
\r
2013 final long total_memory = rt.totalMemory() / 1000000;
\r
2014 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
\r
2015 about.append( "[locale: " + Locale.getDefault() + "]\n" );
\r
2016 about.append( "References:\n" );
\r
2017 about.append( AptxConstants.PHYLOXML_REFERENCE_SHORT + "\n" );
\r
2018 about.append( "For more information & download:\n" );
\r
2019 about.append( AptxConstants.APTX_WEB_SITE + "\n" );
\r
2020 about.append( "Documentation:\n" );
\r
2021 about.append( AptxConstants.APTX_DOC_SITE + "\n" );
\r
2022 about.append( "Comments: " + AptxConstants.AUTHOR_EMAIL );
\r
2023 JOptionPane.showMessageDialog( null, about, AptxConstants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
\r
2026 static void chooseNodeSize( final Options options, final Component parent ) {
\r
2027 final String s = ( String ) JOptionPane.showInputDialog( parent,
\r
2028 "Please enter the default size for node shapes.\n"
\r
2029 + "[current value: "
\r
2030 + options.getDefaultNodeShapeSize() + "]\n",
\r
2031 "Node Shape Size",
\r
2032 JOptionPane.QUESTION_MESSAGE,
\r
2035 options.getDefaultNodeShapeSize() );
\r
2036 if ( !ForesterUtil.isEmpty( s ) ) {
\r
2037 boolean success = true;
\r
2039 final String m_str = s.trim();
\r
2040 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
2042 m = Double.parseDouble( m_str );
\r
2044 catch ( final Exception ex ) {
\r
2051 if ( success && ( m >= 0.0 ) ) {
\r
2052 final short size = ForesterUtil.roundToShort( m );
\r
2053 if ( size >= 0.0 ) {
\r
2054 options.setDefaultNodeShapeSize( size );
\r
2060 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
\r
2061 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
\r
2064 static JMenu createMenu( final String title, final Configuration conf ) {
\r
2065 final JMenu jmenu = new JMenu( title );
\r
2066 if ( !conf.isUseNativeUI() ) {
\r
2067 jmenu.setFont( MainFrame.menu_font );
\r
2068 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
\r
2069 jmenu.setForeground( conf.getGuiMenuTextColor() );
\r
2074 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
\r
2075 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
\r
2076 if ( !configuration.isUseNativeUI() ) {
\r
2077 label.setBackground( configuration.getGuiMenuBackgroundColor() );
\r
2078 label.setForeground( configuration.getGuiMenuTextColor() );
\r
2079 label.setOpaque( true );
\r
2081 label.setSelected( false );
\r
2082 label.setEnabled( false );
\r
2086 static void cycleNodeFill( final Options op ) {
\r
2087 switch ( op.getDefaultNodeFill() ) {
\r
2089 op.setDefaultNodeFill( NodeFill.SOLID );
\r
2092 op.setDefaultNodeFill( NodeFill.GRADIENT );
\r
2095 op.setDefaultNodeFill( NodeFill.NONE );
\r
2098 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
\r
2102 static void cycleNodeShape( final Options op ) {
\r
2103 switch ( op.getDefaultNodeShape() ) {
\r
2105 op.setDefaultNodeShape( NodeShape.RECTANGLE );
\r
2108 op.setDefaultNodeShape( NodeShape.CIRCLE );
\r
2111 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
\r
2115 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
\r
2116 switch ( op.getOvPlacement() ) {
\r
2118 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
\r
2121 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
\r
2124 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
\r
2127 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
\r
2130 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
\r
2132 if ( tree_panel != null ) {
\r
2133 tree_panel.updateOvSettings();
\r
2137 static void exceptionOccuredDuringSaveAs( final Exception e, final TreePanel tp, final Component comp ) {
\r
2139 tp.setArrowCursor();
\r
2141 catch ( final Exception ex ) {
\r
2144 JOptionPane.showMessageDialog( comp, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
\r
2147 static void print( final TreePanel tp, final Options op, final Component c ) {
\r
2148 if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) {
\r
2151 final String job_name = AptxConstants.PRG_NAME;
\r
2152 boolean error = false;
\r
2153 String printer_name = null;
\r
2155 printer_name = Printer.print( tp, job_name );
\r
