lib/bio-ucsc/mm9/rmsk.rb in bio-ucsc-api-0.3.1 vs lib/bio-ucsc/mm9/rmsk.rb in bio-ucsc-api-0.4.0

@@ -11,25 +11,28 @@
 module Bio
   module Ucsc
     module Mm9
 
       class Rmsk
+        include DBConnector
+        DBConnection.database "mm9"
+ 
         Bio::Ucsc::Mm9::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_Rmsk < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_rmsk"
-              set_primary_key nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_rmsk"
+              self.primary_key = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              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})
+              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)
+              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
@@ -58,16 +61,16 @@
               end
             end
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        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})
+        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