Module: Bio::Ucsc::Hg18

Extended by:
TableClassDetector
Defined in:
lib/bio-ucsc/hg18.rb,
lib/bio-ucsc/hg18/gap.rb,
lib/bio-ucsc/hg18/gold.rb,
lib/bio-ucsc/hg18/rmsk.rb,
lib/bio-ucsc/hg18/chainfr2.rb,
lib/bio-ucsc/hg18/chainmm9.rb,
lib/bio-ucsc/hg18/chainrn4.rb,
lib/bio-ucsc/hg18/chainself.rb,
lib/bio-ucsc/hg18/intronest.rb,
lib/bio-ucsc/hg18/rmskrm327.rb,
lib/bio-ucsc/hg18/chainanocar1.rb,
lib/bio-ucsc/hg18/chainbostau4.rb,
lib/bio-ucsc/hg18/chainbraflo1.rb,
lib/bio-ucsc/hg18/chaincaljac1.rb,
lib/bio-ucsc/hg18/chaincanfam2.rb,
lib/bio-ucsc/hg18/chaincavpor3.rb,
lib/bio-ucsc/hg18/chaindanrer5.rb,
lib/bio-ucsc/hg18/chainequcab1.rb,
lib/bio-ucsc/hg18/chainfelcat3.rb,
lib/bio-ucsc/hg18/chaingalgal3.rb,
lib/bio-ucsc/hg18/chaingasacu1.rb,
lib/bio-ucsc/hg18/chainmondom4.rb,
lib/bio-ucsc/hg18/chainornana1.rb,
lib/bio-ucsc/hg18/chainorylat2.rb,
lib/bio-ucsc/hg18/chainpantro2.rb,
lib/bio-ucsc/hg18/chainpetmar1.rb,
lib/bio-ucsc/hg18/chainponabe2.rb,
lib/bio-ucsc/hg18/chainrhemac2.rb,
lib/bio-ucsc/hg18/chainstrpur2.rb,
lib/bio-ucsc/hg18/chaintaegut1.rb,
lib/bio-ucsc/hg18/chaintetnig2.rb,
lib/bio-ucsc/hg18/chainxentro2.rb

Defined Under Namespace

Classes: ChainAnoCar1, ChainBosTau4, ChainBraFlo1, ChainCalJac1, ChainCanFam2, ChainCavPor3, ChainDanRer5, ChainEquCab1, ChainFelCat3, ChainFr2, ChainGalGal3, ChainGasAcu1, ChainMm9, ChainMonDom4, ChainOrnAna1, ChainOryLat2, ChainPanTro2, ChainPetMar1, ChainPonAbe2, ChainRheMac2, ChainRn4, ChainSelf, ChainStrPur2, ChainTaeGut1, ChainTetNig2, ChainXenTro2, DBConnection, Gap, Gold, IntronEst, Rmsk, RmskRM327

Constant Summary collapse

CHROMS = 
%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)

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/hg18.rb', line 25

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/hg18.rb', line 21

def self.default
  DBConnection.default
end