import org.forester.go.PfamToGoMapping;
import org.forester.go.PfamToGoParser;
import org.forester.io.parsers.HmmPfamOutputParser;
import org.forester.go.PfamToGoMapping;
import org.forester.go.PfamToGoParser;
import org.forester.io.parsers.HmmPfamOutputParser;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
if ( p_array.length < 1 ) {
ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "file [" + intree_file
+ "] does not contain any phylogeny in phyloXML format" );
if ( p_array.length < 1 ) {
ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "file [" + intree_file
+ "] does not contain any phylogeny in phyloXML format" );
true,
surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
surfacing_hmmpfam.PRG_NAME,
true,
surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
surfacing_hmmpfam.PRG_NAME,