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: www.phylosoft.org/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         _textframe = 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
  77                         .showMessageDialog( this,
  78                                             ArchaeopteryxA.NAME + ": Could not create URL from: \""
  79                                                     + _applet.getUrlString() + "\"\nError: " + e,
  80                                             "Failed to create URL",
  81                                             JOptionPane.ERROR_MESSAGE );
  82                 close();
  83             }
  84         }
  85         // Load the tree from URL
  86         if ( url != null ) {
  87             try {
  88                 phys = Util.readPhylogeniesFromUrl( url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
  89             }
  90             catch ( final Exception e ) {
  91                 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
  92                 e.printStackTrace();
  93                 JOptionPane.showMessageDialog( this, ArchaeopteryxA.NAME + ": Failed to read phylogenies: "
  94                         + "\nError: " + e, "Failed to read phylogenies", JOptionPane.ERROR_MESSAGE );
  95                 close();
  96             }
  97         }
  98         if ( ( phys == null ) || ( phys.length < 1 ) ) {
  99             ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "phylogenies from [" + url + "] are null or empty" );
 100             JOptionPane.showMessageDialog( this, ArchaeopteryxA.NAME + ": phylogenies from [" + url
 101                     + "] are null or empty", "Failed to read phylogenies", JOptionPane.ERROR_MESSAGE );
 102         }
 103         else {
 104             Util.printAppletMessage( ArchaeopteryxA.NAME, "loaded " + phys.length + " phylogenies from: " + url );
 105         }
 106         _mainpanel = new MainPanelApplets( _configuration, this );
 107         // build the menu bar
 108         _jmenubar = new JMenuBar();
 109         if ( !_configuration.isUseNativeUI() ) {
 110             _jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() );
 111         }
 112         buildToolsMenu();
 113         buildViewMenu();
 114         buildFontSizeMenu();
 115         buildOptionsMenu();
 116         buildTypeMenu();
 117         buildHelpMenu();
 118         setJMenuBar( _jmenubar );
 119         _contentpane = getContentPane();
 120         _contentpane.setLayout( new BorderLayout() );
 121         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 122         setSize( FRAME_X_SIZE, FRAME_Y_SIZE );
 123         addWindowListener( new WindowAdapter() {
 124
 125             @Override
 126             public void windowClosing( final WindowEvent e ) {
 127                 close();
 128             }
 129         } );
 130         addComponentListener( new ComponentAdapter() {
 131
 132             @Override
 133             public void componentResized( final ComponentEvent e ) {
 134                 if ( _mainpanel.getCurrentTreePanel() != null ) {
 135                     _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel()
 136                                                                                        .getWidth(),
 137                                                                                _mainpanel.getCurrentTreePanel()
 138                                                                                        .getHeight(),
 139                                                                                false );
 140                 }
 141             }
 142         } );
 143         setFocusable( true );
 144         requestFocus();
 145         requestFocusInWindow();
 146         // All done: hello, world!
 147         setVisible( true );
 148         System.gc();
 149     }
 150
 151     void buildOptionsMenu() {
 152         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 153         _options_jmenu.addChangeListener( new ChangeListener() {
 154
 155             @Override
 156             public void stateChanged( final ChangeEvent e ) {
 157                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getCurrentTreePanel() );
 158                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 159                 MainFrame
 160                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 161                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel()
 162                         .getTreeFontSet() ) );
 163                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 164                                                                      _show_scale_cbmi,
 165                                                                      _show_branch_length_values_cbmi,
 166                                                                      _non_lined_up_cladograms_rbmi,
 167                                                                      _uniform_cladograms_rbmi,
 168                                                                      _ext_node_dependent_cladogram_rbmi,
 169                                                                      _label_direction_cbmi );
 170             }
 171         } );
 172         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 173                                                                 getConfiguration() ) );
 174         _options_jmenu
 175                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 176         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 177         _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
 178         _radio_group_1 = new ButtonGroup();
 179         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 180         _radio_group_1.add( _uniform_cladograms_rbmi );
 181         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 182         _options_jmenu.add( _show_node_boxes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
 183         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 184         _options_jmenu
 185                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 186         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 187         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
 188         _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
 189         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
 190         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 191         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 192         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 193         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 194         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 195             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
 196         }
 197         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 198         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 199         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 200         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 201         _options_jmenu.addSeparator();
 202         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 203                                                                 getConfiguration() ) );
 204         _options_jmenu
 205                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 206         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 207         _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
 208         customizeJMenuItem( _choose_font_mi );
 209         customizeJMenuItem( _switch_colors_mi );
 210         customizeJMenuItem( _choose_minimal_confidence_mi );
 211         customizeJMenuItem( _overview_placment_mi );
 212         customizeCheckBoxMenuItem( _show_node_boxes_cbmi, getOptions().isShowNodeBoxes() );
 213         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 214         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 215         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 216         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 217         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 218         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 219         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 220         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 221                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 222         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 223                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 224         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 225                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 226         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 227         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 228         customizeCheckBoxMenuItem( _label_direction_cbmi,
 229                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 230         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 231         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 232         _jmenubar.add( _options_jmenu );
 233     }
 234
 235     void buildToolsMenu() {
 236         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 237         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 238         customizeJMenuItem( _confcolor_item );
 239         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 240         customizeJMenuItem( _taxcolor_item );
 241         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 242         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 243         customizeJMenuItem( _remove_branch_color_item );
 244         _tools_menu.addSeparator();
 245         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 246         customizeJMenuItem( _midpoint_root_item );
 247         _tools_menu.addSeparator();
 248         _tools_menu
 249                 .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
 250         customizeJMenuItem( _infer_common_sn_names_item );
 251         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 252         customizeJMenuItem( _collapse_species_specific_subtrees );
 253         _jmenubar.add( _tools_menu );
 254     }
 255
 256     JApplet getApplet() {
 257         return _applet;
 258     }
 259
 260     @Override
 261     MainPanel getMainPanel() {
 262         return _mainpanel;
 263     }
 264
 265     @Override
 266     void readPhylogeniesFromURL() {
 267         throw new NoSuchMethodError( "not implemented" );
 268     }
 269 }