double _min_not_collapse_bl = 0.001;\r
// Phylogeny Inference menu\r
private JMenu _inference_menu;\r
double _min_not_collapse_bl = 0.001;\r
// Phylogeny Inference menu\r
private JMenu _inference_menu;\r
try {\r
final SynthLookAndFeel synth = new SynthLookAndFeel();\r
synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),\r
try {\r
final SynthLookAndFeel synth = new SynthLookAndFeel();\r
synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),\r
if ( _configuration.isUseNativeUI() ) {\r
UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );\r
}\r
if ( _configuration.isUseNativeUI() ) {\r
UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );\r
}\r
setInferenceManager( InferenceManager.createInstance( _configuration ) );\r
setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );\r
// set title\r
setInferenceManager( InferenceManager.createInstance( _configuration ) );\r
setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );\r
// set title\r
_mainpanel = new MainPanel( _configuration, this );\r
// The file dialogs\r
_open_filechooser = new JFileChooser();\r
_mainpanel = new MainPanel( _configuration, this );\r
// The file dialogs\r
_open_filechooser = new JFileChooser();\r
_options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );\r
_search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );\r
_options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );\r
_options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );\r
_search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );\r
_options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );\r
_options_jmenu.addSeparator();\r
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),\r
getConfiguration() ) );\r
_options_jmenu.addSeparator();\r
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),\r
getConfiguration() ) );\r
_options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );\r
_options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );\r
_options_jmenu.addSeparator();\r
_options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );\r
_options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );\r
_options_jmenu.addSeparator();\r
_options_jmenu\r
.add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );\r
_options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
_options_jmenu\r
.add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );\r
_options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
_radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
_radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
_radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
_radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
_radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
_radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
_options_jmenu\r
.add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
_use_brackets_for_conf_in_nh_export_cbmi\r
_options_jmenu\r
.add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
_use_brackets_for_conf_in_nh_export_cbmi\r
customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );\r
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );\r
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );\r
customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );\r
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );\r
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );\r
customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );\r
customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()\r
customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );\r
customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()\r