2 // FORESTER -- software libraries and applications
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3 // for evolutionary biology research and applications.
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5 // Copyright (C) 2008-2010 Christian M. Zmasek
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6 // All rights reserved
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8 // This library is free software; you can redistribute it and/or
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9 // modify it under the terms of the GNU Lesser General Public
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10 // License as published by the Free Software Foundation; either
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11 // version 2.1 of the License, or (at your option) any later version.
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13 // This library is distributed in the hope that it will be useful,
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14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
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15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 // Lesser General Public License for more details.
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18 // You should have received a copy of the GNU Lesser General Public
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19 // License along with this library; if not, write to the Free Software
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20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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22 // Contact: phylosoft @ gmail . com
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23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
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25 package org.forester.archaeopteryx;
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27 import java.awt.Color;
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28 import java.awt.Component;
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29 import java.awt.Container;
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30 import java.awt.Font;
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31 import java.awt.event.ActionEvent;
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32 import java.awt.event.ActionListener;
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33 import java.io.File;
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34 import java.io.IOException;
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35 import java.util.ArrayList;
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36 import java.util.LinkedList;
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37 import java.util.List;
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38 import java.util.Locale;
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39 import java.util.NoSuchElementException;
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41 import javax.swing.Box;
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42 import javax.swing.JApplet;
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43 import javax.swing.JCheckBoxMenuItem;
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44 import javax.swing.JFileChooser;
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45 import javax.swing.JFrame;
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46 import javax.swing.JLabel;
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47 import javax.swing.JMenu;
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48 import javax.swing.JMenuBar;
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49 import javax.swing.JMenuItem;
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50 import javax.swing.JOptionPane;
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51 import javax.swing.JPanel;
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52 import javax.swing.JRadioButtonMenuItem;
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53 import javax.swing.JTextField;
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54 import javax.swing.SwingUtilities;
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55 import javax.swing.filechooser.FileFilter;
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57 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
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58 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
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59 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
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60 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
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61 import org.forester.archaeopteryx.tools.InferenceManager;
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62 import org.forester.archaeopteryx.tools.ProcessPool;
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63 import org.forester.archaeopteryx.tools.ProcessRunning;
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64 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
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65 import org.forester.io.writers.PhylogenyWriter;
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66 import org.forester.phylogeny.Phylogeny;
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67 import org.forester.phylogeny.PhylogenyMethods;
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68 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
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69 import org.forester.phylogeny.PhylogenyNode;
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70 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
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71 import org.forester.phylogeny.data.Annotation;
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72 import org.forester.phylogeny.data.NodeDataField;
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73 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
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74 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
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75 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
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76 import org.forester.sdi.GSDI;
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77 import org.forester.sdi.GSDIR;
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78 import org.forester.sdi.SDIException;
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79 import org.forester.util.ForesterConstants;
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80 import org.forester.util.ForesterUtil;
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81 import org.forester.util.WindowsUtils;
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83 class DefaultFilter extends FileFilter {
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86 public boolean accept( final File f ) {
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87 final String file_name = f.getName().trim().toLowerCase();
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88 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
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89 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
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90 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
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91 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
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92 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
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93 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
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94 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
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95 || file_name.endsWith( ".con" ) || f.isDirectory();
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99 public String getDescription() {
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100 return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
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104 class GraphicsFileFilter extends FileFilter {
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107 public boolean accept( final File f ) {
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108 final String file_name = f.getName().trim().toLowerCase();
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109 return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
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110 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
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114 public String getDescription() {
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115 return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
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119 public abstract class MainFrame extends JFrame implements ActionListener {
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122 * Display the about box.
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124 static void about() {
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125 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
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126 about.append( "Copyright (C) 2014 Christian M Zmasek\n" );
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127 about.append( "All Rights Reserved\n" );
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128 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
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129 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
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130 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
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131 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
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132 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
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133 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
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134 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
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136 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
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137 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
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138 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
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139 + ForesterUtil.OS_VERSION + "]\n" );
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141 final Runtime rt = java.lang.Runtime.getRuntime();
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142 final long free_memory = rt.freeMemory() / 1000000;
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143 final long total_memory = rt.totalMemory() / 1000000;
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144 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
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145 about.append( "[locale: " + Locale.getDefault() + "]\n" );
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146 about.append( "References:\n" );
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147 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
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148 about.append( "For more information & download:\n" );
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149 about.append( Constants.APTX_WEB_SITE + "\n" );
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150 about.append( "Documentation:\n" );
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151 about.append( Constants.APTX_DOC_SITE + "\n" );
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152 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
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153 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
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156 static void chooseNodeSize( final Options options, final Component parent ) {
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157 final String s = ( String ) JOptionPane.showInputDialog( parent,
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158 "Please enter the default size for node shapes.\n"
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159 + "[current value: "
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160 + options.getDefaultNodeShapeSize() + "]\n",
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162 JOptionPane.QUESTION_MESSAGE,
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165 options.getDefaultNodeShapeSize() );
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166 if ( !ForesterUtil.isEmpty( s ) ) {
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167 boolean success = true;
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169 final String m_str = s.trim();
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170 if ( !ForesterUtil.isEmpty( m_str ) ) {
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172 m = Double.parseDouble( m_str );
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174 catch ( final Exception ex ) {
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181 if ( success && ( m >= 0.0 ) ) {
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182 final short size = ForesterUtil.roundToShort( m );
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183 if ( size >= 0.0 ) {
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184 options.setDefaultNodeShapeSize( size );
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190 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
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191 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
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194 static JMenu createMenu( final String title, final Configuration conf ) {
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195 final JMenu jmenu = new JMenu( title );
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196 if ( !conf.isUseNativeUI() ) {
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197 jmenu.setFont( MainFrame.menu_font );
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198 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
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199 jmenu.setForeground( conf.getGuiMenuTextColor() );
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204 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
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205 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
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206 if ( !configuration.isUseNativeUI() ) {
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207 label.setBackground( configuration.getGuiMenuBackgroundColor() );
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208 label.setForeground( configuration.getGuiMenuTextColor() );
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209 label.setOpaque( true );
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211 label.setSelected( false );
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212 label.setEnabled( false );
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216 private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {
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217 switch ( op.getExtDescNodeDataToReturn() ) {
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219 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
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222 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
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224 case DOMAINS_COLLAPSED_PER_PROTEIN:
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225 op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
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227 case SEQ_ANNOTATIONS:
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228 op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
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231 op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
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233 case SEQUENCE_MOL_SEQ_FASTA:
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234 if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )
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235 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )
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236 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )
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237 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )
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238 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )
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239 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {
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240 op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );
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243 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
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247 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
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251 static void cycleNodeFill( final Options op ) {
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252 switch ( op.getDefaultNodeFill() ) {
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254 op.setDefaultNodeFill( NodeFill.SOLID );
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257 op.setDefaultNodeFill( NodeFill.GRADIENT );
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260 op.setDefaultNodeFill( NodeFill.NONE );
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263 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
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267 static void cycleNodeShape( final Options op ) {
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268 switch ( op.getDefaultNodeShape() ) {
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270 op.setDefaultNodeShape( NodeShape.RECTANGLE );
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273 op.setDefaultNodeShape( NodeShape.CIRCLE );
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276 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
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280 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
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281 switch ( op.getOvPlacement() ) {
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283 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
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286 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
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289 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
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292 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
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295 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
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297 if ( tree_panel != null ) {
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298 tree_panel.updateOvSettings();
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302 static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {
