}
AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
final Phylogeny[] phys = factory.create( url.openStream(), parser );
- for( final Phylogeny phy : phys ) {
- System.out.println( phy.toString() );
- }
- if ( nhx_or_nexus && internal_numbers_are_confidences ) {
- for( final Phylogeny phy : phys ) {
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
+ if ( phys != null ) {
+ if ( nhx_or_nexus && internal_numbers_are_confidences ) {
+ for( final Phylogeny phy : phys ) {
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
+ }
}
- }
- if ( midpoint_reroot ) {
- for( final Phylogeny phy : phys ) {
- PhylogenyMethods.midpointRoot( phy );
- PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ if ( midpoint_reroot ) {
+ for( final Phylogeny phy : phys ) {
+ PhylogenyMethods.midpointRoot( phy );
+ PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ }
}
}
return phys;