Module: Bio::Ucsc::SacCer2

Extended by:
TableClassDetector
Defined in:
lib/bio-ucsc/saccer2.rb,
lib/bio-ucsc/saccer2/est.rb,
lib/bio-ucsc/saccer2/gap.rb,
lib/bio-ucsc/saccer2/gold.rb,
lib/bio-ucsc/saccer2/mrna.rb,
lib/bio-ucsc/saccer2/intronest.rb,
lib/bio-ucsc/saccer2/t2micron_est.rb,
lib/bio-ucsc/saccer2/t2micron_gap.rb,
lib/bio-ucsc/saccer2/t2micron_gold.rb,
lib/bio-ucsc/saccer2/t2micron_mrna.rb,
lib/bio-ucsc/saccer2/t2micron_intronEst.rb

Defined Under Namespace

Classes: DBConnection, Est, Gap, Gold, IntronEst, Mrna, T2micron_est, T2micron_gap, T2micron_gold, T2micron_intronEst, T2micron_mrna

Constant Summary collapse

CHROMS = 
%w(chrI chrII chrIII chrIV chrV chrVI chrVII chrVIII chrIX chrX
chrXI chrXII chrXIII chrXIV chrXV chrXVI chrM 2micron)

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/saccer2.rb', line 23

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/saccer2.rb', line 19

def self.default
  DBConnection.default
end