Module: ViennaRna::Global::RunExtensions::InstanceMethods

Defined in:
lib/vienna_rna/global/run_extensions.rb

Instance Method Summary collapse

Instance Method Details

#base_flags(flags) ⇒ Object 



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# File 'lib/vienna_rna/global/run_extensions.rb', line 66

def base_flags(flags)
  default_flags.respond_to?(:call) ? default_flags[self, flags] : default_flags
end

#exec_name ⇒ Object 



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# File 'lib/vienna_rna/global/run_extensions.rb', line 48

def exec_name
  executable_name.respond_to?(:call) ? executable_name[self] : executable_name
end

#pre_run_check ⇒ Object 



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# File 'lib/vienna_rna/global/run_extensions.rb', line 42

def pre_run_check
  if %x[which #{exec_name}].empty?
    raise RuntimeError.new("#{exec_name} is not defined on this machine")
  end
end

#recursively_merge_flags(flags) ⇒ Object 



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# File 'lib/vienna_rna/global/run_extensions.rb', line 52

def recursively_merge_flags(flags)
  rmerge = ->(old_hash, new_hash) do
    inner_hash = {}

    old_hash.merge(new_hash) do |key, old_value, new_value|
      inner_hash[key] = [old_value, new_value].map(&:class).uniq == [Hash] ? rmerge[old_value, new_value] : new_value
    end
  end
  
  rmerge[base_flags(flags), flags].tap do |merged_flags|
    ViennaRna.debugger { "%s: %s" % [self.class.name, merged_flags.inspect] }
  end
end

#run(flags = {}) ⇒ Object 



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# File 'lib/vienna_rna/global/run_extensions.rb', line 21

def run(flags = {})
  unless response
    tap do
      @runtime = Benchmark.measure do
        pre_run_check
        merged_flags     = recursively_merge_flags(flags)
        runnable_command = run_command(merged_flags)
        
        ViennaRna.debugger { runnable_command }
        
        @response        = %x[#{runnable_command}]
        post_process if respond_to?(:post_process)
      end

      ViennaRna.debugger { "Total runtime: %.3f sec." % runtime.real }
    end
  else
    self
  end
end

#run_command(flags) ⇒ Object 



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# File 'lib/vienna_rna/global/run_extensions.rb', line 70

def run_command(flags)
  "echo %s | %s %s" % [
    "'%s'" % call_with.map { |datum| data.send(datum) }.join(?\n),
    exec_name,
    stringify_flags(flags)
  ]
end

#stringify_flags(flags) ⇒ Object 



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# File 'lib/vienna_rna/global/run_extensions.rb', line 78

def stringify_flags(flags)
  flags.inject("") do |string, (flag, value)| 
    (string + (value == :empty || value.class == TrueClass ? " -%s" % flag : " -%s %s" % [flag, value])).strip
  end.tap do
    @flags = flags
  end
end