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303 if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {
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304 mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" );
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307 mi.setText( "Cycle Node Return Data..." );
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311 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
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312 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
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313 mi.setText( "Cycle Node Shape Fill Type... (current: "
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314 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
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317 mi.setText( "Cycle Node Shape Fill Type..." );
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321 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
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322 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
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323 mi.setText( "Cycle Node Shape Fill Type... (current: "
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324 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
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327 mi.setText( "Cycle Node Shape Fill Type..." );
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331 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
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332 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
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333 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
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336 mi.setText( "Cycle Overview Placement..." );
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340 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
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341 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
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342 mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
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346 mi.setText( "Select Color Scheme..." );
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350 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
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351 mi.setText( "Select Default Font... (current: " + font_desc + ")" );
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354 static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
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355 mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
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356 + o.getPrintSizeY() + ")" );
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359 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
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360 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
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363 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
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364 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
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365 mi.setEnabled( true );
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367 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
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368 mi.setEnabled( true );
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371 mi.setEnabled( false );
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373 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
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376 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
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377 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
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380 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
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381 for( final TreePanel tree_panel : treepanels ) {
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382 tree_panel.setTextAntialias();
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385 final static NHFilter nhfilter = new NHFilter();
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386 final static NHXFilter nhxfilter = new NHXFilter();
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387 final static XMLFilter xmlfilter = new XMLFilter();
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388 final static TolFilter tolfilter = new TolFilter();
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389 final static NexusFilter nexusfilter = new NexusFilter();
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390 final static PdfFilter pdffilter = new PdfFilter();
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391 final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
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392 final static MsaFileFilter msafilter = new MsaFileFilter();
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393 final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
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394 final static DefaultFilter defaultfilter = new DefaultFilter();
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395 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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396 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
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397 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
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398 private static final long serialVersionUID = 3655000897845508358L;
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399 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
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402 static final String TYPE_MENU_HEADER = "Type";
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403 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
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404 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
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405 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
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406 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
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407 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
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408 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
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409 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
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410 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
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411 static final String OPTIONS_HEADER = "Options";
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412 static final String SEARCH_SUBHEADER = "Search:";
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413 static final String DISPLAY_SUBHEADER = "Display:";
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414 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
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415 static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions";
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416 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
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417 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
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418 static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";
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419 static final String DISPLAY_SCALE_LABEL = "Scale";
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420 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
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421 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
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422 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
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423 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
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424 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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425 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
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426 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
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427 static final String BG_GRAD_LABEL = "Background Color Gradient";
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428 static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";
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429 static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";
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430 static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";
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431 static final String SHOW_OVERVIEW_LABEL = "Overview";
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432 static final String FONT_SIZE_MENU_LABEL = "Font Size";
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433 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
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434 static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";
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435 static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";
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436 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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437 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
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438 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
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439 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
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440 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
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441 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
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442 static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";
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443 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
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444 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
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445 static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";
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446 static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";
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447 static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";
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448 JMenuBar _jmenubar;
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452 JMenu _options_jmenu;
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453 JMenu _font_size_menu;
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455 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
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457 JMenu _analysis_menu;
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458 JMenuItem _load_species_tree_item;
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459 JMenuItem _gsdi_item;
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460 JMenuItem _gsdir_item;
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461 JMenuItem _lineage_inference;
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463 JMenuItem _open_item;
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464 JMenuItem _open_url_item;
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465 JMenuItem _save_item;
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466 JMenuItem _save_all_item;
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467 JMenuItem _close_item;
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468 JMenuItem _exit_item;
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469 JMenuItem _new_item;
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470 JMenuItem _print_item;
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471 JMenuItem _write_to_pdf_item;
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472 JMenuItem _write_to_jpg_item;
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473 JMenuItem _write_to_gif_item;
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474 JMenuItem _write_to_tif_item;
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475 JMenuItem _write_to_png_item;
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476 JMenuItem _write_to_bmp_item;
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478 JMenuItem _midpoint_root_item;
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479 JMenuItem _taxcolor_item;
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480 JMenuItem _confcolor_item;
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481 JMenuItem _color_rank_jmi;
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482 JMenuItem _collapse_species_specific_subtrees;
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483 JMenuItem _obtain_detailed_taxonomic_information_jmi;
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484 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
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485 JMenuItem _obtain_seq_information_jmi;
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486 JMenuItem _move_node_names_to_tax_sn_jmi;
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487 JMenuItem _move_node_names_to_seq_names_jmi;
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488 JMenuItem _extract_tax_code_from_node_names_jmi;
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489 JMenuItem _annotate_item;
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490 JMenuItem _remove_branch_color_item;
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491 JMenuItem _remove_visual_styles_item;
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492 JMenuItem _delete_selected_nodes_item;
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493 JMenuItem _delete_not_selected_nodes_item;
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495 JMenuItem _super_tiny_fonts_item;
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496 JMenuItem _tiny_fonts_item;
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497 JMenuItem _small_fonts_item;
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498 JMenuItem _medium_fonts_item;
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499 JMenuItem _large_fonts_item;
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501 // _ screen and print
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502 JMenuItem _choose_font_mi;
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503 JMenuItem _switch_colors_mi;
\r
504 JCheckBoxMenuItem _label_direction_cbmi;
\r
505 // _ screen display
\r
506 JCheckBoxMenuItem _screen_antialias_cbmi;
\r
507 JCheckBoxMenuItem _background_gradient_cbmi;
\r
508 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
\r
509 JRadioButtonMenuItem _uniform_cladograms_rbmi;
\r
510 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
\r
511 JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
\r
512 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
\r
513 JCheckBoxMenuItem _show_overview_cbmi;
\r
514 JCheckBoxMenuItem _show_domain_labels;
\r
515 JCheckBoxMenuItem _show_annotation_ref_source;
\r
516 JCheckBoxMenuItem _abbreviate_scientific_names;
\r
517 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
\r
518 JMenuItem _overview_placment_mi;
\r
519 JMenuItem _choose_minimal_confidence_mi;
\r
520 JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
\r
521 JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
\r
522 JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
\r
523 JMenuItem _cycle_node_shape_mi;
\r
524 JMenuItem _cycle_node_fill_mi;
\r
525 JMenuItem _choose_node_size_mi;
\r
526 JMenuItem _cycle_data_return;
\r
527 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
\r
528 JCheckBoxMenuItem _right_line_up_domains_cbmi;
\r
529 JCheckBoxMenuItem _line_up_renderable_data_cbmi;
\r
531 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
\r
532 JCheckBoxMenuItem _antialias_print_cbmi;
\r
533 JCheckBoxMenuItem _print_black_and_white_cbmi;
\r
534 JCheckBoxMenuItem _print_using_actual_size_cbmi;
\r
535 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
\r
536 JMenuItem _print_size_mi;
\r
537 JMenuItem _choose_pdf_width_mi;
\r
539 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
\r
540 JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
\r
541 JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
\r
542 JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
\r
543 JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
\r
544 JCheckBoxMenuItem _replace_underscores_cbmi;
\r
545 JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
\r
546 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
\r
547 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
\r
549 JCheckBoxMenuItem _search_case_senstive_cbmi;
\r
550 JCheckBoxMenuItem _search_whole_words_only_cbmi;
\r
551 JCheckBoxMenuItem _inverse_search_result_cbmi;
\r
552 JCheckBoxMenuItem _search_with_regex_cbmi;
\r
555 JCheckBoxMenuItem _rectangular_type_cbmi;
\r
556 JCheckBoxMenuItem _triangular_type_cbmi;
\r
557 JCheckBoxMenuItem _curved_type_cbmi;
\r
558 JCheckBoxMenuItem _convex_type_cbmi;
\r
559 JCheckBoxMenuItem _euro_type_cbmi;
\r
560 JCheckBoxMenuItem _rounded_type_cbmi; ;
\r
561 JCheckBoxMenuItem _unrooted_type_cbmi;
\r
562 JCheckBoxMenuItem _circular_type_cbmi;
\r
563 // view as text menu:
\r
564 JMenuItem _view_as_NH_item;
\r
565 JMenuItem _view_as_XML_item;
\r
566 JMenuItem _view_as_nexus_item;
\r
567 JMenuItem _display_basic_information_item;
\r
569 JMenuItem _about_item;
\r
570 JMenuItem _help_item;
\r
571 JMenuItem _website_item;
\r
572 JMenuItem _phyloxml_website_item;
\r
573 JMenuItem _phyloxml_ref_item;
\r
574 JMenuItem _aptx_ref_item;
\r
576 JFileChooser _writetopdf_filechooser;
\r
578 JFileChooser _save_filechooser;
\r
579 JFileChooser _writetographics_filechooser;
\r
581 JMenu _process_menu;
\r
582 // Handy pointers to child components:
\r
583 MainPanel _mainpanel;
\r
584 Container _contentpane;
\r
585 final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>();
\r
586 Configuration _configuration;
\r
588 private Phylogeny _species_tree;
\r
589 InferenceManager _inference_manager;
\r
590 final ProcessPool _process_pool;
\r
591 private String _previous_node_annotation_ref;
\r
594 _process_pool = ProcessPool.createInstance();
\r
595 _writetopdf_filechooser = new JFileChooser();
\r
596 _save_filechooser = new JFileChooser();
\r
597 _save_filechooser.setCurrentDirectory( new File( "." ) );
\r
598 _save_filechooser.setMultiSelectionEnabled( false );
\r
599 _save_filechooser.setFileFilter( MainFrame.xmlfilter );
\r
600 _save_filechooser.addChoosableFileFilter( nhfilter );
\r
601 _save_filechooser.addChoosableFileFilter( nexusfilter );
\r
602 _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
\r
603 _writetographics_filechooser = new JFileChooser();
\r
604 _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter );
\r
608 * Action performed.
