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

@@ -1,49 +1,79 @@
-# -*- coding: utf-8 -*-
 # = hg18/gap.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)
 #
-# = Table description in UCSC Table Browser This track depicts gaps in
-# the assembly. These gaps - with the exception of intractable
-# heterochromatic gaps - will be closed during the finishing process.
-#
-# = ommitted dynamic method(s) due to the method name collision
-# none
-#
-# = Note
-# In the hg18 database, the Gap table is actually separated
-# into "chr1_gap", "chr2_gap", etc. The Gap class dynamically
-# define Gap::Chr1_Gap, Gap::Chr2_Gap, etc. The
-# Gap.find_by_interval calls an appropreate class automatically.
+# 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 Gap
-        %w(
-Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9
-Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19
-Chr20 Chr21 Chr22 ).each do |chr|
-          klass = Class.new(DBConnection) do
-            extend Bio::Ucsc::Hg18::QueryUsingChromBin
-            set_table_name "#{chr.downcase}_gap"
-            set_primary_key nil
-            columns_hash.delete("type")  
-          end
-           self.const_set("#{chr}_Gap", klass)
-        end
+        Bio::Ucsc::Hg18::CHROMS.each do |chr|
+          class_eval %!
+            class #{chr[0..0].upcase + chr[1..-1]}_Gap < DBConnection
+              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_gap"
+              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
+      chrom = :chrom
+AND   bin in (:bins)
+AND ((chromStart BETWEEN :zstart AND :zend)
+ OR  (chromEnd BETWEEN :zstart AND :zend)
+ OR  (chromStart <= :zstart AND chromEnd >= :zend))
+                  SQL
+                else
+                  where = <<-SQL
+      chrom = :chrom
+AND   bin in (:bins)
+AND ((chromStart BETWEEN :zstart AND :zend)
+AND  (chromEnd 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}_Gap")
+          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_Gap")
           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}_Gap")
+          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
+          chr_klass = self.const_get("#{chrom}_Gap")
           chr_klass.__send__(:find_all_by_interval, interval, opt)
         end
-      end
-    end
-  end
-end
+      end # class
+
+    end # module Hg18 
+  end # module Ucsc
+end # module Bio