class Align::PairwiseAlgorithm
Provides a base for algorithms that align two sequences.
Attributes
scoring[R]
seq1[R]
seq2[R]
Public Class Methods
new(seq1, seq2, scoring)
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# File lib/align/pairwise_algorithm.rb, line 6 def initialize(seq1, seq2, scoring) @seq1 = seq1 @seq2 = seq2 @scoring = scoring end
Public Instance Methods
align()
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Returns the sequences in aligned arrays. Gaps are filled with :skip_obj @return Two arrays containing the sequences, and their elements.
# File lib/align/pairwise_algorithm.rb, line 34 def align raise NotImplementedError.new("#{self.class}#align") end
max2(a,b)
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Max of 2
# File lib/align/pairwise_algorithm.rb, line 13 def max2(a,b) a >= b ? a : b end
max3(a,b,c)
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Determines the maximum value of three variables. 3-4 times faster than [a,b,c].max.
# File lib/align/pairwise_algorithm.rb, line 19 def max3(a,b,c) (a >= b) ? ((a >= c)? a : c) : ((b >= c)? b : c) end
max4(a,b,c,d)
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Returns the max of 4 integers
# File lib/align/pairwise_algorithm.rb, line 24 def max4(a,b,c,d) x = a >= b ? a : b y = c >= d ? c : d (x >= y) ? x : y end