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     DEFAULT_FRAME_X_SIZE = 640;
  57     private final static int     DEFAULT_FRAME_Y_SIZE = 580;
  58     private final ArchaeopteryxA _applet;
  59     private ButtonGroup          _radio_group_1;
  60
  61     MainFrameApplet( final ArchaeopteryxA parent_applet, final Configuration configuration ) {
  62         setTitle( ArchaeopteryxA.NAME );
  63         _applet = parent_applet;
  64         setConfiguration( configuration );
  65         setOptions( Options.createInstance( configuration ) );
  66         //_textframes = null; //~~~~
  67         URL url = null;
  68         Phylogeny[] phys = null;
  69         // Get URL to tree file
  70         if ( _applet.getTreeUrlStr() != null ) {
  71             try {
  72                 url = new URL( _applet.getTreeUrlStr() );
  73             }
  74             catch ( final Exception e ) {
  75                 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
  76                 e.printStackTrace();
  77                 JOptionPane.showMessageDialog( this,
  78                                                ArchaeopteryxA.NAME + ": Could not create URL from: \""
  79                                                        + _applet.getTreeUrlStr() + "\"\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 = AptxUtil.readPhylogeniesFromUrl( url,
  89                                                         configuration.isValidatePhyloXmlAgainstSchema(),
  90                                                         configuration.isReplaceUnderscoresInNhParsing(),
  91                                                         configuration.isInternalNumberAreConfidenceForNhParsing(),
  92                                                         configuration.getTaxonomyExtraction() );
  93             }
  94             catch ( final Exception e ) {
  95                 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
  96                 e.printStackTrace();
  97                 JOptionPane.showMessageDialog( this, ArchaeopteryxA.NAME + ": Failed to read phylogenies: "
  98                         + "\nError: " + e, "Failed to read phylogenies", JOptionPane.ERROR_MESSAGE );
  99                 close();
 100             }
 101         }
 102         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 103             ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "phylogenies from [" + url + "] are null or empty" );
 104             JOptionPane.showMessageDialog( this, ArchaeopteryxA.NAME + ": phylogenies from [" + url
 105                     + "] are null or empty", "Failed to read phylogenies", JOptionPane.ERROR_MESSAGE );
 106         }
 107         else {
 108             AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "loaded " + phys.length + " phylogenies from: " + url );
 109         }
 110         _mainpanel = new MainPanelApplets( _configuration, this );
 111         // build the menu bar
 112         _jmenubar = new JMenuBar();
 113         if ( !_configuration.isUseNativeUI() ) {
 114             _jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() );
 115         }
 116         if ( _species_tree != null ) {
 117             buildAnalysisMenu();
 118         }
 119         buildToolsMenu();
 120         buildViewMenu();
 121         buildFontSizeMenu();
 122         buildOptionsMenu();
 123         buildTypeMenu();
 124         buildHelpMenu();
 125         setJMenuBar( _jmenubar );
 126         _contentpane = getContentPane();
 127         _contentpane.setLayout( new BorderLayout() );
 128         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 129         setSize( getConfiguration().getFrameXSize() > 40 ? getConfiguration().getFrameXSize() : DEFAULT_FRAME_X_SIZE,
 130                  getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE );
 131         addWindowListener( new WindowAdapter() {
 132
 133             @Override
 134             public void windowClosing( final WindowEvent e ) {
 135                 close();
 136             }
 137         } );
 138         addComponentListener( new ComponentAdapter() {
 139
 140             @Override
 141             public void componentResized( final ComponentEvent e ) {
 142                 if ( _mainpanel.getCurrentTreePanel() != null ) {
 143                     _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
 144                                                                                         .getWidth(),
 145                                                                                 _mainpanel.getCurrentTreePanel()
 146                                                                                         .getHeight(),
 147                                                                                 getOptions().isAllowFontSizeChange() );
 148                 }
 149             }
 150         } );
 151         setFocusable( true );
 152         requestFocus();
 153         requestFocusInWindow();
 154         setVisible( true );
 155         System.gc();
 156     }
 157
 158     @Override
 159     public MainPanel getMainPanel() {
 160         return _mainpanel;
 161     }
 162
 163     void buildAnalysisMenu() {
 164         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 165         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 166         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 167         customizeJMenuItem( _gsdi_item );
 168         customizeJMenuItem( _gsdir_item );
 169         //  _analysis_menu.addSeparator();
 170         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 171         //  customizeJMenuItem( _lineage_inference );
 172         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 173         _jmenubar.add( _analysis_menu );
 174     }
 175
 176     void buildOptionsMenu() {
 177         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 178         _options_jmenu.addChangeListener( new ChangeListener() {
 179
 180             @Override
 181             public void stateChanged( final ChangeEvent e ) {
 182                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 183                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 184                 MainFrame
 185                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 186                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel()
 187                         .getTreeFontSet() ) );
 188                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 189                                                                      _show_scale_cbmi,
 190                                                                      _show_branch_length_values_cbmi,
