+ if ( !ForesterUtil.isEmpty( getSpeciesTreeUrlStr() ) ) {
+ final URL species_tree_url = new URL( getSpeciesTreeUrlStr() );
+ final Phylogeny[] species_trees = AptxUtil
+ .readPhylogeniesFromUrl( species_tree_url,
+ configuration.isValidatePhyloXmlAgainstSchema(),
+ configuration.isReplaceUnderscoresInNhParsing(),
+ false,
+ TAXONOMY_EXTRACTION.NO );
+ if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
+ AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
+ if ( species_trees[ 0 ].isEmpty() ) {
+ ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
+ }
+ else if ( !species_trees[ 0 ].isRooted() ) {
+ ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
+ }
+ else {
+ getMainFrameApplet().setSpeciesTree( species_trees[ 0 ] );
+ }
+ }
+ else {
+ ForesterUtil.printErrorMessage( NAME, "failed to read species tree from " + getSpeciesTreeUrlStr() );
+ }
+ }