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: https://sites.google.com/site/cmzmasek/home/software/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;
36 import java.io.FileNotFoundException;
37 import java.io.IOException;
38 import java.net.MalformedURLException;
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;
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;
56 public final class MainFrameApplet extends MainFrame {
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;
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 ) ) {
74 readSpeciesTree( configuration, species_tree_url_str );
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() );
83 _jmenubar = new JMenuBar();
84 if ( !_configuration.isUseNativeUI() ) {
85 _jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() );
87 if ( getSpeciesTree() != null ) {
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() {
105 public void windowClosing( final WindowEvent e ) {
109 addComponentListener( new ComponentAdapter() {
112 public void componentResized( final ComponentEvent e ) {
113 if ( _mainpanel.getCurrentTreePanel() != null ) {
114 _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
116 _mainpanel.getCurrentTreePanel()
118 getOptions().isAllowFontSizeChange() );
122 setFocusable( true );
124 requestFocusInWindow();
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,
134 .isValidatePhyloXmlAgainstSchema(),
136 .isReplaceUnderscoresInNhParsing(),
138 TAXONOMY_EXTRACTION.NO,
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" );
145 else if ( !species_trees[ 0 ].isRooted() ) {
146 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is not rooted" );
149 setSpeciesTree( species_trees[ 0 ] );
150 AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "species tree OK" );
154 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from "
155 + species_tree_url_str );
160 public MainPanel getMainPanel() {
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 );
177 void buildOptionsMenu() {
178 _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
179 _options_jmenu.addChangeListener( new ChangeListener() {
182 public void stateChanged( final ChangeEvent e ) {
183 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
184 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
186 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
187 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel()
188 .getTreeFontSet() ) );
189 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
191 _show_branch_length_values_cbmi,
192 _non_lined_up_cladograms_rbmi,
193 _uniform_cladograms_rbmi,
194 _ext_node_dependent_cladogram_rbmi,
195 _label_direction_cbmi );
196 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
197 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
198 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
201 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
202 getConfiguration() ) );
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 );
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 ) );
215 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
217 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
219 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
220 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
221 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
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 ) );
226 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
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( "" ) );
243 _options_jmenu.addSeparator();
244 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
245 getConfiguration() ) );
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_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
277 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
278 customizeCheckBoxMenuItem( _label_direction_cbmi,
279 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
280 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
281 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
282 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
283 _jmenubar.add( _options_jmenu );
286 void buildToolsMenu() {
287 _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
288 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
289 customizeJMenuItem( _confcolor_item );
290 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
291 customizeJMenuItem( _taxcolor_item );
292 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
293 _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
294 customizeJMenuItem( _remove_branch_color_item );
295 _tools_menu.addSeparator();
296 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
297 customizeJMenuItem( _midpoint_root_item );
298 _tools_menu.addSeparator();
299 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
300 customizeJMenuItem( _collapse_species_specific_subtrees );
301 _jmenubar.add( _tools_menu );
304 JApplet getApplet() {
309 void readPhylogeniesFromURL() {
310 throw new NoSuchMethodError( "not implemented" );