static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
- static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
- static final String COLOR_BY_TAXONOMIC_GROUP = "Color by Taxonomic Group";
- static final String DISPLAY_SCALE_LABEL = "Display Scale";
+ static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Branch Length Values";
+ static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";
+ static final String DISPLAY_SCALE_LABEL = "Scale";
static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
static final String LABEL_DIRECTION_LABEL = "Radial Labels";
static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
static final String LABEL_DIRECTION_LABEL = "Radial Labels";
static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
- static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Show External Node Shapes";
- static final String DISPLAY_NODE_BOXES_LABEL_INT = "Show Internal Node Shapes";
- static final String SHOW_OVERVIEW_LABEL = "Show Overview";
+ static final String DISPLAY_NODE_BOXES_LABEL_EXT = "External Node Shapes";
+ static final String DISPLAY_NODE_BOXES_LABEL_INT = "Internal Node Shapes";
+ static final String SHOW_OVERVIEW_LABEL = "Overview";
static final String FONT_SIZE_MENU_LABEL = "Font Size";
static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
static final String FONT_SIZE_MENU_LABEL = "Font Size";
static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
- static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
- static final String SHOW_ANN_REF_SOURCE_LABEL = "Show Seq Annotation Ref Sources";
+ static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";
+ static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";
static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
JMenuItem _cycle_node_shape_mi;
JMenuItem _cycle_node_fill_mi;
JMenuItem _choose_node_size_mi;
JMenuItem _cycle_node_shape_mi;
JMenuItem _cycle_node_fill_mi;
JMenuItem _choose_node_size_mi;
JCheckBoxMenuItem _show_confidence_stddev_cbmi;
// _ print
JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
JCheckBoxMenuItem _show_confidence_stddev_cbmi;
// _ print
JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
_view_jmenu = createMenu( "View", getConfiguration() );
_view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
_view_jmenu.addSeparator();
_view_jmenu = createMenu( "View", getConfiguration() );
_view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
_view_jmenu.addSeparator();
- _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
- _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
- _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
+ _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
+ _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
+ _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
customizeJMenuItem( _display_basic_information_item );
customizeJMenuItem( _view_as_NH_item );
customizeJMenuItem( _view_as_XML_item );
customizeJMenuItem( _display_basic_information_item );
customizeJMenuItem( _view_as_NH_item );
customizeJMenuItem( _view_as_XML_item );
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "Basic Information";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "Basic Information";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
&& _show_default_node_shapes_internal_cbmi.isSelected() );
options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
&& _show_default_node_shapes_external_cbmi.isSelected() );
&& _show_default_node_shapes_internal_cbmi.isSelected() );
options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
&& _show_default_node_shapes_external_cbmi.isSelected() );
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
}
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
}
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "Nexus";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "Nexus";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "New Hampshire";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "New Hampshire";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
}
showTextFrame( _mainpanel.getCurrentPhylogeny()
.toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
}
showTextFrame( _mainpanel.getCurrentPhylogeny()
.toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "phyloXML";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "phyloXML";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
if ( ( nodes == null ) || nodes.isEmpty() ) {
JOptionPane
.showMessageDialog( this,
if ( ( nodes == null ) || nodes.isEmpty() ) {
JOptionPane
.showMessageDialog( this,