\r
611 public void actionPerformed( final ActionEvent e ) {
\r
612 final Object o = e.getSource();
\r
613 boolean is_applet = false;
\r
614 JApplet applet = null;
\r
615 if ( getCurrentTreePanel() != null ) {
\r
616 is_applet = getCurrentTreePanel().isApplet();
\r
618 applet = getCurrentTreePanel().obtainApplet();
\r
621 if ( o == _exit_item ) {
\r
624 else if ( o == _gsdi_item ) {
\r
625 if ( isSubtreeDisplayed() ) {
\r
630 else if ( o == _gsdir_item ) {
\r
631 if ( isSubtreeDisplayed() ) {
\r
636 else if ( o == _taxcolor_item ) {
\r
639 else if ( o == _confcolor_item ) {
\r
642 else if ( o == _color_rank_jmi ) {
\r
645 else if ( o == _collapse_species_specific_subtrees ) {
\r
646 if ( isSubtreeDisplayed() ) {
\r
649 if ( getCurrentTreePanel() != null ) {
\r
650 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
\r
653 else if ( o == _remove_branch_color_item ) {
\r
654 if ( isSubtreeDisplayed() ) {
\r
657 removeBranchColors();
\r
659 else if ( o == _remove_visual_styles_item ) {
\r
660 if ( isSubtreeDisplayed() ) {
\r
663 removeVisualStyles();
\r
665 else if ( o == _midpoint_root_item ) {
\r
666 if ( isSubtreeDisplayed() ) {
\r
671 else if ( o == _delete_selected_nodes_item ) {
\r
672 if ( isSubtreeDisplayed() ) {
\r
675 deleteSelectedNodes( true );
\r
677 else if ( o == _delete_not_selected_nodes_item ) {
\r
678 if ( isSubtreeDisplayed() ) {
\r
681 deleteSelectedNodes( false );
\r
683 else if ( o == _annotate_item ) {
\r
684 annotateSequences();
\r
686 else if ( o == _switch_colors_mi ) {
\r
689 else if ( o == _display_basic_information_item ) {
\r
690 if ( getCurrentTreePanel() != null ) {
\r
691 displayBasicInformation( getCurrentTreePanel().getTreeFile() );
\r
694 else if ( o == _view_as_NH_item ) {
\r
697 else if ( o == _view_as_XML_item ) {
\r
700 else if ( o == _view_as_nexus_item ) {
\r
703 else if ( o == _super_tiny_fonts_item ) {
\r
704 if ( getCurrentTreePanel() != null ) {
\r
705 getCurrentTreePanel().setSuperTinyFonts();
\r
706 getCurrentTreePanel().repaint();
\r
709 else if ( o == _tiny_fonts_item ) {
\r
710 if ( getCurrentTreePanel() != null ) {
\r
711 getCurrentTreePanel().setTinyFonts();
\r
712 getCurrentTreePanel().repaint();
\r
715 else if ( o == _small_fonts_item ) {
\r
716 if ( getCurrentTreePanel() != null ) {
\r
717 getCurrentTreePanel().setSmallFonts();
\r
718 getCurrentTreePanel().repaint();
\r
721 else if ( o == _medium_fonts_item ) {
\r
722 if ( getCurrentTreePanel() != null ) {
\r
723 getCurrentTreePanel().setMediumFonts();
\r
724 getCurrentTreePanel().repaint();
\r
727 else if ( o == _large_fonts_item ) {
\r
728 if ( getCurrentTreePanel() != null ) {
\r
729 getCurrentTreePanel().setLargeFonts();
\r
730 getCurrentTreePanel().repaint();
\r
733 else if ( o == _choose_font_mi ) {
\r
736 else if ( o == _choose_minimal_confidence_mi ) {
\r
737 chooseMinimalConfidence();
\r
739 else if ( o == _choose_node_size_mi ) {
\r
740 chooseNodeSize( getOptions(), this );
\r
742 else if ( o == _overview_placment_mi ) {
\r
743 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
\r
745 else if ( o == _cycle_node_fill_mi ) {
\r
746 MainFrame.cycleNodeFill( getOptions() );
\r
748 else if ( o == _cycle_node_shape_mi ) {
\r
749 MainFrame.cycleNodeShape( getOptions() );
\r
751 else if ( o == _cycle_data_return ) {
\r
752 MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );
\r
754 else if ( o == _screen_antialias_cbmi ) {
\r
755 updateOptions( getOptions() );
\r
756 updateScreenTextAntialias( getMainPanel().getTreePanels() );
\r
758 else if ( o == _background_gradient_cbmi ) {
\r
759 updateOptions( getOptions() );
\r
761 else if ( o == _show_domain_labels ) {
\r
762 updateOptions( getOptions() );
\r
764 else if ( o == _show_annotation_ref_source ) {
\r
765 updateOptions( getOptions() );
\r
767 else if ( o == _abbreviate_scientific_names ) {
\r
768 updateOptions( getOptions() );
\r
770 else if ( o == _color_labels_same_as_parent_branch ) {
\r
771 updateOptions( getOptions() );
\r
773 else if ( o == _show_default_node_shapes_internal_cbmi ) {
\r
774 updateOptions( getOptions() );
\r
776 else if ( o == _show_default_node_shapes_external_cbmi ) {
\r
777 updateOptions( getOptions() );
\r
779 else if ( o == _show_default_node_shapes_for_marked_cbmi ) {
\r
780 updateOptions( getOptions() );
\r
782 else if ( o == _non_lined_up_cladograms_rbmi ) {
\r
783 updateOptions( getOptions() );
\r
786 else if ( o == _uniform_cladograms_rbmi ) {
\r
787 updateOptions( getOptions() );
\r
790 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
\r
791 updateOptions( getOptions() );
\r
794 else if ( o == _search_case_senstive_cbmi ) {
\r
795 updateOptions( getOptions() );
\r
796 getMainPanel().getControlPanel().search0();
\r
797 getMainPanel().getControlPanel().search1();
\r
799 else if ( o == _search_whole_words_only_cbmi ) {
\r
800 if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
\r
801 _search_with_regex_cbmi.setSelected( false );
\r
803 updateOptions( getOptions() );
\r
804 getMainPanel().getControlPanel().search0();
\r
805 getMainPanel().getControlPanel().search1();
\r
807 else if ( o == _inverse_search_result_cbmi ) {
\r
808 updateOptions( getOptions() );
\r
809 getMainPanel().getControlPanel().search0();
\r
810 getMainPanel().getControlPanel().search1();
\r
812 else if ( o == _search_with_regex_cbmi ) {
\r
813 if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
\r
814 _search_whole_words_only_cbmi.setSelected( false );
\r
816 if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
\r
817 _search_case_senstive_cbmi.setSelected( true );
\r
819 updateOptions( getOptions() );
\r
820 getMainPanel().getControlPanel().search0();
\r
821 getMainPanel().getControlPanel().search1();
\r
823 else if ( o == _show_scale_cbmi ) {
\r
824 updateOptions( getOptions() );
\r
826 else if ( o == _color_by_taxonomic_group_cbmi ) {
\r
827 updateOptions( getOptions() );
\r
829 else if ( o == _show_confidence_stddev_cbmi ) {
\r
830 updateOptions( getOptions() );
\r
832 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
\r
833 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
834 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
\r
836 updateOptions( getOptions() );
\r
838 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
\r
839 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
840 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
\r
842 updateOptions( getOptions() );
\r
844 else if ( o == _label_direction_cbmi ) {
\r
845 updateOptions( getOptions() );
\r
847 else if ( o == _show_overview_cbmi ) {
\r
848 updateOptions( getOptions() );
\r
849 if ( getCurrentTreePanel() != null ) {
\r
850 getCurrentTreePanel().updateOvSizes();
\r
853 else if ( o == _line_up_renderable_data_cbmi ) {
\r
854 if ( !_line_up_renderable_data_cbmi.isSelected() ) {
\r
855 _right_line_up_domains_cbmi.setSelected( false );
\r
857 updateOptions( getOptions() );
\r
859 else if ( o == _right_line_up_domains_cbmi ) {
\r
860 if ( _right_line_up_domains_cbmi.isSelected() ) {
\r
861 _line_up_renderable_data_cbmi.setSelected( true );
\r
863 updateOptions( getOptions() );
\r
865 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
\r
866 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
\r
867 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
\r
870 else if ( o == _about_item ) {
\r
873 else if ( o == _help_item ) {
\r
875 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );
\r
877 catch ( final IOException e1 ) {
\r
878 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
881 else if ( o == _website_item ) {
\r
883 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
\r
885 catch ( final IOException e1 ) {