2157 catch ( final Exception e ) {
\r
2159 JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
\r
2161 if ( !error && ( printer_name != null ) ) {
\r
2162 String msg = "Printing data sent to printer";
\r
2163 if ( printer_name.length() > 1 ) {
\r
2164 msg += " [" + printer_name + "]";
\r
2166 JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
\r
2168 if ( !op.isPrintUsingActualSize() ) {
\r
2169 tp.getControlPanel().showWhole();
\r
2173 static void printPhylogenyToPdf( final String file_name,
\r
2174 final Options opts,
\r
2175 final TreePanel tp,
\r
2176 final Component comp ) {
\r
2178 String pdf_written_to = "";
\r
2179 boolean error = false;
\r
2181 if ( opts.isPrintUsingActualSize() ) {
\r
2182 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth() , tp.getHeight() );
\r
2188 catch ( final IOException e ) {
\r
2190 JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
\r
2193 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
\r
2194 JOptionPane.showMessageDialog( comp,
\r
2195 "Wrote PDF to: " + pdf_written_to,
\r
2197 JOptionPane.INFORMATION_MESSAGE );
\r
2200 JOptionPane.showMessageDialog( comp,
\r
2201 "There was an unknown problem when attempting to write to PDF file: \""
\r
2202 + file_name + "\"",
\r
2204 JOptionPane.ERROR_MESSAGE );
\r
2207 if ( !opts.isPrintUsingActualSize() ) {
\r
2208 tp.getControlPanel().showWhole();
\r
2212 static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {
\r
2213 if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {
\r
2214 mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" );
\r
2217 mi.setText( "Cycle Node Return Data..." );
\r
2221 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
\r
2222 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
\r
2223 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
2224 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
\r
2227 mi.setText( "Cycle Node Shape Fill Type..." );
\r
2231 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
\r
2232 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
\r
2233 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
2234 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
\r
2237 mi.setText( "Cycle Node Shape Fill Type..." );
\r
2241 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
\r
2242 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
\r
2243 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
\r
2246 mi.setText( "Cycle Overview Placement..." );
\r
2250 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
\r
2251 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
\r
2252 mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
\r
2256 mi.setText( "Select Color Scheme..." );
\r
2260 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
\r
2261 mi.setText( "Select Default Font... (current: " + font_desc + ")" );
\r
2264 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
\r
2265 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
\r
2268 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
\r
2269 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
\r
2270 mi.setEnabled( true );
\r
2272 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
\r
2273 mi.setEnabled( true );
\r
2276 mi.setEnabled( false );
\r
2278 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
\r
2281 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
\r
2282 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
\r
2285 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
\r
2286 for( final TreePanel tree_panel : treepanels ) {
\r
2287 tree_panel.setTextAntialias();
\r
2291 static boolean writeAsNewHampshire( final TreePanel tp, final Options op, boolean exception, final File file ) {
\r
2293 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2294 writer.toNewHampshire( tp.getPhylogeny(), true, op.getNhConversionSupportValueStyle(), file );
\r
2296 catch ( final Exception e ) {
\r
2298 exceptionOccuredDuringSaveAs( e, tp, tp );
\r
2303 static boolean writeAsNexus( final TreePanel tp, final Options op, boolean exception, final File file ) {
\r
