Class: ViennaRna::Fold

Inherits:
Base
  • Object
show all
Defined in:
lib/vienna_rna/modules/fold.rb

Defined Under Namespace

Modules: Batch

Constant Summary collapse

BASE_FLAGS = 
{
  "-noPS" => :empty
}

Instance Attribute Summary collapse

Attributes inherited from Base

#data, #response, #runtime

Instance Method Summary collapse

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 Attribute Details

#mfe ⇒ Object (readonly)

Returns the value of attribute mfe.



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# File 'lib/vienna_rna/modules/fold.rb', line 7

def mfe
  @mfe
end

#mfe_rna ⇒ Object (readonly)

Returns the value of attribute mfe_rna.



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# File 'lib/vienna_rna/modules/fold.rb', line 7

def mfe_rna
  @mfe_rna
end

#structure ⇒ Object (readonly)

Returns the value of attribute structure.



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# File 'lib/vienna_rna/modules/fold.rb', line 7

def structure
  @structure
end

Instance Method Details

#post_process ⇒ Object 



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# File 'lib/vienna_rna/modules/fold.rb', line 9

def post_process
  structure = Parser.rnafold_mfe_structure(@response)
  
  unless data.seq.length == structure.length
    raise "Sequence: '#{data.seq}'\nStructure: '#{structure}'"
  else
    @mfe_rna, @structure, @mfe = Rna.init_from_string(data.seq, structure), structure, Parser.rnafold_mfe(@response)
  end
end