Class: Macroape::PWMCompare

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/macroape/pwm_compare.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(first, second) ⇒ PWMCompare

Returns a new instance of PWMCompare.



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# File 'lib/macroape/pwm_compare.rb', line 6

def initialize(first, second)
  @first = first
  @second = second
end

Instance Attribute Details

#first ⇒ Object (readonly)

Returns the value of attribute first.



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# File 'lib/macroape/pwm_compare.rb', line 5

def first
  @first
end

#max_pair_hash_size ⇒ Object

sets or gets limit of summary size of calculation hash. It’s a defence against overuse CPU resources by non-appropriate data



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# File 'lib/macroape/pwm_compare.rb', line 4

def max_pair_hash_size
  @max_pair_hash_size
end

#second ⇒ Object (readonly)

Returns the value of attribute second.



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# File 'lib/macroape/pwm_compare.rb', line 5

def second
  @second
end

Instance Method Details

#each_alignment ⇒ Object Also known as: each 



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# File 'lib/macroape/pwm_compare.rb', line 29

def each_alignment
  (-second.length..first.length).to_a.product([:direct,:revcomp]) do |shift, orientation|
    yield PWMCompareAligned.new(first, second, shift, orientation).tap{|x| x.max_pair_hash_size = max_pair_hash_size }
  end
end

#jaccard(threshold_first, threshold_second) ⇒ Object 



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# File 'lib/macroape/pwm_compare.rb', line 11

def jaccard(threshold_first, threshold_second)
  self.map_each_alignment do |alignment|
    alignment.alignment_infos.merge( alignment.jaccard(threshold_first, threshold_second) )
  end.max_by {|alignment_infos| alignment_infos[:similarity] }
end

#jaccard_by_pvalue(pvalue) ⇒ Object 



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# File 'lib/macroape/pwm_compare.rb', line 17

def jaccard_by_pvalue(pvalue)
  threshold_first = first.threshold(pvalue)
  threshold_second = second.threshold(pvalue)
  jaccard(threshold_first, threshold_second)
end

#jaccard_by_weak_pvalue(pvalue) ⇒ Object 



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# File 'lib/macroape/pwm_compare.rb', line 23

def jaccard_by_weak_pvalue(pvalue)
  threshold_first = first.weak_threshold(pvalue)
  threshold_second = second.weak_threshold(pvalue)
  jaccard(threshold_first, threshold_second)
end