\r
886 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
889 else if ( o == _phyloxml_website_item ) {
\r
891 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
\r
893 catch ( final IOException e1 ) {
\r
894 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
897 else if ( o == _aptx_ref_item ) {
\r
899 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
\r
901 catch ( final IOException e1 ) {
\r
902 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
905 else if ( o == _phyloxml_ref_item ) {
\r
907 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
\r
909 catch ( final IOException e1 ) {
\r
910 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
913 else if ( o == _write_to_pdf_item ) {
\r
914 writeToPdf( _mainpanel.getCurrentPhylogeny() );
\r
916 else if ( o == _save_item ) {
\r
917 writeToFile( _mainpanel.getCurrentPhylogeny() );
\r
918 // If subtree currently displayed, save it, instead of complete
\r
921 else if ( o == _write_to_png_item ) {
\r
922 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
\r
924 else if ( o == _graphics_export_visible_only_cbmi ) {
\r
925 updateOptions( getOptions() );
\r
927 else if ( o == _antialias_print_cbmi ) {
\r
928 updateOptions( getOptions() );
\r
930 else if ( o == _print_black_and_white_cbmi ) {
\r
931 updateOptions( getOptions() );
\r
933 else if ( o == _print_using_actual_size_cbmi ) {
\r
934 updateOptions( getOptions() );
\r
936 else if ( o == _graphics_export_using_actual_size_cbmi ) {
\r
937 updateOptions( getOptions() );
\r
939 else if ( o == _print_size_mi ) {
\r
942 else if ( o == _choose_pdf_width_mi ) {
\r
946 if ( _load_phylogeny_from_webservice_menu_items != null ) {
\r
947 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
\r
948 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
\r
949 readPhylogeniesFromWebservice( i );
\r
954 _contentpane.repaint();
\r
957 void activateSaveAllIfNeeded() {
\r
958 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
\r
959 _save_all_item.setEnabled( true );
\r
962 _save_all_item.setEnabled( false );
\r
966 private void annotateSequences() {
\r
967 if ( getCurrentTreePanel() != null ) {
\r
968 List<PhylogenyNode> nodes = null;
\r
969 if ( ( getCurrentTreePanel().getFoundNodes0() != null )
\r
970 || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
971 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
973 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
975 .showMessageDialog( this,
\r
976 "Need to select nodes, either via direct selection or via the \"Search\" function",
\r
977 "No nodes selected for annotation",
\r
978 JOptionPane.ERROR_MESSAGE );
\r
981 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
982 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
983 final JTextField ref_field = new JTextField( 10 );
\r
984 final JTextField desc_filed = new JTextField( 20 );
\r
985 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
\r
986 : getPreviousNodeAnnotationReference() );
\r
987 final JPanel my_panel = new JPanel();
\r
988 my_panel.add( new JLabel( "Reference " ) );
\r
989 my_panel.add( ref_field );
\r
990 my_panel.add( Box.createHorizontalStrut( 15 ) );
\r
991 my_panel.add( new JLabel( "Description " ) );
\r
992 my_panel.add( desc_filed );
\r
993 final int result = JOptionPane.showConfirmDialog( null,
\r
995 "Enter the sequence annotation(s) for the "
\r
996 + nodes.size() + " selected nodes",
\r
997 JOptionPane.OK_CANCEL_OPTION );
\r
998 if ( result == JOptionPane.OK_OPTION ) {
\r
999 String ref = ref_field.getText();
\r
1000 String desc = desc_filed.getText();
\r
1001 if ( !ForesterUtil.isEmpty( ref ) ) {
\r
1003 ref = ref.replaceAll( "\\s+", " " );
\r
1004 if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )
\r
1005 || ( ref.length() < 3 ) ) {
\r
1006 JOptionPane.showMessageDialog( this,
\r
1007 "Reference needs to be in the form of \"GO:1234567\"",
\r
1008 "Illegal Format for Annotation Reference",
\r
1009 JOptionPane.ERROR_MESSAGE );
\r
1013 if ( ref != null ) {
\r
1014 setPreviousNodeAnnotationReference( ref );
\r
1016 if ( desc != null ) {
\r
1017 desc = desc.trim();
\r
1018 desc = desc.replaceAll( "\\s+", " " );
\r
1020 if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
\r
1021 for( final PhylogenyNode n : nodes ) {
\r
1022 ForesterUtil.ensurePresenceOfSequence( n );
\r
1023 final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
\r
1024 : new Annotation( ref );
\r
1025 if ( !ForesterUtil.isEmpty( desc ) ) {
\r
1026 ann.setDesc( desc );
\r
1028 n.getNodeData().getSequence().addAnnotation( ann );
\r
1031 getMainPanel().getControlPanel().showAnnotations();
\r
1037 // void buildFileMenu() {
\r
1038 // _file_jmenu = createMenu( "File", getConfiguration() );
\r
1039 // _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
\r
1040 // customizeJMenuItem( _exit_item );
\r
1041 // _jmenubar.add( _file_jmenu );
\r
1043 void buildFileMenu() {
\r
1044 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
\r
1045 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
\r
1046 // _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
\r
1047 // _save_all_item.setToolTipText( "Write all phylogenies to one file." );
\r
1048 // _save_all_item.setEnabled( false );
\r
1049 // _file_jmenu.addSeparator();
\r
1050 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
\r
1051 // if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
\r
1052 // _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
\r
1054 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
\r
1055 // _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
\r
1056 // if ( AptxUtil.canWriteFormat( "gif" ) ) {
\r
1057 // _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
\r
1059 // if ( AptxUtil.canWriteFormat( "bmp" ) ) {
\r
1060 // _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
\r
1062 // _file_jmenu.addSeparator();
\r
1063 // _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
\r
1064 _file_jmenu.addSeparator();
\r
1065 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
\r
1066 customizeJMenuItem( _save_item );
\r
1067 // customizeJMenuItem( _close_item );
\r
1068 //customizeJMenuItem( _save_all_item );
\r
1069 customizeJMenuItem( _write_to_pdf_item );
\r
1070 customizeJMenuItem( _write_to_png_item );
\r
1071 // customizeJMenuItem( _write_to_jpg_item );
\r
1072 // customizeJMenuItem( _write_to_gif_item );
\r
1073 // customizeJMenuItem( _write_to_tif_item );
\r
1074 // customizeJMenuItem( _write_to_bmp_item );
\r
1075 // customizeJMenuItem( _print_item );
\r
1076 customizeJMenuItem( _exit_item );
\r
1077 _jmenubar.add( _file_jmenu );
\r
1080 void buildFontSizeMenu() {
\r
1081 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
\r
1082 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
\r
1083 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
\r
1084 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
\r
1085 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
\r
1086 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
\r
1087 customizeJMenuItem( _super_tiny_fonts_item );
\r
1088 customizeJMenuItem( _tiny_fonts_item );
\r
1089 customizeJMenuItem( _small_fonts_item );
\r
1090 customizeJMenuItem( _medium_fonts_item );
\r
1091 customizeJMenuItem( _large_fonts_item );
\r
1092 _jmenubar.add( _font_size_menu );
\r
1095 void buildHelpMenu() {
\r
1096 _help_jmenu = createMenu( "Help", getConfiguration() );
\r
1097 _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
\r
1098 _help_jmenu.addSeparator();
\r
1099 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
\r
1100 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...