 191                                                                      _non_lined_up_cladograms_rbmi,
 192                                                                      _uniform_cladograms_rbmi,
 193                                                                      _ext_node_dependent_cladogram_rbmi,
 194                                                                      _label_direction_cbmi );
 195                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 196                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 197                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 198             }
 199         } );
 200         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 201                                                                 getConfiguration() ) );
 202         _options_jmenu
 203                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 204         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 205         _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
 206         _radio_group_1 = new ButtonGroup();
 207         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 208         _radio_group_1.add( _uniform_cladograms_rbmi );
 209         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 210         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 211         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 212         _options_jmenu
 213                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 214         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
 215         _options_jmenu
 216                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
 217         _options_jmenu
 218                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
 219         _options_jmenu
 220                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 221         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 222         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 223         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 224         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
 225         _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
 226         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
 227         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 228         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 229         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 230         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 231         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 232             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
 233         }
 234         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 235         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 236         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 237         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 238         _options_jmenu.addSeparator();
 239         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 240                                                                 getConfiguration() ) );
 241         _options_jmenu
 242                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 243         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 244         _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
 245         customizeJMenuItem( _choose_font_mi );
 246         customizeJMenuItem( _switch_colors_mi );
 247         customizeJMenuItem( _choose_minimal_confidence_mi );
 248         customizeJMenuItem( _overview_placment_mi );
 249         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 250                 .isShowDefaultNodeShapesInternal() );
 251         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 252                 .isShowDefaultNodeShapesExternal() );
 253         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 254         customizeJMenuItem( _cycle_node_shape_mi );
 255         customizeJMenuItem( _cycle_node_fill_mi );
 256         customizeJMenuItem( _choose_node_size_mi );
 257         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 258         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 259         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 260         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 261         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 262         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 263         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 264         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 265                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 266         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 267                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 268         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 269                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 270         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 271         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 272         customizeCheckBoxMenuItem( _label_direction_cbmi,
 273                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 274         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 275         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 276         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 277         _jmenubar.add( _options_jmenu );
 278     }
 279
 280     void buildToolsMenu() {
 281         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 282         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 283         customizeJMenuItem( _confcolor_item );
 284         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 285         customizeJMenuItem( _taxcolor_item );
 286         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 287         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 288         customizeJMenuItem( _remove_branch_color_item );
 289         _tools_menu.addSeparator();
 290         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 291         customizeJMenuItem( _midpoint_root_item );
 292         _tools_menu.addSeparator();
 293         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 294         customizeJMenuItem( _collapse_species_specific_subtrees );
 295         _jmenubar.add( _tools_menu );
 296     }
 297
 298     JApplet getApplet() {
 299         return _applet;
 300     }
 301
 302     @Override
 303     void readPhylogeniesFromURL() {
 304         throw new NoSuchMethodError( "not implemented" );
 305     }
 306
 307     void setSpeciesTree( final Phylogeny species_tree ) {
 308         _species_tree = species_tree;
 309     }
 310 }