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 JMenuItem _gsdi_item;
private JMenuItem _gsdir_item;
private Phylogeny _species_tree;
-
- private JCheckBoxMenuItem _right_line_up_domains_cbmi;
- private JCheckBoxMenuItem _line_up_renderable_data_cbmi;
-
+ private JCheckBoxMenuItem _right_line_up_domains_cbmi;
+ private JCheckBoxMenuItem _line_up_renderable_data_cbmi;
@Override
public void actionPerformed( final ActionEvent e ) {
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() );
}
else if ( o == _color_by_taxonomic_group_cbmi ) {
updateOptions( getOptions() );
}
-
-
-
else if ( o == _line_up_renderable_data_cbmi ) {
if ( !_line_up_renderable_data_cbmi.isSelected() ) {
_right_line_up_domains_cbmi.setSelected( false );
}
updateOptions( getOptions() );
}
-
repaint();
}
}
}
//
- setVisible( false );
- setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
- _jmenubar = new JMenuBar();
- if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
- if ( !getConfiguration().isUseNativeUI() ) {
- _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ 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 ( getSpeciesTree() != null ) {
- buildAnalysisMenu();
+ 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();
+ }
}
- 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() );
+ 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() );
}
- } );
- if ( getConfiguration().isUseTabbedDisplay() ) {
- AptxUtil.printAppletMessage( NAME, "using tabbed display" );
- AptxUtil.addPhylogeniesToTabs( phys,
- new File( phys_url.getFile() ).getName(),
- phys_url.toString(),
- getConfiguration(),
- getMainPanel() );
- }
- else {
- AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
- if ( getSpeciesTree() != null ) {
- AptxUtil.printAppletMessage( NAME,
- "Warning: gsdi (gene duplication inference) only available tabbed display" );
+ validate();
+ setName( NAME );
+ getMainPanel().getControlPanel().showWholeAll();
+ getMainPanel().getControlPanel().showWhole();
+ /* GUILHEM_BEG */
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
+ for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
+ .getRelevantSequenceRelationTypes() ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
+ }
+ final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
+ if ( default_relation != null ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
}
- AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
- }
- validate();
- setName( NAME );
- getMainPanel().getControlPanel().showWholeAll();
- getMainPanel().getControlPanel().showWhole();
- /* GUILHEM_BEG */
- getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
- for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
- .getRelevantSequenceRelationTypes() ) {
- getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
- }
- final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
- if ( default_relation != null ) {
- getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
- }
- final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
- if ( default_sequence != null ) {
- getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
- }
- /* GUILHEM_END */
- System.gc();
- AptxUtil.printAppletMessage( NAME, "successfully initialized" );
- setVisible( true );
+ final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
+ if ( default_sequence != null ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
+ }
+ /* GUILHEM_END */
+ System.gc();
+ AptxUtil.printAppletMessage( NAME, "successfully initialized" );
+ setVisible( true );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, e.toString() );
+ e.printStackTrace();
+ }
}
public void showTextFrame( final String s, final String title ) {
.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 ),
_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 ) );
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() );
customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
+ customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
+ customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
_jmenubar.add( _options_jmenu );
}
return _options;
}
-
-
void initializeTypeMenu( final Options options ) {
setTypeMenuToAllUnselected();
try {
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 )
if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
}
-
-
if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
}
-
-
if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
}
-
}
void updateTypeCheckboxes( final Options options, final Object o ) {
}
}
- private MainPanel getMainPanel() {
+ MainPanel getMainPanel() {
return _mainpanel;
}
git://source.jalview.org / jalview.git / blobdiff