Module: Bio::Ucsc::Mm9

Extended by:
TableClassDetector
Defined in:
lib/bio-ucsc/mm9.rb,
lib/bio-ucsc/mm9/est.rb,
lib/bio-ucsc/mm9/gap.rb,
lib/bio-ucsc/mm9/gold.rb,
lib/bio-ucsc/mm9/mrna.rb,
lib/bio-ucsc/mm9/rmsk.rb,
lib/bio-ucsc/mm9/chainfr2.rb,
lib/bio-ucsc/mm9/chainrn4.rb,
lib/bio-ucsc/mm9/intronest.rb,
lib/bio-ucsc/mm9/chainbraflo1.rb,
lib/bio-ucsc/mm9/chaincanfam2.rb,
lib/bio-ucsc/mm9/chaincavpor3.rb,
lib/bio-ucsc/mm9/chainfr2link.rb,
lib/bio-ucsc/mm9/chaingalgal3.rb,
lib/bio-ucsc/mm9/chaingasacu1.rb,
lib/bio-ucsc/mm9/chainornana1.rb,
lib/bio-ucsc/mm9/chainorylat2.rb,
lib/bio-ucsc/mm9/chainpetmar1.rb,
lib/bio-ucsc/mm9/chainponabe2.rb,
lib/bio-ucsc/mm9/chainrhemac2.rb,
lib/bio-ucsc/mm9/chainrn4link.rb,
lib/bio-ucsc/mm9/chainbraflo1link.rb,
lib/bio-ucsc/mm9/chaincanfam2link.rb,
lib/bio-ucsc/mm9/chaincavpor3link.rb,
lib/bio-ucsc/mm9/chaingalgal3link.rb,
lib/bio-ucsc/mm9/chaingasacu1link.rb,
lib/bio-ucsc/mm9/chainornana1link.rb,
lib/bio-ucsc/mm9/chainorylat2link.rb,
lib/bio-ucsc/mm9/chainpetmar1link.rb,
lib/bio-ucsc/mm9/chainponabe2link.rb,
lib/bio-ucsc/mm9/chainrhemac2link.rb

Defined Under Namespace

Classes: ChainBraFlo1, ChainBraFlo1Link, ChainCanFam2, ChainCanFam2Link, ChainCavPor3, ChainCavPor3Link, ChainFr2, ChainFr2Link, ChainGalGal3, ChainGalGal3Link, ChainGasAcu1, ChainGasAcu1Link, ChainOrnAna1, ChainOrnAna1Link, ChainOryLat2, ChainOryLat2Link, ChainPetMar1, ChainPetMar1Link, ChainPonAbe2, ChainPonAbe2Link, ChainRheMac2, ChainRheMac2Link, ChainRn4, ChainRn4Link, DBConnection, Est, Gap, Gold, IntronEst, Mrna, Rmsk

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
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/mm9.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/mm9.rb', line 21

def self.default
  DBConnection.default
end