Class: Bio::PolyploidTools::PrimerRegion

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/PolyploidTools/PrimerRegion.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ PrimerRegion

Returns a new instance of PrimerRegion.



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# File 'lib/bio/PolyploidTools/PrimerRegion.rb', line 9

def initialize

  @chromosome_specific = Array.new
  @almost_chromosome_specific = Array.new
  @crhomosome_specific_intron  = Array.new
  @almost_crhomosome_specific_intron = Array.new
  #For deletions
  @chromosome_specific_in_mask = Array.new
  @almost_chromosome_specific_in_mask = Array.new
  @position_in_mask_from_template = Hash.new
end

Instance Attribute Details

#almost_chromosome_specific ⇒ Object

Returns the value of attribute almost_chromosome_specific.



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# File 'lib/bio/PolyploidTools/PrimerRegion.rb', line 5

def almost_chromosome_specific
  @almost_chromosome_specific
end

#almost_chromosome_specific_in_mask ⇒ Object

Returns the value of attribute almost_chromosome_specific_in_mask.



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# File 'lib/bio/PolyploidTools/PrimerRegion.rb', line 3

def almost_chromosome_specific_in_mask
  @almost_chromosome_specific_in_mask
end

#almost_crhomosome_specific_intron ⇒ Object

Returns the value of attribute almost_crhomosome_specific_intron.



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# File 'lib/bio/PolyploidTools/PrimerRegion.rb', line 6

def almost_crhomosome_specific_intron
  @almost_crhomosome_specific_intron
end

#chromosome_specific ⇒ Object

Returns the value of attribute chromosome_specific.



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# File 'lib/bio/PolyploidTools/PrimerRegion.rb', line 5

def chromosome_specific
  @chromosome_specific
end

#chromosome_specific_in_mask ⇒ Object

Returns the value of attribute chromosome_specific_in_mask.



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# File 'lib/bio/PolyploidTools/PrimerRegion.rb', line 4

def chromosome_specific_in_mask
  @chromosome_specific_in_mask
end

#crhomosome_specific_intron ⇒ Object

Returns the value of attribute crhomosome_specific_intron.



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# File 'lib/bio/PolyploidTools/PrimerRegion.rb', line 6

def crhomosome_specific_intron
  @crhomosome_specific_intron
end

#homoeologous ⇒ Object

Returns the value of attribute homoeologous.



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# File 'lib/bio/PolyploidTools/PrimerRegion.rb', line 7

def homoeologous
  @homoeologous
end

#position_in_mask_from_template ⇒ Object

Returns the value of attribute position_in_mask_from_template.



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# File 'lib/bio/PolyploidTools/PrimerRegion.rb', line 7

def position_in_mask_from_template
  @position_in_mask_from_template
end

#sequence ⇒ Object

Returns the value of attribute sequence.



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# File 'lib/bio/PolyploidTools/PrimerRegion.rb', line 4

def sequence
  @sequence
end

#snp_pos ⇒ Object

Returns the value of attribute snp_pos.



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# File 'lib/bio/PolyploidTools/PrimerRegion.rb', line 3

def snp_pos
  @snp_pos
end

Instance Method Details

#tail_candidates ⇒ Object 



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# File 'lib/bio/PolyploidTools/PrimerRegion.rb', line 21

def tail_candidates
  @chromosome_specific.size + @almost_chromosome_specific.size
end

#to_fasta ⇒ Object 



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# File 'lib/bio/PolyploidTools/PrimerRegion.rb', line 25

def to_fasta
  ">Primer_#{snp_pos}_#{chromosome_specific.to_s}_#{almost_chromosome_specific.to_s}_#{crhomosome_specific_intron.to_s}_#{almost_crhomosome_specific_intron.to_s}\n#{sequence}\n"
end