URL url = null;
Phylogeny[] phys = null;
// Get URL to tree file
- if ( _applet.getUrlString() != null ) {
+ if ( _applet.getTreeUrlStr() != null ) {
try {
- url = new URL( _applet.getUrlString() );
+ url = new URL( _applet.getTreeUrlStr() );
}
catch ( final Exception e ) {
ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
e.printStackTrace();
JOptionPane.showMessageDialog( this,
ArchaeopteryxA.NAME + ": Could not create URL from: \""
- + _applet.getUrlString() + "\"\nError: " + e,
+ + _applet.getTreeUrlStr() + "\"\nError: " + e,
"Failed to create URL",
JOptionPane.ERROR_MESSAGE );
close();
if ( !_configuration.isUseNativeUI() ) {
_jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() );
}
+ //TODO if species tree...
+ buildAnalysisMenu();
buildToolsMenu();
buildViewMenu();
buildFontSizeMenu();
System.gc();
}
+ void buildAnalysisMenu() {
+ _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
+ _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
+ _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
+ customizeJMenuItem( _gsdi_item );
+ customizeJMenuItem( _gsdir_item );
+ // _analysis_menu.addSeparator();
+ // _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
+ // customizeJMenuItem( _lineage_inference );
+ // _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
+ _jmenubar.add( _analysis_menu );
+ }
+
void buildOptionsMenu() {
_options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
_options_jmenu.addChangeListener( new ChangeListener() {
void readPhylogeniesFromURL() {
throw new NoSuchMethodError( "not implemented" );
}
+
+ void setSpeciesTree( final Phylogeny species_tree ) {
+ _species_tree = species_tree;
+ }
}