2305 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2306 writer.toNexus( file, tp.getPhylogeny(), op.getNhConversionSupportValueStyle() );
\r
2308 catch ( final Exception e ) {
\r
2310 exceptionOccuredDuringSaveAs( e, tp, tp );
\r
2315 static boolean writeAsPhyloXml( final TreePanel tp, final Options op, boolean exception, final File file ) {
\r
2317 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2318 writer.toPhyloXML( file, tp.getPhylogeny(), 0 );
\r
2320 catch ( final Exception e ) {
\r
2322 exceptionOccuredDuringSaveAs( e, tp, tp );
\r
2327 static void writePhylogenyToGraphicsFile( final String file_name,
\r
2328 final GraphicsExportType type,
\r
2329 final MainPanel mp,
\r
2330 final Component comp,
\r
2331 final Container contentpane ) {
\r
2332 mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(),
\r
2333 mp.getCurrentTreePanel().getHeight() );
\r
2334 String file_written_to = "";
\r
2335 boolean error = false;
\r
2337 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
\r
2338 mp.getCurrentTreePanel().getWidth(),
\r
2339 mp.getCurrentTreePanel().getHeight(),
\r
2340 mp.getCurrentTreePanel(),
\r
2341 mp.getControlPanel(),
\r
2343 mp.getOptions() );
\r
2345 catch ( final IOException e ) {
\r
2347 JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
\r
2350 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
\r
2351 JOptionPane.showMessageDialog( comp,
\r
2352 "Wrote image to: " + file_written_to,
\r
2353 "Graphics Export",
\r
2354 JOptionPane.INFORMATION_MESSAGE );
\r
2357 JOptionPane.showMessageDialog( comp,
\r
2358 "There was an unknown problem when attempting to write to an image file: \""
\r
2359 + file_name + "\"",
\r
2361 JOptionPane.ERROR_MESSAGE );
\r
2364 contentpane.repaint();
\r
2367 static File writeToFile( final Phylogeny t,
\r
2368 final MainPanel mp,
\r
2369 final JFileChooser save_filechooser,
\r
2370 final File current_dir,
\r
2371 final Container contentpane,
\r
2372 final Component comp ) {
\r
2373 File new_file = null;
\r
2374 if ( t == null ) {
\r
2377 String initial_filename = null;
\r
2378 if ( mp.getCurrentTreePanel().getTreeFile() != null ) {
\r
2380 initial_filename = mp.getCurrentTreePanel().getTreeFile().getCanonicalPath();
\r
2382 catch ( final IOException e ) {
\r
2383 initial_filename = null;
\r
2386 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
\r
2387 save_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2390 save_filechooser.setSelectedFile( new File( "" ) );
\r
2392 final File my_dir = current_dir;
\r
2393 if ( my_dir != null ) {
\r
2394 save_filechooser.setCurrentDirectory( my_dir );
\r
2396 final int result = save_filechooser.showSaveDialog( contentpane );
\r
2397 final File file = save_filechooser.getSelectedFile();
\r
2398 new_file = save_filechooser.getCurrentDirectory();
\r
2399 boolean exception = false;
\r
2400 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2401 if ( file.exists() ) {
\r
2402 final int i = JOptionPane.showConfirmDialog( comp,
\r
2403 file + " already exists.\nOverwrite?",
\r
2405 JOptionPane.OK_CANCEL_OPTION,
\r
2406 JOptionPane.QUESTION_MESSAGE );
\r
2407 if ( i != JOptionPane.OK_OPTION ) {
\r
2411 final File to = new File( file.getAbsoluteFile().toString() + AptxConstants.BACKUP_FILE_SUFFIX );
\r
2413 ForesterUtil.copyFile( file, to );
\r
2415 catch ( final Exception e ) {
\r
2416 JOptionPane.showMessageDialog( comp,
\r
2417 "Failed to create backup copy " + to,
\r
2418 "Failed to Create Backup Copy",
\r
2419 JOptionPane.WARNING_MESSAGE );
\r
2424 catch ( final Exception e ) {
\r
2425 JOptionPane.showMessageDialog( comp,
\r
2426 "Failed to delete: " + file,
\r
2427 "Failed to Delete",
\r
2428 JOptionPane.WARNING_MESSAGE );
\r
2432 if ( save_filechooser.getFileFilter() == MainFrame.nhfilter ) {
\r
2433 exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
\r
2435 else if ( save_filechooser.getFileFilter() == MainFrame.xmlfilter ) {
\r
2436 exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
\r
2438 else if ( save_filechooser.getFileFilter() == MainFrame.nexusfilter ) {
\r
2439 exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
\r
2443 final String file_name = file.getName().trim().toLowerCase();
