import org.forester.go.PfamToGoMapping;
import org.forester.go.PfamToGoParser;
import org.forester.io.parsers.HmmPfamOutputParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
}
try {
final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
- .create( intree_file, ForesterUtil.createParserDependingOnFileType( intree_file, true ) );
+ .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
if ( p_array.length < 1 ) {
ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "file [" + intree_file
+ "] does not contain any phylogeny in phyloXML format" );
.writeDomainSimilaritiesToFile( html_desc,
new StringBuilder( number_of_genomes + " genomes" ),
writer,
+ null,
similarities,
number_of_genomes == 2,
species_order,
true,
surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
surfacing_hmmpfam.PRG_NAME,
- display_histograms,
out_dir,
write_pwc_files );
String matrix_output_file = new String( output_file.toString() );