X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=2796e00a54aa7c977b8244e148237b415e9f25c7;hb=de53b1cdab3596db4f79609b934b44ea687fc879;hp=77355eacbf0ed3837ae2c6dd513c1387e3af3352;hpb=226d82be9b70ce0c67b5b1055654d484073ea184;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 77355ea..2796e00 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -117,12 +117,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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; @@ -263,9 +263,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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() ); } @@ -570,66 +567,62 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } // - 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(); @@ -736,16 +729,16 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { .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 ), @@ -759,20 +752,19 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _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 @@ -792,7 +784,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _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() ) ); @@ -817,6 +808,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { .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 ); @@ -829,7 +822,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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() ); @@ -943,7 +935,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } 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() + "\""; @@ -1319,6 +1312,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { && _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 ); } @@ -1344,9 +1339,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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 ) @@ -1475,7 +1467,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } - private MainPanel getMainPanel() { + MainPanel getMainPanel() { return _mainpanel; }