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lib/Bio/Palantir/Parser/Root.pm  view on Meta::CPAN

            $_->_set_rank($domain_rank++) 
                for sort { $a->begin <=> $b->begin } $gene->all_domains;

            $gene->_set_rank($gene_rank++);
        }

        # fix antiSMASH 5.1 and its module delineation
        if ($self->_root->{modulelist}) {     # Add new module feature from version 5.1

            # TODO see how synchronize domain rank in @genes and @modules
            my @cluster_modules = 
                sort {$a->genomic_prot_begin <=> $b->genomic_prot_begin } 
                grep { $_->genomic_dna_begin < $end
                    && $_->genomic_dna_end > $begin }
                @modules;
            ;
            
            my $mrank = 1;
            $_->_set_rank($mrank++) for @cluster_modules;