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.net.URL;
  37
  38 import javax.swing.ButtonGroup;
  39 import javax.swing.JApplet;
  40 import javax.swing.JCheckBoxMenuItem;
  41 import javax.swing.JMenuBar;
  42 import javax.swing.JMenuItem;
  43 import javax.swing.JOptionPane;
  44 import javax.swing.JRadioButtonMenuItem;
  45 import javax.swing.event.ChangeEvent;
  46 import javax.swing.event.ChangeListener;
  47
  48 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  49 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  50 import org.forester.phylogeny.Phylogeny;
  51 import org.forester.util.ForesterUtil;
  52
  53 public final class MainFrameApplet extends MainFrame {
  54
  55     private static final long    serialVersionUID = 1941019292746717053L;
  56     private final static int     FRAME_X_SIZE     = 640, FRAME_Y_SIZE = 580;
  57     private final ArchaeopteryxA _applet;
  58     private ButtonGroup          _radio_group_1;
  59
  60     MainFrameApplet( final ArchaeopteryxA parent_applet, final Configuration configuration ) {
  61         setTitle( ArchaeopteryxA.NAME );
  62         _applet = parent_applet;
  63         setConfiguration( configuration );
  64         setOptions( Options.createInstance( configuration ) );
  65         //_textframes = null; //~~~~
  66         URL url = null;
  67         Phylogeny[] phys = null;
  68         // Get URL to tree file
  69         if ( _applet.getUrlString() != null ) {
  70             try {
  71                 url = new URL( _applet.getUrlString() );
  72             }
  73             catch ( final Exception e ) {
  74                 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
  75                 e.printStackTrace();
  76                 JOptionPane.showMessageDialog( this,
  77                                                ArchaeopteryxA.NAME + ": Could not create URL from: \""
  78                                                        + _applet.getUrlString() + "\"\nError: " + e,
  79                                                "Failed to create URL",
  80                                                JOptionPane.ERROR_MESSAGE );
  81                 close();
  82             }
  83         }
  84         // Load the tree from URL
  85         if ( url != null ) {
  86             try {
  87                 phys = AptxUtil.readPhylogeniesFromUrl( url,
  88                                                         configuration.isValidatePhyloXmlAgainstSchema(),
  89                                                         configuration.isReplaceUnderscoresInNhParsing(),
  90                                                         configuration.isInternalNumberAreConfidenceForNhParsing(),
  91                                                         configuration.getTaxonomyExtraction() );
  92             }
  93             catch ( final Exception e ) {
  94                 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
  95                 e.printStackTrace();
  96                 JOptionPane.showMessageDialog( this, ArchaeopteryxA.NAME + ": Failed to read phylogenies: "
  97                         + "\nError: " + e, "Failed to read phylogenies", JOptionPane.ERROR_MESSAGE );
  98                 close();
  99             }
 100         }
 101         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 102             ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "phylogenies from [" + url + "] are null or empty" );
 103             JOptionPane.showMessageDialog( this, ArchaeopteryxA.NAME + ": phylogenies from [" + url
 104                     + "] are null or empty", "Failed to read phylogenies", JOptionPane.ERROR_MESSAGE );
 105         }
 106         else {
 107             AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "loaded " + phys.length + " phylogenies from: " + url );
 108         }
 109         _mainpanel = new MainPanelApplets( _configuration, this );
 110         // build the menu bar
 111         _jmenubar = new JMenuBar();
 112         if ( !_configuration.isUseNativeUI() ) {
 113             _jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() );
 114         }
 115         buildToolsMenu();
 116         buildViewMenu();
 117         buildFontSizeMenu();
 118         buildOptionsMenu();
 119         buildTypeMenu();
 120         buildHelpMenu();
 121         setJMenuBar( _jmenubar );
 122         _contentpane = getContentPane();
 123         _contentpane.setLayout( new BorderLayout() );
 124         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 125         setSize( FRAME_X_SIZE, FRAME_Y_SIZE );
 126         addWindowListener( new WindowAdapter() {
 127
 128             @Override
 129             public void windowClosing( final WindowEvent e ) {
 130                 close();
 131             }
 132         } );
 133         addComponentListener( new ComponentAdapter() {
 134
 135             @Override
 136             public void componentResized( final ComponentEvent e ) {
 137                 if ( _mainpanel.getCurrentTreePanel() != null ) {
 138                     _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel()
 139                                                                                        .getWidth(),
 140                                                                                _mainpanel.getCurrentTreePanel()
 141                                                                                        .getHeight(),
 142                                                                                false );
 143                 }
 144             }
 145         } );
 146         setFocusable( true );
 147         requestFocus();
 148         requestFocusInWindow();
 149         setVisible( true );
 150         System.gc();
 151     }
 152
 153     void buildOptionsMenu() {
 154         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 155         _options_jmenu.addChangeListener( new ChangeListener() {
 156
 157             @Override
 158             public void stateChanged( final ChangeEvent e ) {
 159                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 160                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 161                 MainFrame
 162                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 163                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel()
 164                         .getTreeFontSet() ) );
 165                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 166                                                                      _show_scale_cbmi,
