- html_desc.append( "<tr><td>" + input_file_properties[ i ][ 0 ] + " [species: "
- + input_file_properties[ i ][ 1 ] + "]" + ":</td><td>domains analyzed: "
- + parser.getDomainsStored() + "; domains ignored: [ind score cutoffs: "
- + parser.getDomainsIgnoredDueToIndividualScoreCutoff() + "] [E-value cutoff: "
- + parser.getDomainsIgnoredDueToEval() + "] [DUF: " + parser.getDomainsIgnoredDueToDuf()
- + "] [virus like ids: " + parser.getDomainsIgnoredDueToVirusLikeIds()
- + "] [negative domain filter: " + parser.getDomainsIgnoredDueToNegativeDomainFilter()
- + "] [overlap: " + parser.getDomainsIgnoredDueToOverlap() + "]" );
- if ( negative_filter_file != null ) {
- html_desc.append( "; proteins ignored due to negative filter: "
- + parser.getProteinsIgnoredDueToFilter() );
- }
- if ( positive_filter_file != null ) {
- html_desc.append( "; proteins ignored due to positive filter: "
- + parser.getProteinsIgnoredDueToFilter() );
- }
- html_desc.append( "</td></tr>" + nl );