forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // Copyright (C) 2000-2001 Washington University School of Medicine
   8 // and Howard Hughes Medical Institute
   9 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
  10 // All rights reserved
  11 //
  12 // This library is free software; you can redistribute it and/or
  13 // modify it under the terms of the GNU Lesser General Public
  14 // License as published by the Free Software Foundation; either
  15 // version 2.1 of the License, or (at your option) any later version.
  16 //
  17 // This library is distributed in the hope that it will be useful,
  18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  20 // Lesser General Public License for more details.
  21 //
  22 // You should have received a copy of the GNU Lesser General Public
  23 // License along with this library; if not, write to the Free Software
  24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  25 //
  26 // Contact: phylosoft @ gmail . com
  27 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  28
  29 package org.forester.archaeopteryx;
  30
  31 import java.awt.BorderLayout;
  32 import java.awt.event.ComponentAdapter;
  33 import java.awt.event.ComponentEvent;
  34 import java.awt.event.WindowAdapter;
  35 import java.awt.event.WindowEvent;
  36 import java.io.FileNotFoundException;
  37 import java.io.IOException;
  38 import java.net.MalformedURLException;
  39 import java.net.URL;
  40
  41 import javax.swing.ButtonGroup;
  42 import javax.swing.JApplet;
  43 import javax.swing.JCheckBoxMenuItem;
  44 import javax.swing.JMenuBar;
  45 import javax.swing.JMenuItem;
  46 import javax.swing.JRadioButtonMenuItem;
  47 import javax.swing.event.ChangeEvent;
  48 import javax.swing.event.ChangeListener;
  49
  50 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  51 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  52 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  53 import org.forester.phylogeny.Phylogeny;
  54 import org.forester.util.ForesterUtil;
  55
  56 public final class MainFrameApplet extends MainFrame {
  57
  58     private static final long    serialVersionUID     = 1941019292746717053L;
  59     private final static int     DEFAULT_FRAME_X_SIZE = 640;
  60     private final static int     DEFAULT_FRAME_Y_SIZE = 580;
  61     private final ArchaeopteryxA _applet;
  62     private ButtonGroup          _radio_group_1;
  63
  64     MainFrameApplet( final ArchaeopteryxA parent_applet,
  65                      final Configuration configuration,
  66                      final String species_tree_url_str ) {
  67         setTitle( ArchaeopteryxA.NAME );
  68         _applet = parent_applet;
  69         setConfiguration( configuration );
  70         setOptions( Options.createInstance( configuration ) );
  71         _mainpanel = new MainPanelApplets( _configuration, this );
  72         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
  73             try {
  74                 readSpeciesTree( configuration, species_tree_url_str );
  75             }
  76             catch ( final Exception e ) {
  77                 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from "
  78                         + species_tree_url_str );
  79                 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
  80             }
  81         }
  82         // build the menu bar
  83         _jmenubar = new JMenuBar();
  84         if ( !_configuration.isUseNativeUI() ) {
  85             _jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() );
  86         }
  87         if ( getSpeciesTree() != null ) {
  88             buildAnalysisMenu();
  89         }
  90         buildToolsMenu();
  91         buildViewMenu();
  92         buildFontSizeMenu();
  93         buildOptionsMenu();
  94         buildTypeMenu();
  95         buildHelpMenu();
  96         setJMenuBar( _jmenubar );
  97         _contentpane = getContentPane();
  98         _contentpane.setLayout( new BorderLayout() );
  99         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 100         setSize( getConfiguration().getFrameXSize() > 40 ? getConfiguration().getFrameXSize() : DEFAULT_FRAME_X_SIZE,
 101                  getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE );
 102         addWindowListener( new WindowAdapter() {
 103
 104             @Override
 105             public void windowClosing( final WindowEvent e ) {
 106                 close();
 107             }
 108         } );
 109         addComponentListener( new ComponentAdapter() {
 110
 111             @Override
 112             public void componentResized( final ComponentEvent e ) {
 113                 if ( _mainpanel.getCurrentTreePanel() != null ) {
 114                     _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
 115                                                                                         .getWidth(),
 116                                                                                 _mainpanel.getCurrentTreePanel()
 117                                                                                         .getHeight(),
 118                                                                                 getOptions().isAllowFontSizeChange() );
 119                 }
 120             }
 121         } );
 122         setFocusable( true );
 123         requestFocus();
 124         requestFocusInWindow();
 125         setVisible( true );
 126         System.gc();
 127     }
 128
 129     private void readSpeciesTree( final Configuration configuration, final String species_tree_url_str )
 130             throws MalformedURLException, FileNotFoundException, IOException {
 131         final URL species_tree_url = new URL( species_tree_url_str );
 132         final Phylogeny[] species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 133                                                                            configuration
 134                                                                                    .isValidatePhyloXmlAgainstSchema(),
 135                                                                            configuration
 136                                                                                    .isReplaceUnderscoresInNhParsing(),
 137                                                                            false,
 138                                                                            TAXONOMY_EXTRACTION.NO,
 139                                                                            false );
 140         if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 141             AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "successfully read species tree" );
 142             if ( species_trees[ 0 ].isEmpty() ) {
 143                 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is empty" );
 144             }
 145             else if ( !species_trees[ 0 ].isRooted() ) {
 146                 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is not rooted" );
 147             }
 148             else {
 149                 setSpeciesTree( species_trees[ 0 ] );
 150                 AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "species tree OK" );
 151             }
 152         }
 153         else {
 154             ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from "
 155                     + species_tree_url_str );
 156         }
 157     }
 158
 159     @Override
 160     public MainPanel getMainPanel() {
 161         return _mainpanel;
 162     }
 163
 164     void buildAnalysisMenu() {
 165         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 166         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 167         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 168         customizeJMenuItem( _gsdi_item );
 169         customizeJMenuItem( _gsdir_item );
 170         //  _analysis_menu.addSeparator();