\r
1101 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
\r
1102 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
\r
1103 _help_jmenu.addSeparator();
\r
1104 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
\r
1105 customizeJMenuItem( _help_item );
\r
1106 customizeJMenuItem( _website_item );
\r
1107 customizeJMenuItem( _phyloxml_website_item );
\r
1108 customizeJMenuItem( _aptx_ref_item );
\r
1109 customizeJMenuItem( _phyloxml_ref_item );
\r
1110 customizeJMenuItem( _about_item );
\r
1111 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
\r
1112 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
\r
1113 _jmenubar.add( _help_jmenu );
\r
1116 void buildTypeMenu() {
\r
1117 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
\r
1118 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
\r
1119 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
\r
1120 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
\r
1121 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
\r
1122 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
\r
1123 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
\r
1124 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
\r
1125 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
\r
1126 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
\r
1127 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
\r
1128 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
\r
1129 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
\r
1130 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
\r
1131 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
\r
1132 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
\r
1133 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
\r
1134 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
1135 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
1136 initializeTypeMenu( getOptions() );
\r
1137 _jmenubar.add( _type_menu );
\r
1140 void buildViewMenu() {
\r
1141 _view_jmenu = createMenu( "View", getConfiguration() );
\r
1142 _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
\r
1143 _view_jmenu.addSeparator();
\r
1144 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
\r
1145 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
\r
1146 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
\r
1147 customizeJMenuItem( _display_basic_information_item );
\r
1148 customizeJMenuItem( _view_as_NH_item );
\r
1149 customizeJMenuItem( _view_as_XML_item );
\r
1150 customizeJMenuItem( _view_as_nexus_item );
\r
1151 _jmenubar.add( _view_jmenu );
\r
1154 void checkTextFrames() {
\r
1155 if ( _textframes.size() > 5 ) {
\r
1157 if ( _textframes.getFirst() != null ) {
\r
1158 _textframes.getFirst().removeMe();
\r
1161 _textframes.removeFirst();
\r
1164 catch ( final NoSuchElementException e ) {
\r
1170 private void chooseFont() {
\r
1171 final FontChooser fc = new FontChooser();
\r
1172 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
\r
1173 fc.showDialog( this, "Select the Base Font" );
\r
1174 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
\r
1177 private void chooseMinimalConfidence() {
\r
1178 final String s = ( String ) JOptionPane
\r
1179 .showInputDialog( this,
\r
1180 "Please enter the minimum for confidence values to be displayed.\n"
\r
1181 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
\r
1182 "Minimal Confidence Value",
\r
1183 JOptionPane.QUESTION_MESSAGE,
\r
1186 getOptions().getMinConfidenceValue() );
\r
1187 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1188 boolean success = true;
\r
1190 final String m_str = s.trim();
\r
1191 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1193 m = Double.parseDouble( m_str );
\r
1195 catch ( final Exception ex ) {
\r
1202 if ( success && ( m >= 0.0 ) ) {
\r
1203 getOptions().setMinConfidenceValue( m );
\r
1208 void choosePdfWidth() {
\r
1209 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
1210 "Please enter the default line width for PDF export.\n"
\r
1211 + "[current value: "
\r
1212 + getOptions().getPrintLineWidth() + "]\n",
\r
1213 "Line Width for PDF Export",
\r
1214 JOptionPane.QUESTION_MESSAGE,
\r
1217 getOptions().getPrintLineWidth() );
\r
1218 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1219 boolean success = true;
\r
1221 final String m_str = s.trim();
\r
1222 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1224 f = Float.parseFloat( m_str );
\r
1226 catch ( final Exception ex ) {
\r
1233 if ( success && ( f > 0.0 ) ) {
\r
1234 getOptions().setPrintLineWidth( f );
\r
1239 void choosePrintSize() {
\r
1240 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
1241 "Please enter values for width and height,\nseparated by a comma.\n"
\r
1242 + "[current values: "
\r
1243 + getOptions().getPrintSizeX() + ", "
\r
1244 + getOptions().getPrintSizeY() + "]\n"
\r
1245 + "[A4: " + Constants.A4_SIZE_X + ", "
\r
1246 + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
\r
1247 + Constants.US_LETTER_SIZE_X + ", "
\r
1248 + Constants.US_LETTER_SIZE_Y + "]",
\r
1249 "Default Size for Graphics Export",
\r
1250 JOptionPane.QUESTION_MESSAGE,
\r
1253 getOptions().getPrintSizeX() + ", "
\r
1254 + getOptions().getPrintSizeY() );
\r
1255 if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
\r
1256 boolean success = true;
\r
1259 final String[] str_ary = s.split( "," );
\r
1260 if ( str_ary.length == 2 ) {
\r
1261 final String x_str = str_ary[ 0 ].trim();
\r
1262 final String y_str = str_ary[ 1 ].trim();
\r
1263 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
\r
1265 x = Integer.parseInt( x_str );
\r
1266 y = Integer.parseInt( y_str );
\r
1268 catch ( final Exception ex ) {
\r
1279 if ( success && ( x > 1 ) && ( y > 1 ) ) {
\r
1280 getOptions().setPrintSizeX( x );
\r
1281 getOptions().setPrintSizeY( y );
\r
1287 removeAllTextFrames();
\r
1288 if ( _mainpanel != null ) {
\r
1289 _mainpanel.terminate();
\r
1291 if ( _contentpane != null ) {
\r
1292 _contentpane.removeAll();
\r
1294 setVisible( false );
\r
1298 void colorRank() {
\r
1299 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1300 final String[] ranks = AptxUtil.getAllPossibleRanks();
\r
1301 final String rank = ( String ) JOptionPane
\r
1302 .showInputDialog( this,
\r
1303 "What rank should the colorization be based on",
\r
1305 JOptionPane.QUESTION_MESSAGE,
\r
1309 if ( !ForesterUtil.isEmpty( rank ) ) {
\r
1310 _mainpanel.getCurrentTreePanel().colorRank( rank );
\r
1315 void confColor() {
\r
1316 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1317 _mainpanel.getCurrentTreePanel().confColor();
\r
1321 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
\r
1322 if ( item != null ) {
\r
1323 item.setFont( MainFrame.menu_font );
\r
1324 if ( !getConfiguration().isUseNativeUI() ) {
\r
1325 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
1326 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
1328 item.setSelected( is_selected );
\r
1329 item.addActionListener( this );
\r
1333 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
\r
1334 if ( jmi != null ) {
\r
1335 jmi.setFont( MainFrame.menu_font );
\r
1336 if ( !getConfiguration().isUseNativeUI() ) {
\r
1337 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
1338 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
1340 jmi.addActionListener( this );
\r
1345 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
\r
1346 if ( item != null ) {
\r
1347 item.setFont( MainFrame.menu_font );
\r
1348 if ( !getConfiguration().isUseNativeUI() ) {
\r
1349 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
1350 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
1352 item.setSelected( is_selected );
\r
1353 item.addActionListener( this );
\r
1357 private void deleteSelectedNodes( final boolean delete ) {
\r
1358 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
1359 if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {
\r
1362 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
1363 if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
1364 final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
1365 for( final PhylogenyNode n : all_selected_nodes ) {
\r
1366 if ( n.isExternal() ) {
\r
1371 String function = "Retain";
\r
1373 function = "Delete";
\r
1375 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
1377 .showMessageDialog( this,
\r
1378 "Need to select external nodes, either via direct selection or via the \"Search\" function",
\r
1379 "No external nodes selected to " + function.toLowerCase(),
\r
1380 JOptionPane.ERROR_MESSAGE );
\r
1383 final int todo = nodes.size();
\r
1384 final int ext = phy.getNumberOfExternalNodes();
\r
1390 JOptionPane.showMessageDialog( this,
\r
1391 "Cannot delete all nodes",
\r
1392 "Attempt to delete all nodes ",
\r
1393 JOptionPane.ERROR_MESSAGE );
\r
1396 final int result = JOptionPane.showConfirmDialog( null, function + " " + todo
\r
1397 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res
\r
1398 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );
\r
1399 if ( result == JOptionPane.OK_OPTION ) {
\r
1401 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
\r
1402 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
\r
1403 final PhylogenyNode n = it.next();
\r
1404 if ( !nodes.contains( n ) ) {
\r
1405 to_delete.add( n );
\r
1408 for( final PhylogenyNode n : to_delete ) {
\r
1409 phy.deleteSubtree( n, true );
\r
1413 for( final PhylogenyNode n : nodes ) {
\r
1414 phy.deleteSubtree( n, true );
\r
1418 getCurrentTreePanel().setNodeInPreorderToNull();
\r
1419 phy.externalNodesHaveChanged();
\r
1420 phy.clearHashIdToNodeMap();
\r
1421 phy.recalculateNumberOfExternalDescendants( true );
\r
1422 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
1423 getCurrentTreePanel().setEdited( true );
\r
1428 void displayBasicInformation( final File treefile ) {
\r
1429 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1430 String title = "Basic Information";
\r
1431 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1432 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
\r
1434 showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
\r
1438 private void doUpdateProcessMenu() {
\r
1439 if ( _process_pool.size() > 0 ) {
\r
1440 if ( _process_menu == null ) {
\r
1441 _process_menu = createMenu( "", getConfiguration() );
\r
1442 _process_menu.setForeground( Color.RED );
\r
1444 _process_menu.removeAll();
\r
1445 final String text = "processes running: " + _process_pool.size();
\r
1446 _process_menu.setText( text );
\r
1447 _jmenubar.add( _process_menu );
\r
1448 for( int i = 0; i < _process_pool.size(); ++i ) {
\r
1449 final ProcessRunning p = _process_pool.getProcessByIndex( i );
\r
1450 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
\r
1454 if ( _process_menu != null ) {
\r
1455 _process_menu.removeAll();
\r
1456 _jmenubar.remove( _process_menu );
\r
1459 _jmenubar.validate();
\r
1460 _jmenubar.repaint();
\r
1464 void exceptionOccuredDuringOpenFile( final Exception e ) {
\r
1466 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
1468 catch ( final Exception ex ) {
\r
1471 JOptionPane.showMessageDialog( this,
\r
