module BioDSL::Ambiguity
Namespace for Ambiguity
.
Public Instance Methods
add_ambiguity_macro(inline_builder)
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Add C functions to Inline::C object.
@param inline_builder [Inline::C] Inline C object.
# File lib/BioDSL/seq/ambiguity.rb, line 35 def add_ambiguity_macro(inline_builder) # Macro for matching nucleotides including ambiguity codes. inline_builder.prefix %( #define MATCH(A,B) ((bitmap[(int) A] & bitmap[(int) B]) != 0) ) # Bitmap for matching nucleotides including ambiguity codes. # For each value bits are set from the left: bit pos 1 for A, # bit pos 2 for T, bit pos 3 for C, and bit pos 4 for G. inline_builder.prefix %( char bitmap[256] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,14, 4,11, 0, 0, 8, 7, 0, 0,10, 0, 5,15, 0, 0, 0, 9,12, 2, 2,13, 3, 0, 6, 0, 0, 0, 0, 0, 0, 0, 1,14, 4,11, 0, 0, 8, 7, 0, 0,10, 0, 5,15, 0, 0, 0, 9,12, 2, 2,13, 3, 0, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }; ) end