 171         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 172         //  customizeJMenuItem( _lineage_inference );
 173         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 174         _jmenubar.add( _analysis_menu );
 175     }
 176
 177     void buildOptionsMenu() {
 178         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 179         _options_jmenu.addChangeListener( new ChangeListener() {
 180
 181             @Override
 182             public void stateChanged( final ChangeEvent e ) {
 183                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 184                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 185                 MainFrame
 186                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 187                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel()
 188                         .getTreeFontSet() ) );
 189                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 190                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 191                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 192                 try {
 193                     getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
 194                     getMainPanel().getControlPanel().setVisibilityOfX();
 195                 }
 196                 catch ( final Exception ignore ) {
 197                     // do nothing, not important.
 198                 }
 199             }
 200         } );
 201         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 202                                                                 getConfiguration() ) );
 203         _options_jmenu
 204                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 205         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 206         _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
 207         _radio_group_1 = new ButtonGroup();
 208         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 209         _radio_group_1.add( _uniform_cladograms_rbmi );
 210         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 211         ////////////
 212         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 213         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 214         _options_jmenu
 215                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 216         _options_jmenu
 217                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 218         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 219             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 220             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
 221         }
 222         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
 223         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
 224         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 225         _options_jmenu
 226                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
 227         _options_jmenu
 228                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 229         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 230         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 231         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 232         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 233         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 234         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 235         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 236         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 237         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 238         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 239         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 240         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 241         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 242         //////
 243         _options_jmenu.addSeparator();
 244         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 245                                                                 getConfiguration() ) );
 246         _options_jmenu
 247                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 248         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 249         _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
 250         customizeJMenuItem( _choose_font_mi );
 251         customizeJMenuItem( _switch_colors_mi );
 252         customizeJMenuItem( _choose_minimal_confidence_mi );
 253         customizeJMenuItem( _overview_placment_mi );
 254         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 255                 .isShowDefaultNodeShapesInternal() );
 256         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 257                 .isShowDefaultNodeShapesExternal() );
 258         customizeJMenuItem( _cycle_node_shape_mi );
 259         customizeJMenuItem( _cycle_node_fill_mi );
 260         customizeJMenuItem( _choose_node_size_mi );
 261         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
 262         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 263         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 264         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 265         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 266         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
 267         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 268         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 269         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 270         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 271                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 272         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 273                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 274         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 275                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 276         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 277         customizeCheckBoxMenuItem( _label_direction_cbmi,
 278                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 279         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 280         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 281         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 282         customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
 283         customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
 284         _jmenubar.add( _options_jmenu );
 285     }
 286
 287     void buildToolsMenu() {
 288         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 289         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 290         customizeJMenuItem( _confcolor_item );
 291         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 292         customizeJMenuItem( _taxcolor_item );
 293         _tools_menu.addSeparator();
 294         _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
 295         _remove_visual_styles_item
 296                 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
 297         customizeJMenuItem( _remove_visual_styles_item );
 298         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
 299         _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
 300         customizeJMenuItem( _remove_branch_color_item );
 301         _tools_menu.addSeparator();
 302         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 303         customizeJMenuItem( _midpoint_root_item );
 304         _tools_menu.addSeparator();
 305         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 306         customizeJMenuItem( _collapse_species_specific_subtrees );
 307         _jmenubar.add( _tools_menu );
 308     }
 309
 310     JApplet getApplet() {
 311         return _applet;
 312     }
 313 }