1472 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
1473 "Error during File|Open",
\r
1474 JOptionPane.ERROR_MESSAGE );
\r
1477 void exceptionOccuredDuringSaveAs( final Exception e ) {
\r
1479 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
1481 catch ( final Exception ex ) {
\r
1484 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
\r
1487 void executeGSDI() {
\r
1488 if ( !isOKforSDI( false, true ) ) {
\r
1491 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
\r
1492 JOptionPane.showMessageDialog( this,
\r
1493 "Gene tree is not rooted.",
\r
1494 "Cannot execute GSDI",
\r
1495 JOptionPane.ERROR_MESSAGE );
\r
1498 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
1499 gene_tree.setAllNodesToNotCollapse();
\r
1500 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
1502 final Phylogeny species_tree = getSpeciesTree().copy();
\r
1504 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
\r
1506 catch ( final SDIException e ) {
\r
1507 JOptionPane.showMessageDialog( this,
\r
1508 e.getLocalizedMessage(),
\r
1509 "Error during GSDI",
\r
1510 JOptionPane.ERROR_MESSAGE );
\r
1513 catch ( final Exception e ) {
\r
1514 AptxUtil.unexpectedException( e );
\r
1517 gene_tree.setRerootable( false );
\r
1518 gene_tree.clearHashIdToNodeMap();
\r
1519 gene_tree.recalculateNumberOfExternalDescendants( true );
\r
1520 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
\r
1521 getMainPanel().getControlPanel().setShowEvents( true );
\r
1523 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
1524 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
1526 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
1528 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
1529 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
1530 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
1531 JOptionPane.showMessageDialog( this,
\r
1532 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
1533 + "Potential duplications: "
\r
1534 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
1535 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
1536 + "Stripped gene tree nodes: "
\r
1537 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1538 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
1539 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1540 "GSDI successfully completed",
\r
1541 JOptionPane.WARNING_MESSAGE );
\r
1544 JOptionPane.showMessageDialog( this,
\r
1545 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
1546 + "Potential duplications: "
\r
1547 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
1548 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
1549 + "Stripped gene tree nodes: "
\r
1550 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1551 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
1552 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1553 "GSDI successfully completed",
\r
1554 JOptionPane.INFORMATION_MESSAGE );
\r
1558 void executeGSDIR() {
\r
1559 if ( !isOKforSDI( false, false ) ) {
\r
1562 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
\r
1564 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
\r
1565 JOptionPane.showMessageDialog( this,
\r
1566 "Gene tree is not completely binary",
\r
1567 "Cannot execute GSDI",
\r
1568 JOptionPane.ERROR_MESSAGE );
\r
1571 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
1572 gene_tree.setAllNodesToNotCollapse();
\r
1573 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
1574 GSDIR gsdir = null;
\r
1575 final Phylogeny species_tree = getSpeciesTree().copy();
\r
1577 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
\r
1579 catch ( final SDIException e ) {
\r
1580 JOptionPane.showMessageDialog( this,
\r
1581 e.getLocalizedMessage(),
\r
1582 "Error during GSDIR",
\r
1583 JOptionPane.ERROR_MESSAGE );
\r
1586 catch ( final Exception e ) {
\r
1587 AptxUtil.unexpectedException( e );
\r
1590 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
\r
1591 result_gene_tree.setRerootable( false );
\r
1592 result_gene_tree.clearHashIdToNodeMap();
\r
1593 result_gene_tree.recalculateNumberOfExternalDescendants( true );
\r
1594 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
\r
1595 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
\r
1596 getMainPanel().getControlPanel().setShowEvents( true );
\r
1598 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
1599 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
1601 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
1603 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
1604 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
1605 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
1606 JOptionPane.showMessageDialog( this,
\r
1607 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1608 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1609 + "Stripped gene tree nodes: "
\r
1610 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1611 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1612 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1613 "GSDIR successfully completed",
\r
1614 JOptionPane.WARNING_MESSAGE );
\r
1617 JOptionPane.showMessageDialog( this,
\r
1618 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1619 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1620 + "Stripped gene tree nodes: "
\r
1621 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1622 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1623 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1624 "GSDIR successfully completed",
\r
1625 JOptionPane.INFORMATION_MESSAGE );
\r
1629 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
\r
1630 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
\r
1631 JOptionPane.showMessageDialog( this,
\r
1632 "Gene tree and species tree have no species in common.",
\r
1633 "Error during SDI",
\r
1634 JOptionPane.ERROR_MESSAGE );
\r
1637 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
\r
1638 JOptionPane.showMessageDialog( this,
\r
1639 "Gene tree and species tree have only one species in common.",
\r
1640 "Error during SDI",
\r
1641 JOptionPane.ERROR_MESSAGE );
\r
1649 public Configuration getConfiguration() {
\r
1650 return _configuration;
\r
1653 ControlPanel getControlPanel() {
\r
1654 return getMainPanel().getControlPanel();
\r
1657 File getCurrentDir() {
\r
1658 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
\r
1659 if ( ForesterUtil.isWindows() ) {
\r
1661 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
\r
1663 catch ( final Exception e ) {
\r
1664 _current_dir = null;
\r
1668 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
\r
1669 if ( System.getProperty( "user.home" ) != null ) {
\r
1670 _current_dir = new File( System.getProperty( "user.home" ) );
\r
1672 else if ( System.getProperty( "user.dir" ) != null ) {
\r
1673 _current_dir = new File( System.getProperty( "user.dir" ) );
\r
1676 return _current_dir;
\r
1680 * This method returns the current external node data which
\r
1681 * has been selected by the user by clicking the "Return ..."
\r
1682 * menu item. This method is expected to be called from Javascript or
\r
1683 * something like it.
\r
1685 * @return current external node data as String
\r
1687 public String getCurrentExternalNodesDataBuffer() {
\r
1688 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
\r
1691 public int getCurrentExternalNodesDataBufferChangeCounter() {
\r
1692 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
\r
1695 public int getCurrentExternalNodesDataBufferLength() {
\r
1696 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
\r
1699 TreePanel getCurrentTreePanel() {
\r
1700 return getMainPanel().getCurrentTreePanel();
\r
1703 JMenu getHelpMenu() {
\r
1704 return _help_jmenu;
\r
1707 public InferenceManager getInferenceManager() {
\r
1708 return _inference_manager;
\r
1711 JCheckBoxMenuItem getlabelDirectionCbmi() {
\r
1712 return _label_direction_cbmi;
\r
1715 public MainPanel getMainPanel() {
\r
1716 return _mainpanel;
\r
1719 JMenuBar getMenuBarOfMainFrame() {
\r
1723 public Options getOptions() {
\r
1727 private String getPreviousNodeAnnotationReference() {
\r
1728 return _previous_node_annotation_ref;
\r
1731 public ProcessPool getProcessPool() {
\r
1732 return _process_pool;
\r
1735 final Phylogeny getSpeciesTree() {
\r
1736 return _species_tree;
\r
1739 void initializeTypeMenu( final Options options ) {
\r
1740 setTypeMenuToAllUnselected();
\r
1741 switch ( options.getPhylogenyGraphicsType() ) {
\r
1743 _convex_type_cbmi.setSelected( true );
\r
1746 _curved_type_cbmi.setSelected( true );
\r
1749 _euro_type_cbmi.setSelected( true );
\r
1752 _rounded_type_cbmi.setSelected( true );
\r
1755 _triangular_type_cbmi.setSelected( true );
\r
1758 _unrooted_type_cbmi.setSelected( true );
\r
1761 _circular_type_cbmi.setSelected( true );
\r
1764 _rectangular_type_cbmi.setSelected( true );
\r
1769 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
\r
1770 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1773 else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
\r
1774 JOptionPane.showMessageDialog( this,
\r
1775 "No species tree loaded",
\r
1776 "Cannot execute GSDI",
\r
1777 JOptionPane.ERROR_MESSAGE );
\r
1780 else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
\r
1781 JOptionPane.showMessageDialog( this,
\r
1782 "Species tree is not completely binary",
\r
1783 "Cannot execute GSDI",
\r
1784 JOptionPane.ERROR_MESSAGE );
\r
1787 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
\r
1788 JOptionPane.showMessageDialog( this,
\r
1789 "Gene tree is not completely binary",
\r
1790 "Cannot execute GSDI",
\r
1791 JOptionPane.ERROR_MESSAGE );
\r
1799 boolean isSubtreeDisplayed() {
\r
1800 if ( getCurrentTreePanel() != null ) {
\r
1801 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
\r
1803 .showMessageDialog( this,
\r
1804 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
\r
1805 "Operation can not be exectuted on a sub-tree",
\r
1806 JOptionPane.WARNING_MESSAGE );
\r
1813 void midpointRoot() {
\r
1814 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1815 _mainpanel.getCurrentTreePanel().midpointRoot();
\r
1819 void printPhylogenyToPdf( final String file_name ) {
\r
1820 if ( !getOptions().isPrintUsingActualSize() ) {
\r
1821 getCurrentTreePanel()
\r
1822 .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() );
\r
1823 getCurrentTreePanel().resetPreferredSize();
\r
1824 getCurrentTreePanel().repaint();
\r
1826 String pdf_written_to = "";
\r
1827 boolean error = false;
\r
1829 if ( getOptions().isPrintUsingActualSize() ) {
\r
1830 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
\r
1831 getCurrentTreePanel(),
\r
1832 getCurrentTreePanel().getWidth(),
\r
1833 getCurrentTreePanel().getHeight() );
\r
1836 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
\r
1837 .getPrintSizeX(), getOptions().getPrintSizeY() );
\r
1840 catch ( final IOException e ) {
\r
1842 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
\r
1845 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
\r
1846 JOptionPane.showMessageDialog( this,
\r
1847 "Wrote PDF to: " + pdf_written_to,
\r
1849 JOptionPane.INFORMATION_MESSAGE );
\r
