// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx;
static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
static final String BG_GRAD_LABEL = "Background Color Gradient";
- static final String DISPLAY_NODE_BOXES_LABEL = "Show Node Shapes";
+ 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 FONT_SIZE_MENU_LABEL = "Font Size";
static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
JCheckBoxMenuItem _color_labels_same_as_parent_branch;
JMenuItem _overview_placment_mi;
JMenuItem _choose_minimal_confidence_mi;
- JCheckBoxMenuItem _show_default_node_shapes_cbmi;
+ JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
+ JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
JMenuItem _cycle_node_shape_mi;
JMenuItem _cycle_node_fill_mi;
JMenuItem _choose_node_size_mi;
JCheckBoxMenuItem _circular_type_cbmi;
// view as text menu:
JMenuItem _view_as_NH_item;
- JMenuItem _view_as_NHX_item;
JMenuItem _view_as_XML_item;
JMenuItem _view_as_nexus_item;
JMenuItem _display_basic_information_item;
else if ( o == _view_as_NH_item ) {
viewAsNH();
}
- else if ( o == _view_as_NHX_item ) {
- viewAsNHX();
- }
else if ( o == _view_as_XML_item ) {
viewAsXML();
}
else if ( o == _color_labels_same_as_parent_branch ) {
updateOptions( getOptions() );
}
- else if ( o == _show_default_node_shapes_cbmi ) {
+ else if ( o == _show_default_node_shapes_internal_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_default_node_shapes_external_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
}
- public int getExtNodeDataBufferChangeCounter() {
+ public int getCurrentExternalNodesDataBufferChangeCounter() {
return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
}
+ public int getCurrentExternalNodesDataBufferLength() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
+ }
+
public InferenceManager getInferenceManager() {
return _inference_manager;
}
_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_NHX_item = new JMenuItem( "View as NHX" ) );
_view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
customizeJMenuItem( _display_basic_information_item );
customizeJMenuItem( _view_as_NH_item );
- customizeJMenuItem( _view_as_NHX_item );
customizeJMenuItem( _view_as_XML_item );
customizeJMenuItem( _view_as_nexus_item );
_jmenubar.add( _view_jmenu );
sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
sb.append( "\n" );
- sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
+ sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
TextFrame.instantiate( sb.toString(), "Help", _textframes );
}
&& _abbreviate_scientific_names.isSelected() );
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
&& _color_labels_same_as_parent_branch.isSelected() );
- options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
- && _show_default_node_shapes_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
+ && _show_default_node_shapes_internal_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
+ && _show_default_node_shapes_external_cbmi.isSelected() );
options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
&& _taxonomy_colorize_node_shapes_cbmi.isSelected() );
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
}
}
- void viewAsNHX() {
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
- String title = "NHX";
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
- title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
- }
- showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshireX(), title );
- }
- }
-
void viewAsXML() {
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "phyloXML";
*/
static void about() {
final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
- about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" );
+ about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );
about.append( "All Rights Reserved\n" );
about.append( "License: GNU Lesser General Public License (LGPL)\n" );
about.append( "Last modified: " + Constants.PRG_DATE + "\n" );