private void init() { _fs_e_value_maximum = HmmscanPerDomainTableParser.E_VALUE_MAXIMUM_DEFAULT; _i_e_value_maximum = HmmscanPerDomainTableParser.E_VALUE_MAXIMUM_DEFAULT; setIgnoreDufs( HmmscanPerDomainTableParser.IGNORE_DUFS_DEFAULT ); setReturnType( HmmscanPerDomainTableParser.RETURN_TYPE_DEFAULT ); _max_allowed_overlap = HmmscanPerDomainTableParser.MAX_ALLOWED_OVERLAP_DEFAULT; setIndividualScoreCutoffs( null ); setIgnoreEngulfedDomains( false ); setIgnoreVirusLikeIds( false ); intitCounts(); }
parser.setIgnoreEngulfedDomains( no_engulfing_overlaps ); if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) { parser.setMaxAllowedOverlap( max_allowed_overlap );