1852 JOptionPane.showMessageDialog( this,
\r
1853 "There was an unknown problem when attempting to write to PDF file: \""
\r
1854 + file_name + "\"",
\r
1856 JOptionPane.ERROR_MESSAGE );
\r
1859 if ( !getOptions().isPrintUsingActualSize() ) {
\r
1860 getControlPanel().showWhole();
\r
1864 void readPhylogeniesFromWebservice( final int i ) {
\r
1865 final UrlTreeReader reader = new UrlTreeReader( this, i );
\r
1866 new Thread( reader ).start();
\r
1869 void removeAllTextFrames() {
\r
1870 for( final TextFrame tf : _textframes ) {
\r
1871 if ( tf != null ) {
\r
1875 _textframes.clear();
\r
1878 private void removeBranchColors() {
\r
1879 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1880 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
\r
1884 private void removeVisualStyles() {
\r
1885 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1886 AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
\r
1890 void resetSearch() {
\r
1891 getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
\r
1892 getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
\r
1893 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );
\r
1894 getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );
\r
1895 getMainPanel().getControlPanel().getSearchTextField0().setText( "" );
\r
1896 getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );
\r
1897 getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );
\r
1898 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );
\r
1899 getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );
\r
1900 getMainPanel().getControlPanel().getSearchTextField1().setText( "" );
\r
1901 getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );
\r
1902 getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );
\r
1905 void setConfiguration( final Configuration configuration ) {
\r
1906 _configuration = configuration;
\r
1909 void setCurrentDir( final File current_dir ) {
\r
1910 _current_dir = current_dir;
\r
1913 void setInferenceManager( final InferenceManager i ) {
\r
1914 _inference_manager = i;
\r
1917 void setOptions( final Options options ) {
\r
1918 _options = options;
\r
1921 private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
\r
1922 _previous_node_annotation_ref = previous_node_annotation_ref;
\r
1925 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
\r
1926 setTypeMenuToAllUnselected();
\r
1929 _circular_type_cbmi.setSelected( true );
\r
1932 _convex_type_cbmi.setSelected( true );
\r
1935 _curved_type_cbmi.setSelected( true );
\r
1938 _euro_type_cbmi.setSelected( true );
\r
1941 _rounded_type_cbmi.setSelected( true );
\r
1944 _rectangular_type_cbmi.setSelected( true );
\r
1947 _triangular_type_cbmi.setSelected( true );
\r
1950 _unrooted_type_cbmi.setSelected( true );
\r
1953 throw new IllegalArgumentException( "unknown type: " + type );
\r
1957 final void setSpeciesTree( final Phylogeny species_tree ) {
\r
1958 _species_tree = species_tree;
\r
1961 void setTypeMenuToAllUnselected() {
\r
1962 _convex_type_cbmi.setSelected( false );
\r
1963 _curved_type_cbmi.setSelected( false );
\r
1964 _euro_type_cbmi.setSelected( false );
\r
1965 _rounded_type_cbmi.setSelected( false );
\r
1966 _triangular_type_cbmi.setSelected( false );
\r
1967 _rectangular_type_cbmi.setSelected( false );
\r
1968 _unrooted_type_cbmi.setSelected( false );
\r
1969 _circular_type_cbmi.setSelected( false );
\r
1972 public void showTextFrame( final String s, final String title ) {
\r
1973 checkTextFrames();
\r
1974 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
\r
1977 public void showWhole() {
\r
1978 _mainpanel.getControlPanel().showWhole();
\r
1981 void switchColors() {
\r
1982 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
\r
1983 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
\r
1984 csc.setVisible( true );
\r
1988 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1989 _mainpanel.getCurrentTreePanel().taxColor();
\r
1993 void typeChanged( final Object o ) {
\r
1994 updateTypeCheckboxes( getOptions(), o );
\r
1995 updateOptions( getOptions() );
\r
1996 if ( getCurrentTreePanel() != null ) {
\r
1997 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
\r
1998 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
\r
1999 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
2000 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
\r
2001 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
2002 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
\r
2003 getCurrentTreePanel().getControlPanel().showWhole();
\r
2005 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
\r
2006 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
\r
2009 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
\r
2011 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
\r
2012 updateScreenTextAntialias( getMainPanel().getTreePanels() );
\r
2013 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
\r
2014 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
\r
2015 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
\r
2018 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
\r
2024 void updateOptions( final Options options ) {
\r
2025 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
\r
2026 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
\r
2027 && _background_gradient_cbmi.isSelected() );
\r
2028 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
\r
2029 options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
\r
2030 && _show_annotation_ref_source.isSelected() );
\r
2031 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
\r
2032 && _abbreviate_scientific_names.isSelected() );
\r
2033 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
\r
2034 && _color_labels_same_as_parent_branch.isSelected() );
\r
2035 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
\r
2036 && _show_default_node_shapes_internal_cbmi.isSelected() );
\r
2037 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
\r
2038 && _show_default_node_shapes_external_cbmi.isSelected() );
\r
2039 options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
\r
2040 && _show_default_node_shapes_for_marked_cbmi.isSelected() );
\r
2041 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
\r
2042 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
\r
2044 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
\r
2045 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
\r
2047 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
\r
2048 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
\r
2050 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
\r
2051 && _search_case_senstive_cbmi.isSelected() );
\r
2052 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
\r
2053 options.setShowScale( _show_scale_cbmi.isSelected() );
\r
2055 if ( _label_direction_cbmi != null ) {
\r
2056 if ( _label_direction_cbmi.isSelected() ) {
\r
2057 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
\r
2060 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
\r
2063 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
\r
2064 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
\r
2065 && _show_confidence_stddev_cbmi.isSelected() );
\r
2066 if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
\r
2067 options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
\r
2069 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
\r
2070 && ( _print_using_actual_size_cbmi.isSelected() ) );
\r
2071 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
\r
2072 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
\r
2073 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
\r
2074 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
\r
2075 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
2076 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
\r
2078 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
\r
2079 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
2080 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
\r
2083 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
\r
2085 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
\r
2086 && _print_black_and_white_cbmi.isSelected() );
\r
2087 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
\r
2088 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
\r
2089 if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
\r
2090 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
\r
2092 else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
\r
2093 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
\r
2095 else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
\r
2096 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
2098 else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
\r
2099 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
\r
2101 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
\r
2102 && _replace_underscores_cbmi.isSelected() );
\r
2103 options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
\r
2104 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
\r
2105 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
\r
2106 && _search_whole_words_only_cbmi.isSelected() );
\r
2107 options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
\r
2108 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
\r
2109 && _inverse_search_result_cbmi.isSelected() );
\r
2110 if ( _graphics_export_visible_only_cbmi != null ) {
\r
2111 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
\r
2112 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
\r
2113 _graphics_export_using_actual_size_cbmi.setSelected( true );
\r
2114 _graphics_export_using_actual_size_cbmi.setEnabled( false );
\r
2117 _graphics_export_using_actual_size_cbmi.setEnabled( true );
\r
2120 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
\r
2121 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
2123 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
\r
2124 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
\r
2126 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
\r
2127 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
\r
2129 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
\r
2130 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
\r
2132 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
\r
2133 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
\r
2135 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
\r
2136 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
\r
2138 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
\r
2139 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
\r
2141 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
\r
2142 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
\r
2144 if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
\r
2145 options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
\r
2147 if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
\r
2148 options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
\r
2152 public void updateProcessMenu() {
\r
2153 // In general Swing is not thread safe.
\r
2154 // See "Swing's Threading Policy".
