public abstract class MainFrame extends JFrame implements ActionListener {\r
\r
static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
- static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME\r
+ static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME\r
static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;\r
private static final long serialVersionUID = 3655000897845508358L;\r
final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),\r
static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";\r
static final String CONVEX_TYPE_CBMI_LABEL = "Convex";\r
static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";\r
- static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO\r
- static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO\r
+ static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO\r
+ static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO\r
static final String OPTIONS_HEADER = "Options";\r
static final String SEARCH_SUBHEADER = "Search:";\r
static final String DISPLAY_SUBHEADER = "Display:";\r
static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";\r
+ static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions";\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 UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";\r
static final String LABEL_DIRECTION_LABEL = "Radial Labels";\r
static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";\r
+ static final String SEARCH_WITH_REGEX_TIP = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits.";\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
static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";\r
static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";\r
- static final String LINE_UP_RENDERABLE_DATA = "Line Up Node Diagrams";\r
+ static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";\r
JMenuBar _jmenubar;\r
JMenu _file_jmenu;\r
JMenu _tools_menu;\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_scale_cbmi; //TODO fix me\r
JCheckBoxMenuItem _show_overview_cbmi;\r
JCheckBoxMenuItem _show_domain_labels;\r
JCheckBoxMenuItem _show_annotation_ref_source;\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
JCheckBoxMenuItem _search_case_senstive_cbmi;\r
JCheckBoxMenuItem _search_whole_words_only_cbmi;\r
JCheckBoxMenuItem _inverse_search_result_cbmi;\r
+ JCheckBoxMenuItem _search_with_regex_cbmi;\r
// type menu:\r
JMenu _type_menu;\r
JCheckBoxMenuItem _rectangular_type_cbmi;\r
// Handy pointers to child components:\r
MainPanel _mainpanel;\r
Container _contentpane;\r
- final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;\r
+ final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;\r
Configuration _configuration;\r
Options _options;\r
private Phylogeny _species_tree;\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
getMainPanel().getControlPanel().search1();\r
}\r
else if ( o == _search_whole_words_only_cbmi ) {\r
+ if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {\r
+ _search_with_regex_cbmi.setSelected( false );\r
+ }\r
updateOptions( getOptions() );\r
getMainPanel().getControlPanel().search0();\r
getMainPanel().getControlPanel().search1();\r
getMainPanel().getControlPanel().search0();\r
getMainPanel().getControlPanel().search1();\r
}\r
- else if ( o == _show_scale_cbmi ) {\r
+ else if ( o == _search_with_regex_cbmi ) {\r
+ if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
+ _search_whole_words_only_cbmi.setSelected( false );\r
+ }\r
+ if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
+ _search_case_senstive_cbmi.setSelected( true );\r
+ }\r
updateOptions( getOptions() );\r
+ getMainPanel().getControlPanel().search0();\r
+ getMainPanel().getControlPanel().search1();\r
}\r
- else if ( o == _show_branch_length_values_cbmi ) {\r
+ else if ( o == _show_scale_cbmi ) {\r
updateOptions( getOptions() );\r
}\r
else if ( o == _color_by_taxonomic_group_cbmi ) {\r
* has been selected by the user by clicking the "Return ..."\r
* menu item. This method is expected to be called from Javascript or\r
* something like it.\r
- * \r
+ *\r
* @return current external node data as String\r
*/\r
public String getCurrentExternalNodesDataBuffer() {\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
&& _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
&& _search_whole_words_only_cbmi.isSelected() );\r
+ options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
&& _inverse_search_result_cbmi.isSelected() );\r
if ( _graphics_export_visible_only_cbmi != null ) {\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