final boolean transfer_taxonomy ) throws SDIException, RIOException, FileNotFoundException, IOException { if ( !parser.hasNext() ) { throw new RIOException( "no gene trees to analyze" ); int counter = 0; final boolean no_range = ( first < 0 ) || ( last < first ); while ( parser.hasNext() ) { final Phylogeny gt = parser.next(); if ( no_range || ( ( i >= first ) && ( i <= last ) ) ) { if ( gt.isEmpty() ) {
p.reset(); checkPreconditions( p, species_tree, rerooting, outgroup, first, last ); _produce_log = produce_log; _removed_gene_tree_nodes = null; _duplications_stats = new BasicDescriptiveStatistics(); p.reset(); inferOrthologs( p, species_tree, algorithm, outgroup, first, last, transfer_taxonomy ); _species_tree = species_tree; final boolean transfer_taxonomy ) throws IOException, SDIException, RIOException { final Phylogeny g0 = p.next(); if ( ( g0 == null ) || g0.isEmpty() || ( g0.getNumberOfExternalNodes() < 2 ) ) { throw new RIOException( "input file does not seem to contain any gene trees" ); true, TAXONOMY_EXTRACTION.NO ); p.reset(); return new RIO( p, species_tree,
ip.setSource( gene_trees_file ); rio = RIO.executeAnalysis( ip, species_tree_file,
final int first, final int last ) throws RIOException, IOException { final Phylogeny g0 = p.next(); if ( ( g0 == null ) || g0.isEmpty() ) { throw new RIOException( "input file does not seem to contain any gene trees" );