+ ForesterUtil.programMessage( PRG_NAME, "wrote output phylogeny to: " + outtree );
+ final SortedSet<String> species_set = new TreeSet<String>();
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( node.getNodeData().isHasTaxonomy() ) {
+ final String sn = node.getNodeData().getTaxonomy().getScientificName();
+ if ( !ForesterUtil.isEmpty( sn ) ) {
+ species_set.add( sn );
+ }
+ }
+ }
+ try {
+ final BufferedWriter out = new BufferedWriter( new FileWriter( present_species ) );
+ for( final String species : species_set ) {
+ out.write( species );
+ out.newLine();
+ }
+ out.close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "failed to write to [" + present_species + "]: " + e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "wrote present species to: " + present_species );
+ try {
+ final BufferedWriter out = new BufferedWriter( new FileWriter( removed_nodes ) );
+ for( final String remove_me : not_found ) {
+ out.write( remove_me );
+ out.newLine();
+ }
+ out.close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "failed to write to [" + removed_nodes + "]: " + e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "wrote removed external nodes labels to: " + removed_nodes );