\r
2444 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2445 || file_name.endsWith( ".tree" ) ) {
\r
2446 exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
\r
2448 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
\r
2449 exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
\r
2451 // XML is default:
\r
2453 exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
\r
2456 if ( !exception ) {
\r
2457 mp.setTitleOfSelectedTab( file.getName() );
\r
2458 mp.getCurrentTreePanel().setTreeFile( file );
\r
2459 mp.getCurrentTreePanel().setEdited( false );
\r
2465 static File writeToGraphicsFile( final Phylogeny t,
\r
2466 final GraphicsExportType type,
\r
2467 final MainPanel mp,
\r
2468 final JFileChooser writetographics_filechooser,
\r
2469 final Component component,
\r
2470 final Container contentpane,
\r
2471 final File current_dir ) {
\r
2472 File new_dir = null;
\r
2473 if ( ( t == null ) || t.isEmpty() ) {
\r
2476 String initial_filename = "";
\r
2477 if ( mp.getCurrentTreePanel().getTreeFile() != null ) {
\r
2478 initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();
\r
2480 if ( initial_filename.indexOf( '.' ) > 0 ) {
\r
2481 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
\r
2483 initial_filename = initial_filename + "." + type;
\r
2484 writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2485 final File my_dir = current_dir;
\r
2486 if ( my_dir != null ) {
\r
2487 writetographics_filechooser.setCurrentDirectory( my_dir );
\r
2489 final int result = writetographics_filechooser.showSaveDialog( contentpane );
\r
2490 File file = writetographics_filechooser.getSelectedFile();
\r
2491 //setCurrentDir( writetographics_filechooser.getCurrentDirectory() );
\r
2492 new_dir = writetographics_filechooser.getCurrentDirectory();
\r
2493 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2494 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
\r
2495 file = new File( file.toString() + "." + type );
\r
2497 if ( file.exists() ) {
\r
2498 final int i = JOptionPane.showConfirmDialog( component,
\r
2499 file + " already exists. Overwrite?",
\r
2501 JOptionPane.OK_CANCEL_OPTION,
\r
2502 JOptionPane.WARNING_MESSAGE );
\r
2503 if ( i != JOptionPane.OK_OPTION ) {
\r
2510 catch ( final Exception e ) {
\r
2511 JOptionPane.showMessageDialog( component,
\r
2512 "Failed to delete: " + file,
\r
2514 JOptionPane.WARNING_MESSAGE );
\r
2518 writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane );
\r
2523 static File writeToPdf( final Phylogeny t,
\r
2524 final MainPanel mp,
\r
2525 final JFileChooser writetopdf_filechooser,
\r
2526 final File curr_dir,
\r
2527 final Container contentpane,
\r
2528 final Component component ) {
\r
2529 if ( ( t == null ) || t.isEmpty() ) {
\r
2532 String initial_filename = "";
\r
2533 if ( mp.getCurrentTreePanel().getTreeFile() != null ) {
\r
2534 initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();
\r
2536 if ( initial_filename.indexOf( '.' ) > 0 ) {
\r
2537 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
\r
2539 initial_filename = initial_filename + ".pdf";
\r
2540 writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2541 final File my_dir = curr_dir;
\r
2542 if ( my_dir != null ) {
\r
2543 writetopdf_filechooser.setCurrentDirectory( my_dir );
\r
2545 final int result = writetopdf_filechooser.showSaveDialog( contentpane );
\r
2546 File file = writetopdf_filechooser.getSelectedFile();
\r
2547 // setCurrentDir( writetopdf_filechooser.getCurrentDirectory() );
\r
2548 final File new_current_dir = writetopdf_filechooser.getCurrentDirectory();
\r
2549 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2550 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
\r
2551 file = new File( file.toString() + ".pdf" );
\r
2553 if ( file.exists() ) {
\r
2554 final int i = JOptionPane.showConfirmDialog( component,
\r
2555 file + " already exists. Overwrite?",
\r
2557 JOptionPane.OK_CANCEL_OPTION,
\r
2558 JOptionPane.WARNING_MESSAGE );
\r
2559 if ( i != JOptionPane.OK_OPTION ) {
\r
2563 printPhylogenyToPdf( file.toString(), mp.getOptions(), mp.getCurrentTreePanel(), component );
\r
