2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
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
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.
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.
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
26 // Contact: phylosoft @ gmail . com
27 // WWW: www.phylosoft.org/forester
29 package org.forester.archaeopteryx;
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;
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;
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;
53 public final class MainFrameApplet extends MainFrame {
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;
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; //~~~~
67 Phylogeny[] phys = null;
68 // Get URL to tree file
69 if ( _applet.getUrlString() != null ) {
71 url = new URL( _applet.getUrlString() );
73 catch ( final Exception e ) {
74 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
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 );
84 // Load the tree from URL
87 phys = AptxUtil.readPhylogeniesFromUrl( url,
88 configuration.isValidatePhyloXmlAgainstSchema(),
89 configuration.isReplaceUnderscoresInNhParsing(),
90 configuration.isInternalNumberAreConfidenceForNhParsing(),
91 configuration.getTaxonomyExtraction() );
93 catch ( final Exception e ) {
94 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
96 JOptionPane.showMessageDialog( this, ArchaeopteryxA.NAME + ": Failed to read phylogenies: "
97 + "\nError: " + e, "Failed to read phylogenies", JOptionPane.ERROR_MESSAGE );
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 );
107 AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "loaded " + phys.length + " phylogenies from: " + url );
109 _mainpanel = new MainPanelApplets( _configuration, this );
110 // build the menu bar
111 _jmenubar = new JMenuBar();
112 if ( !_configuration.isUseNativeUI() ) {
113 _jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() );
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() {
129 public void windowClosing( final WindowEvent e ) {
133 addComponentListener( new ComponentAdapter() {
136 public void componentResized( final ComponentEvent e ) {
137 if ( _mainpanel.getCurrentTreePanel() != null ) {
138 _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel()
140 _mainpanel.getCurrentTreePanel()
146 setFocusable( true );
148 requestFocusInWindow();
153 void buildOptionsMenu() {
154 _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
155 _options_jmenu.addChangeListener( new ChangeListener() {
158 public void stateChanged( final ChangeEvent e ) {
159 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
160 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
162 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
163 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel()
164 .getTreeFontSet() ) );
165 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
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() );
177 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
178 getConfiguration() ) );
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 ) );
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 ) );
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 ) );
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() ) );
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 );
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 );
269 JApplet getApplet() {
274 public MainPanel getMainPanel() {
279 void readPhylogeniesFromURL() {
280 throw new NoSuchMethodError( "not implemented" );