private JCheckBoxMenuItem _inverse_search_result_cbmi;
private JCheckBoxMenuItem _show_overview_cbmi;
private JMenuItem _choose_minimal_confidence_mi;
- private JCheckBoxMenuItem _show_branch_length_values_cbmi;
private JMenuItem _collapse_species_specific_subtrees;
private JMenuItem _overview_placment_mi;
private ButtonGroup _radio_group_1;
private JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
private JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
+ private JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
private JMenuItem _cycle_node_shape_mi;
private JMenuItem _cycle_node_fill_mi;
private JMenuItem _choose_node_size_mi;
else if ( o == _show_scale_cbmi ) {
updateOptions( getOptions() );
}
- else if ( o == _show_branch_length_values_cbmi ) {
- updateOptions( getOptions() );
- }
else if ( o == _show_confidence_stddev_cbmi ) {
updateOptions( getOptions() );
}
}
}
//
- setVisible( false );
- setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
- _jmenubar = new JMenuBar();
- if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
- if ( !getConfiguration().isUseNativeUI() ) {
- _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
- }
- if ( getSpeciesTree() != null ) {
- buildAnalysisMenu();
- }
- buildToolsMenu();
- buildViewMenu();
- buildFontSizeMenu();
- buildOptionsMenu();
- buildTypeMenu();
- buildHelpMenu();
- setJMenuBar( _jmenubar );
- }
- final Container contentpane = getContentPane();
- contentpane.setLayout( new BorderLayout() );
- contentpane.add( getMainPanel(), BorderLayout.CENTER );
- addComponentListener( new ComponentAdapter() {
-
- @Override
- public void componentResized( final ComponentEvent e ) {
- if ( getMainPanel().getCurrentTreePanel() != null ) {
- getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
- .getCurrentTreePanel()
- .getWidth(),
- getMainPanel()
- .getCurrentTreePanel()
- .getHeight(),
- getOptions()
- .isAllowFontSizeChange() );
+ try {
+ setVisible( false );
+ setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
+ _jmenubar = new JMenuBar();
+ if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
}
+ if ( getSpeciesTree() != null ) {
+ buildAnalysisMenu();
+ }
+ buildToolsMenu();
+ buildViewMenu();
+ buildFontSizeMenu();
+ buildOptionsMenu();
+ buildTypeMenu();
+ buildHelpMenu();
+ setJMenuBar( _jmenubar );
}
- } );
- if ( getConfiguration().isUseTabbedDisplay() ) {
- try {
- AptxUtil.printAppletMessage( NAME, "using tabbed display" );
- AptxUtil.addPhylogeniesToTabs( phys,
- new File( phys_url.getFile() ).getName(),
- phys_url.toString(),
- getConfiguration(),
- getMainPanel() );
- }
- catch ( final Exception e ) {
- ForesterUtil.printErrorMessage( NAME, e.toString() );
- e.printStackTrace();
+ final Container contentpane = getContentPane();
+ contentpane.setLayout( new BorderLayout() );
+ contentpane.add( getMainPanel(), BorderLayout.CENTER );
+ addComponentListener( new ComponentAdapter() {
+
+ @Override
+ public void componentResized( final ComponentEvent e ) {
+ if ( getMainPanel().getCurrentTreePanel() != null ) {
+ getMainPanel().getCurrentTreePanel()
+ .calcParametersForPainting( getMainPanel().getCurrentTreePanel().getWidth(),
+ getMainPanel().getCurrentTreePanel().getHeight(),
+ getOptions().isAllowFontSizeChange() );
+ }
+ }
+ } );
+ if ( getConfiguration().isUseTabbedDisplay() ) {
+ try {
+ AptxUtil.printAppletMessage( NAME, "using tabbed display" );
+ AptxUtil.addPhylogeniesToTabs( phys,
+ new File( phys_url.getFile() ).getName(),
+ phys_url.toString(),
+ getConfiguration(),
+ getMainPanel() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, e.toString() );
+ e.printStackTrace();
+ }
}
- }
- else {
- AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
- if ( getSpeciesTree() != null ) {
- AptxUtil.printAppletMessage( NAME,
- "Warning: gsdi (gene duplication inference) only available tabbed display" );
+ else {
+ AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
+ if ( getSpeciesTree() != null ) {
+ AptxUtil.printAppletMessage( NAME,
+ "Warning: gsdi (gene duplication inference) only available tabbed display" );
+ }
+ AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
}
- AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
- }
- try {
validate();
setName( NAME );
getMainPanel().getControlPanel().showWholeAll();
.setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
.createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
- MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
- _show_scale_cbmi,
- _show_branch_length_values_cbmi,
- _non_lined_up_cladograms_rbmi,
- _uniform_cladograms_rbmi,
- _ext_node_dependent_cladogram_rbmi,
- _label_direction_cbmi );
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
+ try {
+ getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
+ getMainPanel().getControlPanel().setVisibilityOfX();
+ }
+ catch ( final Exception ignore ) {
+ // do nothing, not important.
+ }
}
} );
_options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
_radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
_radio_group_1.add( _uniform_cladograms_rbmi );
_radio_group_1.add( _non_lined_up_cladograms_rbmi );
- /////
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
_options_jmenu
- .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
- _options_jmenu
.add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
_options_jmenu
.add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
+ _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
- _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
_options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
}
- _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
_options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
_options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
_options_jmenu
_options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
_options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
_options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
- /////
_options_jmenu.addSeparator();
_options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
getConfiguration() ) );
.isShowDefaultNodeShapesExternal() );
customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
.isShowDefaultNodeShapesInternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
+ .isShowDefaultNodeShapesForMarkedNodes() );
customizeJMenuItem( _cycle_node_shape_mi );
customizeJMenuItem( _cycle_node_fill_mi );
customizeJMenuItem( _choose_node_size_mi );
getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
- customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
}
void displayBasicInformation() {
- if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null )
+ && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
String title = "Basic Information";
if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
&& _show_default_node_shapes_internal_cbmi.isSelected() );
options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
&& _show_default_node_shapes_external_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
}
options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
&& _show_confidence_stddev_cbmi.isSelected() );
- if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
- options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
- }
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
&& _search_whole_words_only_cbmi.isSelected() );
options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
}
}
- private MainPanel getMainPanel() {
+ MainPanel getMainPanel() {
return _mainpanel;
}
git://source.jalview.org / jalview.git / blobdiff