- _mainframe_applet = new MainFrameApplet( this, configuration );
- URL url = null;
- url = new URL( getUrlString() );
- final Phylogeny[] phys = Util.readPhylogeniesFromUrl( url, configuration.isValidatePhyloXmlAgainstSchema() );
- Util.addPhylogeniesToTabs( phys, new File( url.getFile() ).getName(), getUrlString(), getMainFrameApplet()
- .getConfiguration(), getMainFrameApplet().getMainPanel() );
+ _mainframe_applet = new MainFrameApplet( this, configuration, getSpeciesTreeUrlStr() );
+ final URL tree_url = new URL( getTreeUrlStr() );
+ final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( tree_url, configuration
+ .isValidatePhyloXmlAgainstSchema(), configuration.isReplaceUnderscoresInNhParsing(), configuration
+ .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction(), configuration
+ .isMidpointReroot() );
+ if ( phys == null ) {
+ ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are null" );
+ }
+ else if ( phys.length < 1 ) {
+ ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are empty" );
+ }
+ else {
+ AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + tree_url );
+ }
+ AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "loaded " + phys.length + " phylogenies from: "
+ + tree_url );
+ AptxUtil.addPhylogeniesToTabs( phys,
+ new File( tree_url.getFile() ).getName(),
+ getTreeUrlStr(),
+ getMainFrameApplet().getConfiguration(),
+ getMainFrameApplet().getMainPanel() );