 167                                                                      _show_branch_length_values_cbmi,
 168                                                                      _non_lined_up_cladograms_rbmi,
 169                                                                      _uniform_cladograms_rbmi,
 170                                                                      _ext_node_dependent_cladogram_rbmi,
 171                                                                      _label_direction_cbmi );
 172                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 173                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 174                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 175             }
 176         } );
 177         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 178                                                                 getConfiguration() ) );
 179         _options_jmenu
 180                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 181         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 182         _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
 183         _radio_group_1 = new ButtonGroup();
 184         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 185         _radio_group_1.add( _uniform_cladograms_rbmi );
 186         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 187         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 188         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 189         _options_jmenu
 190                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 191         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
 192         _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
 193         _options_jmenu
 194                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 195         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 196         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 197         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 198         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
 199         _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
 200         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
 201         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 202         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 203         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 204         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 205         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 206             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
 207         }
 208         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 209         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 210         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 211         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 212         _options_jmenu.addSeparator();
 213         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 214                                                                 getConfiguration() ) );
 215         _options_jmenu
 216                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 217         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 218         _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
 219         customizeJMenuItem( _choose_font_mi );
 220         customizeJMenuItem( _switch_colors_mi );
 221         customizeJMenuItem( _choose_minimal_confidence_mi );
 222         customizeJMenuItem( _overview_placment_mi );
 223         customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
 224         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 225         customizeJMenuItem( _cycle_node_shape_mi );
 226         customizeJMenuItem( _cycle_node_fill_mi );
 227         customizeJMenuItem( _choose_node_size_mi );
 228         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 229         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 230         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 231         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 232         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 233         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 234         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 235         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 236                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 237         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 238                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 239         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 240                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 241         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 242         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 243         customizeCheckBoxMenuItem( _label_direction_cbmi,
 244                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 245         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 246         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 247         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 248         _jmenubar.add( _options_jmenu );
 249     }
 250
 251     void buildToolsMenu() {
 252         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 253         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 254         customizeJMenuItem( _confcolor_item );
 255         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 256         customizeJMenuItem( _taxcolor_item );
 257         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 258         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 259         customizeJMenuItem( _remove_branch_color_item );
 260         _tools_menu.addSeparator();
 261         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 262         customizeJMenuItem( _midpoint_root_item );
 263         _tools_menu.addSeparator();
 264         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 265         customizeJMenuItem( _collapse_species_specific_subtrees );
 266         _jmenubar.add( _tools_menu );
 267     }
 268
 269     JApplet getApplet() {
 270         return _applet;
 271     }
 272
 273     @Override
 274     public MainPanel getMainPanel() {
 275         return _mainpanel;
 276     }
 277
 278     @Override
 279     void readPhylogeniesFromURL() {
 280         throw new NoSuchMethodError( "not implemented" );
 281     }
 282 }