Class: ViennaRna::Rnabor

Inherits:
Xbor show all
Defined in:
lib/vienna_rna/modules/rnabor.rb

Constant Summary collapse

FLAGS = 
{
  nodangle: :empty
}

Constants inherited from Xbor

Xbor::BASE_FLAGS

Instance Attribute Summary

Attributes inherited from Base

#data, #response, #runtime

Instance Method Summary collapse

Methods inherited from Xbor

bootstrap_from_file, #expected_k, #full_distribution, #inspect, #k_p_points, parse, #quick_plot, #run_command

Methods inherited from Base

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

Constructor Details

This class inherits a constructor from ViennaRna::Base

Instance Method Details

#counts ⇒ Object 



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# File 'lib/vienna_rna/modules/rnabor.rb', line 18

def counts
  (non_zero_counts = self.class.parse(response).map { |row| BigDecimal.new(row[2]).to_i }) + [0] * (data.seq.length - non_zero_counts.length + 1)
end

#distribution(options = {}) ⇒ Object 



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# File 'lib/vienna_rna/modules/rnabor.rb', line 22

def distribution(options = {})
  options = { precision: 4 }.merge(options)
  
  distribution_before_precision = (non_zero_distribution = non_zero_shells.map { |i| i / partition }) + [0.0] * (data.seq.length - non_zero_distribution.length + 1)
  distribution_before_precision.map { |value| options[:precision].zero? ? value : (value * 10 ** options[:precision]).truncate / 10.0 ** options[:precision] }
end

#non_zero_shells ⇒ Object 



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# File 'lib/vienna_rna/modules/rnabor.rb', line 29

def non_zero_shells
  self.class.parse(response).map { |row| BigDecimal.new(row[1]) }
end

#partition ⇒ Object 



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# File 'lib/vienna_rna/modules/rnabor.rb', line 10

def partition
  non_zero_shells.inject(&:+)
end

#total_count ⇒ Object 



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# File 'lib/vienna_rna/modules/rnabor.rb', line 14

def total_count
  counts.inject(&:+)
end