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 ) {
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 ) {