Class: Bio::DB::Primer3::PrimerPair

Inherits:
Object
  • Object
show all
Includes:
Comparable
Defined in:
lib/bio/db/primer3.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(record, index) ⇒ PrimerPair

Returns a new instance of PrimerPair.

Raises:



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# File 'lib/bio/db/primer3.rb', line 595

def initialize(record, index)
  raise Primer3Exception.new(), "Index #{index} is greater than the number of records" unless index < record.size
  @record = record
  @left = Primer.new
  @right = Primer.new
  @values = Hash.new
  

  @left.set_value("added", false)
  @right.set_value("added", false)
  @left.pair = self
  @right.pair = self
  index_s = index.to_s
  record.properties.each do |key, value|
    tokens = key.to_s.split("_")
    if tokens.size > 2 and tokens[2] == index_s
      primer = nil
      primer = @right if tokens[1] == "right"
      primer = @left if tokens[1] == "left"
      if primer != nil
        primer.set_value("added", true)
        if tokens.size == 3
          primer.set_value("coordinates", parse_coordinates(value) )
        else

          to_add = value
          to_add = value.to_f unless tokens[3]=="sequence"
          n_key = tokens[3..6].join("_")
          primer.set_value(n_key, to_add)
        end
      else
        n_key = tokens[3..6].join("_")
        @values[n_key] = value  
      end

    end
  end

  raise Primer3Exception.new(), "The pair is not complete (l:#{left.added}, r:#{right.added})" if @left.added == false or @right.added == false

end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method

#method_missing(m, *args, &block) ⇒ Object

Raises:

  • (NoMethodError.new()) 


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# File 'lib/bio/db/primer3.rb', line 637

def method_missing(m, *args, &block)  

  return @values[m.to_s] if @values[m.to_s]
  raise NoMethodError.new(), "There's no method called #{m}. Available methods: #{@values.keys.to_s}"
end

Instance Attribute Details

#left ⇒ Object (readonly)

Returns the value of attribute left.



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# File 'lib/bio/db/primer3.rb', line 578

def left
  @left
end

#record ⇒ Object (readonly)

Returns the value of attribute record.



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# File 'lib/bio/db/primer3.rb', line 577

def record
  @record
end

#right ⇒ Object (readonly)

Returns the value of attribute right.



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# File 'lib/bio/db/primer3.rb', line 578

def right
  @right
end

Instance Method Details

#<=>(anOther) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 591

def <=>(anOther)
  penalty.to_f <=> anOther.penalty.to_f
end

#parse_coordinates(str) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 580

def parse_coordinates(str)
  coords = str.split(',')
  coords[0] = coords[0].to_i
  coords[1] = coords[1].to_i
  coords
end

#size ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 587

def size
  return product_size.to_i
end