Class: Environment

Inherits:
Object
  • Object
show all
Defined in:
lib/environment.rb

Constant Summary collapse

@@amino_acids = 
"ACDEFGHIKLMNPQRSTVWYJ".split("")

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(number, label) ⇒ Environment

Returns a new instance of Environment.



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# File 'lib/environment.rb', line 17

def initialize(number, label)
  @number             = number
  @label              = label
  @freq_array         = NArray.int(21)
  @prob_array         = NArray.float(21)
  @logodd_array       = NArray.float(21)
  @smooth_prob_array  = NArray.float(21)
end

Instance Attribute Details

#freq_array ⇒ Object

Returns the value of attribute freq_array.



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# File 'lib/environment.rb', line 10

def freq_array
  @freq_array
end

#label ⇒ Object

Returns the value of attribute label.



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# File 'lib/environment.rb', line 10

def label
  @label
end

#logodd_array ⇒ Object

Returns the value of attribute logodd_array.



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# File 'lib/environment.rb', line 10

def logodd_array
  @logodd_array
end

#number ⇒ Object

Returns the value of attribute number.



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# File 'lib/environment.rb', line 10

def number
  @number
end

#prob_array ⇒ Object

Returns the value of attribute prob_array.



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# File 'lib/environment.rb', line 10

def prob_array
  @prob_array
end

#smooth_prob_array ⇒ Object

Returns the value of attribute smooth_prob_array.



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# File 'lib/environment.rb', line 10

def smooth_prob_array
  @smooth_prob_array
end

Instance Method Details

#add_residue_count(a, inc = 1) ⇒ Object 



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# File 'lib/environment.rb', line 26

def add_residue_count(a, inc = 1)
  @freq_array[@@amino_acids.index(a.upcase)] += inc
end

#label_set ⇒ Object 



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# File 'lib/environment.rb', line 30

def label_set
  label.split("").map_with_index { |l, i| "#{i}#{l}" }.to_set
end

#to_s ⇒ Object 



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# File 'lib/environment.rb', line 34

def to_s
  "#{number}-#{label}"
end