static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";\r
static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";\r
static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";\r
- static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Branch Length Values";\r
static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";\r
static final String DISPLAY_SCALE_LABEL = "Scale";\r
static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";\r
static final String SCREEN_ANTIALIAS_LABEL = "Antialias";\r
static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";\r
static final String BG_GRAD_LABEL = "Background Color Gradient";\r
- static final String DISPLAY_NODE_BOXES_LABEL_EXT = "External Node Shapes";\r
- static final String DISPLAY_NODE_BOXES_LABEL_INT = "Internal Node Shapes";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";\r
static final String SHOW_OVERVIEW_LABEL = "Overview";\r
static final String FONT_SIZE_MENU_LABEL = "Font Size";\r
static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";\r
JMenuItem _confcolor_item;\r
JMenuItem _color_rank_jmi;\r
JMenuItem _collapse_species_specific_subtrees;\r
- JMenuItem _collapse_below_threshold; //TODO implememt me\r
JMenuItem _obtain_detailed_taxonomic_information_jmi;\r
JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;\r
JMenuItem _obtain_seq_information_jmi;\r
JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;\r
JRadioButtonMenuItem _uniform_cladograms_rbmi;\r
JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;\r
- JCheckBoxMenuItem _show_branch_length_values_cbmi;\r
JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;\r
JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me\r
JCheckBoxMenuItem _show_overview_cbmi;\r
JMenuItem _choose_minimal_confidence_mi;\r
JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;\r
JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;\r
+ JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;\r
JMenuItem _cycle_node_shape_mi;\r
JMenuItem _cycle_node_fill_mi;\r
JMenuItem _choose_node_size_mi;\r
switchColors();\r
}\r
else if ( o == _display_basic_information_item ) {\r
- displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
+ if ( getCurrentTreePanel() != null ) {\r
+ displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
+ }\r
}\r
else if ( o == _view_as_NH_item ) {\r
viewAsNH();\r
else if ( o == _show_default_node_shapes_external_cbmi ) {\r
updateOptions( getOptions() );\r
}\r
+ else if ( o == _show_default_node_shapes_for_marked_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
else if ( o == _non_lined_up_cladograms_rbmi ) {\r
updateOptions( getOptions() );\r
showWhole();\r
else if ( o == _show_scale_cbmi ) {\r
updateOptions( getOptions() );\r
}\r
- else if ( o == _show_branch_length_values_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
else if ( o == _color_by_taxonomic_group_cbmi ) {\r
updateOptions( getOptions() );\r
}\r
&& _show_default_node_shapes_internal_cbmi.isSelected() );\r
options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
&& _show_default_node_shapes_external_cbmi.isSelected() );\r
+ options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
}\r
options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
&& _show_confidence_stddev_cbmi.isSelected() );\r
- if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {\r
- options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );\r
- }\r
if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
}\r
mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
}\r
\r
- static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,\r
- final JCheckBoxMenuItem scale,\r
- final JCheckBoxMenuItem branch_lengths,\r
- final JRadioButtonMenuItem non_lined_up,\r
- final JRadioButtonMenuItem uniform_clado,\r
- final JRadioButtonMenuItem nonuniform_clado,\r
- final JCheckBoxMenuItem label_direction_cbmi ) {\r
- final TreePanel tree_panel = main_panel.getCurrentTreePanel();\r
- final ControlPanel control = main_panel.getControlPanel();\r
- final Options options = main_panel.getOptions();\r
- scale.setSelected( options.isShowScale() );\r
- branch_lengths.setSelected( options.isShowBranchLengthValues() );\r
- // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
- if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {\r
- scale.setSelected( false );\r
- scale.setEnabled( false );\r
- branch_lengths.setSelected( false );\r
- branch_lengths.setEnabled( false );\r
- }\r
- else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {\r
- scale.setSelected( false );\r
- scale.setEnabled( false );\r
- branch_lengths.setEnabled( true );\r
- }\r
- else {\r
- scale.setEnabled( true );\r
- branch_lengths.setEnabled( true );\r
- }\r
- if ( ( tree_panel != null )\r
- && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )\r
- && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
- .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
- branch_lengths.setSelected( false );\r
- branch_lengths.setEnabled( false );\r
- }\r
- if ( tree_panel != null ) {\r
- if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )\r
- || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {\r
- non_lined_up.setEnabled( false );\r
- uniform_clado.setEnabled( false );\r
- nonuniform_clado.setEnabled( false );\r
- }\r
- else {\r
- non_lined_up.setEnabled( true );\r
- uniform_clado.setEnabled( true );\r
- nonuniform_clado.setEnabled( true );\r
- }\r
- }\r
- else {\r
- if ( ( tree_panel != null )\r
- && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
- .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
- branch_lengths.setSelected( false );\r
- branch_lengths.setEnabled( false );\r
- }\r
- if ( ( tree_panel != null )\r
- && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel\r
- .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {\r
- non_lined_up.setEnabled( false );\r
- }\r
- else {\r
- // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
- non_lined_up.setEnabled( true );\r
- }\r
- }\r
- label_direction_cbmi.setEnabled( true );\r
- if ( tree_panel != null ) {\r
- if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )\r
- && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
- label_direction_cbmi.setEnabled( false );\r
- }\r
- if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {\r
- scale.setSelected( false );\r
- scale.setEnabled( false );\r
- }\r
- }\r
- }\r
-\r
static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
for( final TreePanel tree_panel : treepanels ) {\r
tree_panel.setTextAntialias();\r
git://source.jalview.org / jalview.git / blobdiff