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();
85 if ( !_configuration.isUseNativeUI() ) {
86 _jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() );
95 setJMenuBar( _jmenubar );
96 _contentpane = getContentPane();
97 _contentpane.setLayout( new BorderLayout() );
98 _contentpane.add( _mainpanel, BorderLayout.CENTER );
99 setSize( getConfiguration().getFrameXSize() > 40 ? getConfiguration().getFrameXSize() : DEFAULT_FRAME_X_SIZE,
100 getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE );
101 addWindowListener( new WindowAdapter() {
104 public void windowClosing( final WindowEvent e ) {
108 addComponentListener( new ComponentAdapter() {
111 public void componentResized( final ComponentEvent e ) {
112 if ( _mainpanel.getCurrentTreePanel() != null ) {
113 _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
115 _mainpanel.getCurrentTreePanel()
120 setFocusable( true );
122 requestFocusInWindow();
128 public MainPanel getMainPanel() {
132 private void readSpeciesTree( final Configuration configuration, final String species_tree_url_str )
133 throws MalformedURLException, FileNotFoundException, IOException {
134 final URL species_tree_url = new URL( species_tree_url_str );
135 final Phylogeny[] species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
137 .isValidatePhyloXmlAgainstSchema(),
139 .isReplaceUnderscoresInNhParsing(),
141 TAXONOMY_EXTRACTION.NO,
143 if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
144 AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "successfully read species tree" );
145 if ( species_trees[ 0 ].isEmpty() ) {
146 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is empty" );
148 else if ( !species_trees[ 0 ].isRooted() ) {
149 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is not rooted" );
152 setSpeciesTree( species_trees[ 0 ] );
153 AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "species tree OK" );
157 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from "
158 + species_tree_url_str );
162 void buildAnalysisMenu() {
163 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
164 if ( getSpeciesTree() != null ) {
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();
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 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
190 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
191 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
192 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
193 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
195 getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
196 getMainPanel().getControlPanel().setVisibilityOfX();
198 catch ( final Exception ignore ) {
199 // do nothing, not important.
203 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
204 getConfiguration() ) );
206 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
207 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
208 _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
209 _radio_group_1 = new ButtonGroup();
210 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
211 _radio_group_1.add( _uniform_cladograms_rbmi );
212 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
213 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
214 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
216 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
218 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
220 .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
221 _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
222 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
223 _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
224 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
226 _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
227 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
229 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
231 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
232 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
233 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
234 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
235 _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
236 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
237 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
238 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
239 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
240 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
241 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
242 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
243 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
244 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
245 _options_jmenu.addSeparator();
246 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
247 getConfiguration() ) );
249 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
250 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
251 _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
252 _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
253 _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
255 _options_jmenu.addSeparator();
256 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
257 getConfiguration() ) );
258 _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
259 _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
261 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
263 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
265 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
266 _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
267 _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
269 customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
270 customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
271 customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
272 customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
273 customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
274 .isGraphicsExportUsingActualSize() );
275 customizeJMenuItem( _print_size_mi );
276 customizeJMenuItem( _choose_pdf_width_mi );
278 customizeJMenuItem( _choose_font_mi );
279 customizeJMenuItem( _switch_colors_mi );
280 customizeJMenuItem( _choose_minimal_confidence_mi );
281 customizeJMenuItem( _overview_placment_mi );
282 customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
283 .isShowDefaultNodeShapesInternal() );
284 customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
285 .isShowDefaultNodeShapesExternal() );
286 customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
287 .isShowDefaultNodeShapesForMarkedNodes() );
288 customizeJMenuItem( _cycle_node_shape_mi );
289 customizeJMenuItem( _cycle_node_fill_mi );
290 customizeJMenuItem( _choose_node_size_mi );
291 customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
292 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
293 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
294 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
295 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
296 customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
297 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
298 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
299 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
300 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
301 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
302 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
303 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
304 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
305 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
306 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
307 customizeCheckBoxMenuItem( _label_direction_cbmi,
308 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
309 customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
310 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
311 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
312 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
313 customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
314 customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
315 _jmenubar.add( _options_jmenu );
318 void buildToolsMenu() {
319 _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
320 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
321 customizeJMenuItem( _confcolor_item );
322 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
323 customizeJMenuItem( _taxcolor_item );
324 _tools_menu.addSeparator();
325 _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
326 _remove_visual_styles_item
327 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
328 customizeJMenuItem( _remove_visual_styles_item );
329 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
330 _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
331 customizeJMenuItem( _remove_branch_color_item );
332 _tools_menu.addSeparator();
333 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
334 customizeJMenuItem( _midpoint_root_item );
335 _tools_menu.addSeparator();
336 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
337 customizeJMenuItem( _collapse_species_specific_subtrees );
338 _jmenubar.add( _tools_menu );
341 JApplet getApplet() {