Module: Bio::Ucsc::Dp3

Extended by:
TableClassDetector
Defined in:
lib/bio-ucsc/dp3.rb,
lib/bio-ucsc/dp3/est.rb,
lib/bio-ucsc/dp3/gap.rb,
lib/bio-ucsc/dp3/gold.rb,
lib/bio-ucsc/dp3/mrna.rb,
lib/bio-ucsc/dp3/rmsk.rb,
lib/bio-ucsc/dp3/chaindm3.rb,
lib/bio-ucsc/dp3/intronest.rb,
lib/bio-ucsc/dp3/chaindm3link.rb

Defined Under Namespace

Classes: ChainDm3, ChainDm3Link, DBConnection, Est, Gap, Gold, IntronEst, Mrna, Rmsk

Constant Summary collapse

CHROMS = 
%w(chr2 chr3 chr4_group1 chr4_group2 chr4_group3 chr4_group4 chr4_group5
chrXL_group1a chrXL_group1e chrXL_group3a chrXL_group3b chrXR_group3a
chrXR_group5 chrXR_group6 chrXR_group8 chrXR_group9 chrU)

Constants included from TableClassDetector

TableClassDetector::COMMON_CLASS_METHODS, TableClassDetector::PARAMETERS, TableClassDetector::RESERVED_METHODS, TableClassDetector::UPPERCASED_TABLE_PREFIX

Class Method Summary collapse

Methods included from TableClassDetector

bed, const_missing, genepred, generic, psl, rmsk

Class Method Details

.connect(param = Hash.new) ⇒ Object 



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# File 'lib/bio-ucsc/dp3.rb', line 24

def self.connect(param = Hash.new)
  DBConnection.db_adapter = param[:db_adapter] if param[:db_adapter]
  DBConnection.db_host = param[:db_host] if param[:db_host]
  DBConnection.db_username = param[:db_username] if param[:db_username]
  DBConnection.password = param[:password] if param[:password]
  DBConnection.connect
end

.default ⇒ Object 



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# File 'lib/bio-ucsc/dp3.rb', line 20

def self.default
  DBConnection.default
end