\r
2155 SwingUtilities.invokeLater( new Runnable() {
\r
2158 public void run() {
\r
2159 doUpdateProcessMenu();
\r
2164 void updateTypeCheckboxes( final Options options, final Object o ) {
\r
2165 setTypeMenuToAllUnselected();
\r
2166 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
\r
2169 void viewAsNexus() {
\r
2170 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
2171 String title = "Nexus";
\r
2172 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
2173 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
2175 showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
\r
2181 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
2182 String title = "New Hampshire";
\r
2183 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
2184 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
2186 showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
\r
2187 .getNhConversionSupportValueStyle() ),
\r
2192 void viewAsXML() {
\r
2193 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
2194 String title = "phyloXML";
\r
2195 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
2196 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
2198 showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
\r
2202 boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
\r
2204 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2205 writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );
\r
2207 catch ( final Exception e ) {
\r
2209 exceptionOccuredDuringSaveAs( e );
\r
2214 boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
\r
2216 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2217 writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
\r
2219 catch ( final Exception e ) {
\r
2221 exceptionOccuredDuringSaveAs( e );
\r
2226 boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
\r
2228 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2229 writer.toPhyloXML( file, t, 0 );
\r
2231 catch ( final Exception e ) {
\r
2233 exceptionOccuredDuringSaveAs( e );
\r
2238 void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
\r
2239 _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
\r
2240 _mainpanel.getCurrentTreePanel().getHeight() );
\r
2241 String file_written_to = "";
\r
2242 boolean error = false;
\r
2244 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
\r
2245 _mainpanel.getCurrentTreePanel().getWidth(),
\r
2246 _mainpanel.getCurrentTreePanel().getHeight(),
\r
2247 _mainpanel.getCurrentTreePanel(),
\r
2248 _mainpanel.getControlPanel(),
\r
2252 catch ( final IOException e ) {
\r
2254 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
\r
2257 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
\r
2258 JOptionPane.showMessageDialog( this,
\r
2259 "Wrote image to: " + file_written_to,
\r
2260 "Graphics Export",
\r
2261 JOptionPane.INFORMATION_MESSAGE );
\r
2264 JOptionPane.showMessageDialog( this,
\r
2265 "There was an unknown problem when attempting to write to an image file: \""
\r
2266 + file_name + "\"",
\r
2268 JOptionPane.ERROR_MESSAGE );
\r
2271 _contentpane.repaint();
\r
2274 void writeToFile( final Phylogeny t ) {
\r
2275 if ( t == null ) {
\r
2278 String initial_filename = null;
\r
2279 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
\r
2281 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
\r
2283 catch ( final IOException e ) {
\r
2284 initial_filename = null;
\r
2287 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
\r
2288 _save_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2291 _save_filechooser.setSelectedFile( new File( "" ) );
\r
2293 final File my_dir = getCurrentDir();
\r
2294 if ( my_dir != null ) {
\r
2295 _save_filechooser.setCurrentDirectory( my_dir );
\r
2297 final int result = _save_filechooser.showSaveDialog( _contentpane );
\r
2298 final File file = _save_filechooser.getSelectedFile();
\r
2299 setCurrentDir( _save_filechooser.getCurrentDirectory() );
\r
2300 boolean exception = false;
\r
2301 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2302 if ( file.exists() ) {
\r
2303 final int i = JOptionPane.showConfirmDialog( this,
\r
2304 file + " already exists.\nOverwrite?",
\r
2306 JOptionPane.OK_CANCEL_OPTION,
\r
2307 JOptionPane.QUESTION_MESSAGE );
\r
2308 if ( i != JOptionPane.OK_OPTION ) {
\r
2312 final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
\r
2314 ForesterUtil.copyFile( file, to );
\r
2316 catch ( final Exception e ) {
\r
2317 JOptionPane.showMessageDialog( this,
\r
2318 "Failed to create backup copy " + to,
\r
2319 "Failed to Create Backup Copy",
\r
2320 JOptionPane.WARNING_MESSAGE );
\r
2325 catch ( final Exception e ) {
\r
2326 JOptionPane.showMessageDialog( this,
\r
2327 "Failed to delete: " + file,
\r
2328 "Failed to Delete",
\r
2329 JOptionPane.WARNING_MESSAGE );
\r
2333 if ( _save_filechooser.getFileFilter() == MainFrame.nhfilter ) {
\r
2334 exception = writeAsNewHampshire( t, exception, file );
\r
2336 else if ( _save_filechooser.getFileFilter() == MainFrame.xmlfilter ) {
\r
2337 exception = writeAsPhyloXml( t, exception, file );
\r
2339 else if ( _save_filechooser.getFileFilter() == MainFrame.nexusfilter ) {
\r
2340 exception = writeAsNexus( t, exception, file );
\r
2344 final String file_name = file.getName().trim().toLowerCase();
\r
2345 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2346 || file_name.endsWith( ".tree" ) ) {
\r
2347 exception = writeAsNewHampshire( t, exception, file );
\r
2349 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
\r
2350 exception = writeAsNexus( t, exception, file );
\r
2352 // XML is default:
\r
2354 exception = writeAsPhyloXml( t, exception, file );
\r
2357 if ( !exception ) {
\r
2358 getMainPanel().setTitleOfSelectedTab( file.getName() );
\r
2359 getMainPanel().getCurrentTreePanel().setTreeFile( file );
\r
2360 getMainPanel().getCurrentTreePanel().setEdited( false );
\r
2365 void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
\r
2366 if ( ( t == null ) || t.isEmpty() ) {
\r
2369 String initial_filename = "";
\r
2370 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
\r
2371 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
\r
2373 if ( initial_filename.indexOf( '.' ) > 0 ) {
\r
2374 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
\r
2376 initial_filename = initial_filename + "." + type;
\r
2377 _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2378 final File my_dir = getCurrentDir();
\r
2379 if ( my_dir != null ) {
\r
2380 _writetographics_filechooser.setCurrentDirectory( my_dir );
\r
2382 final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
\r
2383 File file = _writetographics_filechooser.getSelectedFile();
\r
2384 setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
\r
2385 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2386 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
\r
2387 file = new File( file.toString() + "." + type );
\r
2389 if ( file.exists() ) {
\r
2390 final int i = JOptionPane.showConfirmDialog( this,
\r
2391 file + " already exists. Overwrite?",
\r
2393 JOptionPane.OK_CANCEL_OPTION,
\r
2394 JOptionPane.WARNING_MESSAGE );
\r
2395 if ( i != JOptionPane.OK_OPTION ) {
\r
2402 catch ( final Exception e ) {
\r
2403 JOptionPane.showMessageDialog( this,
\r
2404 "Failed to delete: " + file,
\r
2406 JOptionPane.WARNING_MESSAGE );
\r
2410 writePhylogenyToGraphicsFile( file.toString(), type );
\r
2414 void writeToPdf( final Phylogeny t ) {
\r
2415 if ( ( t == null ) || t.isEmpty() ) {
\r
2418 String initial_filename = "";
\r
2419 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
\r
2420 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
\r
2422 if ( initial_filename.indexOf( '.' ) > 0 ) {
\r
2423 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
\r
2425 initial_filename = initial_filename + ".pdf";
\r
2426 _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2427 final File my_dir = getCurrentDir();
\r
2428 if ( my_dir != null ) {
\r
2429 _writetopdf_filechooser.setCurrentDirectory( my_dir );
\r
2431 final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
\r
2432 File file = _writetopdf_filechooser.getSelectedFile();
\r
2433 setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
\r
2434 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2435 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
\r
2436 file = new File( file.toString() + ".pdf" );
\r
2438 if ( file.exists() ) {
\r
2439 final int i = JOptionPane.showConfirmDialog( this,
\r
2440 file + " already exists. Overwrite?",
\r
2442 JOptionPane.OK_CANCEL_OPTION,
\r
2443 JOptionPane.WARNING_MESSAGE );
\r
2444 if ( i != JOptionPane.OK_OPTION ) {
\r
2448 printPhylogenyToPdf( file.toString() );
\r
2453 class MsaFileFilter extends FileFilter {
\r
2456 public boolean accept( final File f ) {
\r
2457 final String file_name = f.getName().trim().toLowerCase();
\r
2458 return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
\r
2459 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
\r
2463 public String getDescription() {
\r
2464 return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
\r
2468 class NexusFilter extends FileFilter {
\r
2471 public boolean accept( final File f ) {
\r
2472 final String file_name = f.getName().trim().toLowerCase();
\r
2473 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
\r
2474 || file_name.endsWith( ".tre" ) || f.isDirectory();
\r
2478 public String getDescription() {
\r
2479 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
\r
2483 class NHFilter extends FileFilter {
\r
2486 public boolean accept( final File f ) {
\r
2487 final String file_name = f.getName().trim().toLowerCase();
\r
2488 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2489 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
\r
2490 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
\r
2491 || f.isDirectory();
\r
2495 public String getDescription() {
\r
2496 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
\r
2500 class NHXFilter extends FileFilter {
\r
2503 public boolean accept( final File f ) {
\r
2504 final String file_name = f.getName().trim().toLowerCase();
\r
2505 return file_name.endsWith( ".nhx" ) || f.isDirectory();
\r
2509 public String getDescription() {
\r
2510 return "NHX files (*.nhx) [deprecated]";
\r
2514 class PdfFilter extends FileFilter {
\r
2517 public boolean accept( final File f ) {
\r
2518 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
\r
2522 public String getDescription() {
\r
2523 return "PDF files (*.pdf)";
\r
2527 class SequencesFileFilter extends FileFilter {
\r
2530 public boolean accept( final File f ) {
\r
2531 final String file_name = f.getName().trim().toLowerCase();
\r
2532 return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
\r
2533 || file_name.endsWith( ".seqs" ) || f.isDirectory();
\r
2537 public String getDescription() {
\r
2538 return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
\r
2542 class TolFilter extends FileFilter {
\r
2545 public boolean accept( final File f ) {
\r
2546 final String file_name = f.getName().trim().toLowerCase();
\r
2547 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
\r
2548 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
\r
2552 public String getDescription() {
\r
2553 return "Tree of Life files (*.tol, *.tolxml)";
\r
2557 class XMLFilter extends FileFilter {
\r
2560 public boolean accept( final File f ) {
\r
2561 final String file_name = f.getName().trim().toLowerCase();
\r
2562 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
\r
2563 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
\r
2567 public String getDescription() {
\r
2568 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";
\r
git://source.jalview.org / jalview.git / blob