2565 return new_current_dir;
\r
2569 class DefaultFilter extends FileFilter {
\r
2572 public boolean accept( final File f ) {
\r
2573 final String file_name = f.getName().trim().toLowerCase();
\r
2574 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2575 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
\r
2576 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
\r
2577 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
\r
2578 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
\r
2579 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
\r
2580 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
\r
2581 || file_name.endsWith( ".con" ) || f.isDirectory();
\r
2585 public String getDescription() {
\r
2586 return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
\r
2590 class GraphicsFileFilter 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( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
\r
2596 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
\r
2600 public String getDescription() {
\r
2601 return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
\r
2605 class MsaFileFilter extends FileFilter {
\r
2608 public boolean accept( final File f ) {
\r
2609 final String file_name = f.getName().trim().toLowerCase();
\r
2610 return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
\r
2611 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
\r
2615 public String getDescription() {
\r
2616 return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
\r
2620 class NexusFilter extends FileFilter {
\r
2623 public boolean accept( final File f ) {
\r
2624 final String file_name = f.getName().trim().toLowerCase();
\r
2625 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
\r
2626 || file_name.endsWith( ".tre" ) || f.isDirectory();
\r
2630 public String getDescription() {
\r
2631 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
\r
2635 class NHFilter extends FileFilter {
\r
2638 public boolean accept( final File f ) {
\r
2639 final String file_name = f.getName().trim().toLowerCase();
\r
2640 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2641 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
\r
2642 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
\r
2643 || f.isDirectory();
\r
2647 public String getDescription() {
\r
2648 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
\r
2652 class NHXFilter extends FileFilter {
\r
2655 public boolean accept( final File f ) {
\r
2656 final String file_name = f.getName().trim().toLowerCase();
\r
2657 return file_name.endsWith( ".nhx" ) || f.isDirectory();
\r
2661 public String getDescription() {
\r
2662 return "NHX files (*.nhx) [deprecated]";
\r
2666 class PdfFilter extends FileFilter {
\r
2669 public boolean accept( final File f ) {
\r
2670 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
\r
2674 public String getDescription() {
\r
2675 return "PDF files (*.pdf)";
\r
2679 class SequencesFileFilter extends FileFilter {
\r
2682 public boolean accept( final File f ) {
\r
2683 final String file_name = f.getName().trim().toLowerCase();
\r
2684 return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
\r
2685 || file_name.endsWith( ".seqs" ) || f.isDirectory();
\r
2689 public String getDescription() {
\r
2690 return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
\r
2694 class TolFilter extends FileFilter {
\r
2697 public boolean accept( final File f ) {
\r
2698 final String file_name = f.getName().trim().toLowerCase();
\r
2699 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
\r
2700 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
\r
2704 public String getDescription() {
\r
2705 return "Tree of Life files (*.tol, *.tolxml)";
\r
2709 class XMLFilter extends FileFilter {
\r
2712 public boolean accept( final File f ) {
\r
2713 final String file_name = f.getName().trim().toLowerCase();
\r
2714 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
\r
2715 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
\r
2719 public String getDescription() {
\r
2720 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";
\r
git://source.jalview.org / jalview.git / blob