+ _allow_proteins_with_same_name = false;
+ init();
+ }
+
+ public HmmscanPerDomainTableParser( final File input_file,
+ final String species,
+ final Set<DomainId> filter,
+ final FilterType filter_type,
+ final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to,
+ final boolean allow_proteins_with_same_name ) {
+ _input_file = input_file;
+ _species = species;
+ _filter = filter;
+ _filter_type = filter_type;
+ _ind_cutoff = individual_cutoff_applies_to;
+ _allow_proteins_with_same_name = allow_proteins_with_same_name;