lib/bio-ucsc/hg18/chaindanrer5.rb in bio-ucsc-api-0.1.0 vs lib/bio-ucsc/hg18/chaindanrer5.rb in bio-ucsc-api-0.2.0

@@ -1,47 +1,79 @@
-# -*- coding: utf-8 -*-
 # = hg18/chaindanrer5.rb
 # Copyright::
-#  Copyright (C) 2011 MISHIMA, Hiroyuki
-#  <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
-# = Table desfription in UCSC Table Browser 
-# The chain track shows alignments of human (Feb. 2009
-# (GRCh37/hg18)/hg18) to other genomes using a gap scoring system that
-# allows longer gaps than traditional affine gap scoring systems. It
-# can also tolerate gaps in both human and the other genome
-# simultaneously. These "double-sided" gaps can be caused by local
-# inversions and overlapping deletions in both species. 
-#
-# = ommitted dynamic method(s) due to the method name collision
-#  none
+# In the hg18 database, this table is actually separated
+# into "chr1_*", "chr2_*", etc. This class dynamically
+# define *::Chr1_*, *::Chr2_*, etc. The
+# Rmsk.find_by_interval calls an appropreate class automatically.
 
 module Bio
   module Ucsc
     module Hg18
+
       class ChainDanRer5
-        %w(
-ChrM Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9
-Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19
-Chr20 Chr21 Chr22 ChrX ChrY).each do |chr|
-          klass = Class.new(DBConnection) do
-            extend Bio::Ucsc::Hg18::QueryUsingTBin
-            set_table_name "#{chr.downcase}_chainDanRer5"
-            set_primary_key nil
-          end
-          self.const_set("#{chr}_ChainDanRer5", klass)
-        end
+        Bio::Ucsc::Hg18::CHROMS.each do |chr|
+          class_eval %!
+            class #{chr[0..0].upcase + chr[1..-1]}_ChainDanRer5 < DBConnection
+              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_chainDanRer5"
+              set_primary_key nil
+              set_inheritance_column nil
 
+              def self.find_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :first, opt)
+              end
+        
+              def self.find_all_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :all, opt)
+              end
+
+              def self.find_first_or_all_by_interval(interval, first_all, opt)
+                zstart = interval.zero_start
+                zend   = interval.zero_end
+                if opt[:partial] == true
+                  where = <<-SQL
+      tName = :chrom
+AND   bin in (:bins)
+AND ((tStart BETWEEN :zstart AND :zend)
+ OR  (tEnd BETWEEN :zstart AND :zend)
+ OR  (tStart <= :zstart AND tEnd >= :zend))
+                  SQL
+                else
+                  where = <<-SQL
+      tName = :chrom
+AND   bin in (:bins)
+AND ((tStart BETWEEN :zstart AND :zend)
+AND  (tEnd 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})
-          chr_klass = self.const_get("#{interval.chrom.capitalize}_ChainDanRer5")
+          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_ChainDanRer5")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
         def self.find_all_by_interval(interval, opt = {:partial => true})
-          chr_klass = self.const_get("#{interval.chrom.capitalize}_ChainDanRer5")
+          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_ChainDanRer5")
           chr_klass.__send__(:find_all_by_interval, interval, opt)
         end
-      end
-    end # module Hg18
+      end # class
+
+    end # module Hg18 
   end # module Ucsc
-end # Bio
+end # module Bio