Class: ViennaRna::Package::Rna2dfold

Inherits:
EnergyGrid2d show all
Defined in:
lib/vienna_rna/package/rna2dfold.rb

Constant Summary collapse

BASE_FLAGS = 
{
  d:         0,
  p:         :empty,
  "-noBT" => :empty
}

Instance Attribute Summary

Attributes inherited from Base

#data, #response, #runtime

Instance Method Summary collapse

Methods inherited from EnergyGrid2d

aligned_distributions, #each, inherited, #inspect, #quick_plot, set_of_points

Methods inherited from Base

bootstrap, #debugger, exec_exists?, #exec_name, #exec_sequence_format, #initialize, method_added, #pre_run_check, run, #run, #run_with_hooks, #serialize, #stringify_flags

Constructor Details

This class inherits a constructor from ViennaRna::Package::Base

Instance Method Details

#distribution ⇒ Object 



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# File 'lib/vienna_rna/package/rna2dfold.rb', line 22

def distribution
  response.split(/\n/)[6..-1].map { |line| line.split(/\t/).at_indexes([0, 1, 2, 6]) }
end

#run_command(flags = {}) ⇒ Object 



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# File 'lib/vienna_rna/package/rna2dfold.rb', line 12

def run_command(flags = {})
  ViennaRna.debugger { "Running RNA2Dfold on #{data.inspect}" }

  "cat %s  | %s %s" % [
    data.temp_fa_file!,
    exec_name, 
    stringify_flags(BASE_FLAGS.merge(self.class.const_defined?(:FLAGS) ? self.class.const_get(:FLAGS) : {}).merge(flags))
  ]
end