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" );
SurfacingUtil.extractProteinNames( protein_list,
query_domain_ids_array[ j ],
query_domains_writer_ary[ j ],
- "\t" );
+ "\t",
+ surfacing.LIMIT_SPEC_FOR_PROT_EX );
query_domains_writer_ary[ j ].flush();
}
catch ( final IOException e ) {
.writeDomainSimilaritiesToFile( html_desc,
new StringBuilder( number_of_genomes + " genomes" ),
writer,
+ null,
similarities,
number_of_genomes == 2,
species_order,
SurfacingUtil.checkForOutputFileWriteability( out );
try {
final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
- SurfacingUtil.extractProteinNames( protein_lists_per_species, domain, proteins_file_writer, "\t" );
+ SurfacingUtil.extractProteinNames( protein_lists_per_species, domain, proteins_file_writer, "\t", null );
proteins_file_writer.close();
}
catch ( final IOException e ) {