codon.h

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#ifndef CODON_H
#define CODON_H

#include <map>
#include <string>
#include <iostream>

using namespace std;

/* convert base to integer
 * A=>0, C=>1, G=>2, T,U=>3, 
 * S,W,R,Y,K,M,B,V,H,D,N => 4-14
 * regardless of case
 */
int hashbase(char n);
/* convert 3-letter codon to a integer
 * from 0-63
 */
int hashcodon(char c[3]);
int hashcodon(const string &cc);

class codon {
   public:
      /* initialize with the default universal codon */
      codon();
      /* use a given codon table 
       * given as a string of TTT F TTC F ....
       * This class should be able to input from more 
       * formats, such as files etc.
       * */
      codon(const std::string &def);
      char operator[](const string &cd);
      char operator[](char cc[3]);
      map<char,double> getAAUniformFrequency() const;

   private:
      map<string, char> tab;
      char nuc2aa[65]; // last character is ?
      void convert();
};

/* the universal codon table is defined like this
 */
//   char nuc2aa[64]={ /* AAA */  'K', /* AAC */  'N', /* AAG */  'K',
// Any exception must be handled outside this table.

#endif