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 USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";\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 RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";\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
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 _cycle_node_fill_mi;\r
JMenuItem _choose_node_size_mi;\r
JCheckBoxMenuItem _show_confidence_stddev_cbmi;\r
- JCheckBoxMenuItem _right_line_up_domains_cbmi;\r
- JCheckBoxMenuItem _line_up_renderable_data_cbmi;\r
+ JCheckBoxMenuItem _right_line_up_domains_cbmi;\r
+ JCheckBoxMenuItem _line_up_renderable_data_cbmi;\r
// _ print\r
JCheckBoxMenuItem _graphics_export_visible_only_cbmi;\r
JCheckBoxMenuItem _antialias_print_cbmi;\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_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
}\r
updateOptions( getOptions() );\r
}\r
- \r
- \r
else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
|| ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
|| ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
typeChanged( o );\r
}\r
- \r
else if ( o == _about_item ) {\r
about();\r
}\r
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
}\r
}\r
- \r
else {\r
if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
_contentpane.repaint();\r
}\r
\r
- private void deleteSelectedNodes( boolean delete ) {\r
+ private void deleteSelectedNodes( final boolean delete ) {\r
final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
- if ( phy == null || phy.getNumberOfExternalNodes() < 2 ) {\r
+ if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
return;\r
}\r
- List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
- final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+ final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
for( final PhylogenyNode n : all_selected_nodes ) {\r
if ( n.isExternal() ) {\r
nodes.add( n );\r
}\r
}\r
}\r
- \r
String function = "Retain";\r
if ( delete ) {\r
function = "Delete";\r
return _species_tree;\r
}\r
\r
- \r
-\r
void initializeTypeMenu( final Options options ) {\r
setTypeMenuToAllUnselected();\r
switch ( options.getPhylogenyGraphicsType() ) {\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
}\r
if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
- \r
}\r
if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\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