Simple dictionary in C

Question

Moving some code from Python to C     BASEPAIRS      T    A    A    T    G    C    C    G      Thinking maps might be overkill   What would you use

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BASEPAIRS      T    A    A    T    G    C    C    G      What would you use    Maybe   static const char basepairs      ATAGCG      lookup  if  const char  p   strchr basepairs  c          use p 1     -

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If you are into optimization  and assuming the input is always one of the four characters  the function below might be worth a try as a replacement for the map   char map const char in    return   in  amp  2      x8a  - in     x95  - in       It works based on the fact that you are dealing with two symmetric pairs  The conditional works to tell apart the A T pair from the G C one   G  and  C  happen to have the second-least-significant bit in common   The remaining arithmetics performs the symmetric mapping  It s based on the fact that a    a   b  - b is true for any a b

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A table out of char array   char map 256      0    map  T      A    map  A      T   map  C      G   map  G      C

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You can use the following syntax    include  lt map gt   std  map lt char  char gt  my map            A    1            B    2            C    3

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Until I was really concerned about performance  I would use a function  that takes a base and returns its match   char base pair char base        switch base            case  T   return  A               etc         default     handle error           If I was concerned about performance  I would define a base as one fourth of a byte   0 would represent A  1 would represent G  2 would represent C  and 3 would represent T   Then I would pack 4 bases into a byte  and to get their pairs  I would simply take the complement

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This is the fastest  simplest  smallest space solution I can think of   A good optimizing compiler will even remove the cost of accessing the pair and name arrays   This solution works equally well in C    include  lt iostream gt   enum Base enum   A  C  T  G    typedef enum Base enum Base  static const Base pair 4      T  G  A  C    static const char name 4       A    C    T    G     static const Base base 85         -1  -1  -1  -1  -1  -1  -1  -1  -1  -1      -1  -1  -1  -1  -1  -1  -1  -1  -1  -1      -1  -1  -1  -1  -1  -1  -1  -1  -1  -1      -1  -1  -1  -1  -1  -1  -1  -1  -1  -1       -1  -1  -1  -1  -1  -1  -1  -1  -1  -1      -1  -1  -1  -1  -1  -1  -1  -1  -1  -1      -1  -1  -1  -1  -1   A  -1   C  -1  -1      -1   G  -1  -1  -1  -1  -1  -1  -1  -1       -1  -1  -1  -1   T     const Base base2  const char b      switch  b            case  A   return A      case  C   return C      case  T   return T      case  G   return G      default  abort              int main  int argc  char  args       for  Base b   A  b  lt   G  b                std  cout  lt  lt  name b   lt  lt                        lt  lt  name pair b    lt  lt  std  endl          for  Base b   A  b  lt   G  b                std  cout  lt  lt  name base name b     lt  lt                        lt  lt  name pair base name b      lt  lt  std  endl          for  Base b   A  b  lt   G  b                std  cout  lt  lt  name base2 name b     lt  lt                        lt  lt  name pair base2 name b      lt  lt  std  endl             base   is a fast ascii char to Base  i e  int between 0 and 3 inclusive  lookup that is a bit ugly   A good optimizing compiler should be able to handle base2   but I m not sure if any do

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Here s the map solution    include  lt iostream gt   include  lt map gt   typedef std  map lt char  char gt  BasePairMap   int main         BasePairMap m      m  A      T       m  T      A       m  C      G       m  G      C        std  cout  lt  lt   A    lt  lt  m  A    lt  lt  std  endl      std  cout  lt  lt   T    lt  lt  m  T    lt  lt  std  endl      std  cout  lt  lt   C    lt  lt  m  C    lt  lt  std  endl      std  cout  lt  lt   G    lt  lt  m  G    lt  lt  std  endl       return 0

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While using a std  map is fine or using a 256-sized char table would be fine  you could save yourself an enormous amount of space agony by simply using an enum  If you have C  11 features  you can use enum class for strong-typing      First  we define base-pairs  Because regular enums    Pollute the global namespace  I m using  enum class    enum class BasePair       A      T      C      G        Let s cut out the nonsense and make this easy     A is 0  T is 1  C is 2  G is 3     These are indices into our table    Now  everything can be so much easier BasePair Complimentary 4          T     Compliment of A     A     Compliment of T     G     Compliment of C     C     Compliment of G      Usage becomes simple   int main  int argc  char  argv           BasePair bp   BasePair  A      BasePair complimentbp   Complimentary  int bp       If this is too much for you  you can define some helpers to get human-readable ASCII characters and also to get the base pair compliment so you re not doing  int  casts all the time   BasePair Compliment   BasePair bp         return Complimentary  int bp      Move the pain here       Define a conversion table somewhere in your program char BasePairToChar 4       A    T    C    G     char ToCharacter   BasePair bp         return BasePairToChar   int bp        It s clean  it s simple  and its efficient   Now  suddenly  you don t have a 256 byte table  You re also not storing characters  1 byte each   and thus if you re writing this to a file  you can write 2 bits per Base pair instead of 1 byte  8 bits  per base pair  I had to work with Bioinformatics Files that stored data as 1 character each  The benefit is it was human-readable  The con is that what should have been a 250 MB file ended up taking 1 GB of space  Movement and storage and usage was a nightmare  Of coursse  250 MB is being generous when accounting for even Worm DNA  No human is going to read through 1 GB worth of base pairs anyhow

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