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Contents
# Copyright::
# Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
# License:: The Ruby licence (Ryby's / GPLv2 dual)
#
# this table is actually separated
# into "chr1_*", "chr2_*", etc. This class dynamically
# define *::Chr1_*, *::Chr2_*, etc. The
# find_by_interval calls an appropreate class automatically.
module Bio
module Ucsc
module SacCer2
class T2micron_gap < DBConnection
self.table_name = "2micron_gap"
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
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 ((chromStart BETWEEN :zstart AND :zend)
AND (chromEnd BETWEEN :zstart AND :zend))
SQL
end
cond = {
:chrom => interval.chrom,
:bins => Ucsc::UcscBin.bin_all(zstart, zend),
:zstart => zstart,
:zend => zend,}
self.find(first_all,
{ :select => "*",
:conditions => [where, cond], })
end
end # class
end # module
end # module Ucsc
end # module Bio
Version data entries
11 entries across 11 versions & 1 rubygems