X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplet.java;h=baec9097a7d3fee033c9aa4cb66b2451f4361d34;hb=e6ea1a1dcb0a9b96cad1bc08c3b80a6f876344d2;hp=11bbba5f3984ad015bb911c6f2b60fd7eb361f98;hpb=733f051a048f64b6850314a08880f1f77a633db8;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java index 11bbba5..baec909 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java @@ -208,34 +208,38 @@ public final class MainFrameApplet extends MainFrame { _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_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu - .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) ); + .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( DISPLAY_NODE_BOXES_LABEL_EXT ) ); + .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); + if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { + _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); + } + _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 - .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) ); - _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); - _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) ); - _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) ); - _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) ); - _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP ); - _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) ); + .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); + _options_jmenu + .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); + _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); + _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP ); _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) ); _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) ); - if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { - _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) ); - } + _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); + _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) ); + _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) ); _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) ); _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() ) ); @@ -251,14 +255,15 @@ public final class MainFrameApplet extends MainFrame { .isShowDefaultNodeShapesInternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() .isShowDefaultNodeShapesExternal() ); - customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); + customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() ); customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() ); customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() ); + customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() ); customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() ); customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() ); @@ -284,8 +289,13 @@ public final class MainFrameApplet extends MainFrame { customizeJMenuItem( _confcolor_item ); _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) ); customizeJMenuItem( _taxcolor_item ); - _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) ); - _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." ); + _tools_menu.addSeparator(); + _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) ); + _remove_visual_styles_item + .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); + customizeJMenuItem( _remove_visual_styles_item ); + _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) ); + _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." ); customizeJMenuItem( _remove_branch_color_item ); _tools_menu.addSeparator(); _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) ); @@ -299,9 +309,4 @@ public final class MainFrameApplet extends MainFrame { JApplet getApplet() { return _applet; } - - @Override - void readPhylogeniesFromURL() { - throw new NoSuchMethodError( "not implemented" ); - } }