import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Taxonomy;
final PhyloXmlParser xml_parser = new PhyloXmlParser();
final Phylogeny[] phylogenies_0 = factory.create( in, xml_parser );
final Phylogeny phylogeny_0 = phylogenies_0[ 0 ];
final PhyloXmlParser xml_parser = new PhyloXmlParser();
final Phylogeny[] phylogenies_0 = factory.create( in, xml_parser );
final Phylogeny phylogeny_0 = phylogenies_0[ 0 ];
- final PhylogenyWriter writer = new PhylogenyWriter();
- writer.toPhyloXML( out, phylogeny_0, 0 );
+ // final PhylogenyWriter writer = new PhylogenyWriter();
+ // writer.toPhyloXML( out, phylogeny_0, 0 );
//if ( node.isExternal() ) {
// final String c = "" + node.getNodeData().getBinaryCharacters().getPresentCount();
// final String s = node.getNodeData().getTaxonomy().getScientificName();
//if ( node.isExternal() ) {
// final String c = "" + node.getNodeData().getBinaryCharacters().getPresentCount();
// final String s = node.getNodeData().getTaxonomy().getScientificName();
//if ( !ForesterUtil.isEmpty( t.getTaxonomyCode() ) && t.getTaxonomyCode().length() == 5 ) {
// if ( node.getName().equalsIgnoreCase( t.getTaxonomyCode() ) ) {
// node.setName( "" );
// }
//}
//if ( !ForesterUtil.isEmpty( t.getTaxonomyCode() ) && t.getTaxonomyCode().length() == 5 ) {
// if ( node.getName().equalsIgnoreCase( t.getTaxonomyCode() ) ) {
// node.setName( "" );
// }
//}