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// Copyright 2010 Martin C. Frith
// An "Alphabet" consists of two things:
// 1) A mapping from ASCII letters to small integers.
// 2) A distinction between "normal" and "abnormal" letters. The
// letters that map to the first "size" integers are normal. For
// example, for DNA, ACGT would be normal.
#ifndef MCF_ALPHABET_HH
#define MCF_ALPHABET_HH
#include <string>
namespace mcf {
typedef unsigned char uchar;
struct Alphabet {
static const char* dna;
static const char* protein;
static const unsigned capacity = 256;
// Initializes the Alphabet with the given normal letters.
void fromString(const std::string &normalLetters); // case is preserved
// Makes lowercase letters map to the same numbers that uppercase
// letters do.
void makeCaseInsensitive();
// Maps letters to numbers in the given range.
void encodeInPlace(uchar *beg, uchar *end) const;
// Maps numbers back to letters in the given range.
void decodeInPlace(uchar *beg, uchar *end) const;
unsigned size; // number of "normal" letters in the alphabet
uchar lettersToNumbers[capacity];
uchar numbersToLetters[capacity];
uchar numbersToUppercase[capacity];
uchar numbersToLowercase[capacity];
private:
void addLetters(const std::string &letters, uchar &number);
void initCaseConversions();
};
}
#endif
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