# = rmsk.rb
# Copyright::
#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
# License::     The Ruby licence (Ryby's / GPLv2 dual)
#
# In the hg18 database, the Rmsk table is actually separated
# into "chr1_rmsk", "chr2_rmsk", etc. The Rmsk class dynamically
# define Rmsk::Chr1_Rmsk, Rmsk::Chr2_Rmsk, etc. The
# Rmsk.find_by_interval calls an appropreate class automatically.

module Bio
  module Ucsc
    module Rn4

      class Rmsk
        Bio::Ucsc::Rn4::CHROMS.each do |chr|
          class_eval %!
            class #{chr[0..0].upcase + chr[1..-1]}_Rmsk < DBConnection
              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_rmsk"
              self.primary_key = nil

              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                find_first_or_all_by_interval(interval, :first, opt)
              end
        
              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                find_first_or_all_by_interval(interval, :all, opt)
              end

              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
                zstart = interval.zero_start
                zend   = interval.zero_end
                if opt[:partial] == true
                  where = <<-SQL
      genoName = :chrom
AND   bin in (:bins)
AND ((genoStart BETWEEN :zstart AND :zend)
 OR  (genoEnd BETWEEN :zstart AND :zend)
 OR  (genoStart <= :zstart AND genoEnd >= :zend))
                  SQL
                else
                  where = <<-SQL
      genoName = :chrom
AND   bin in (:bins)
AND ((genoStart BETWEEN :zstart AND :zend)
AND  (genoEnd BETWEEN :zstart AND :zend))
                  SQL
                end
                cond = {
                  :chrom  => interval.chrom,
                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
                  :zstart => zstart,
                  :zend   => zend,
                }
                self.find(first_all,
                          { :select => "*",
                            :conditions => [where, cond], })
              end
            end
          !
        end # each chromosome

        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
          chr_klass = self.const_get("#{chrom}_Rmsk")
          chr_klass.__send__(:find_by_interval, interval, opt)
        end

        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
          chr_klass = self.const_get("#{chrom}_Rmsk")
          chr_klass.__send__(:find_all_by_interval, interval, opt)
        end
      end # class Rmsk

    end # module 
  end # module Ucsc
end # module Bio