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// Copyright 2008, 2009, 2010, 2012, 2013, 2014 Martin C. Frith
// This struct maps characters to codes (small integers) and back.
// We allow for both "proper" letters (e.g. ACGT for DNA), which get
// the lowest codes, and "improper" letters. This is because real
// sequence data includes additional letters (e.g. ambiguous bases),
// so we have to handle them. In addition, the space character
// represents a special delimiter.
#ifndef ALPHABET_HH
#define ALPHABET_HH
#include <string>
#include <iosfwd>
namespace cbrc{
typedef unsigned char uchar;
struct Alphabet{
typedef unsigned long long countT;
static const char* dna;
static const char* protein;
static const unsigned capacity = 256;
// does this alphabet start with the standard protein alphabet?
bool isProtein() const{ return letters.find( protein ) == 0; }
// make an Alphabet from a string containing the "proper" letters
void fromString( const std::string& alphString );
// add counts of "proper" letters to "counts" (counting lowercase too)
void count( const uchar* beg, const uchar* end, countT* counts ) const;
// translate (encode) a sequence of letters to numbers, in place
void tr( uchar* beg, uchar* end, bool isKeepLowercase=true ) const;
// reverse-translate (decode) a sequence of numbers to letters
// return the position after the last written position in dest
char* rtCopy( const uchar* beg, const uchar* end, char* dest ) const;
std::string letters; // the "proper" letters, e.g. ACGT for DNA
unsigned size; // same as letters.size(): excludes delimiters
uchar encode[capacity]; // translate ASCII letters to codes (small integers)
uchar decode[capacity]; // translate codes to ASCII letters
uchar numbersToUppercase[capacity]; // translate codes to uppercase codes
uchar numbersToLowercase[capacity]; // translate codes to lowercase codes
uchar lettersToUppercase[capacity]; // translate letters to uppercase codes
uchar complement[capacity]; // translate DNA codes to their complements
void init();
void addLetters( const std::string& lettersToAdd, unsigned& code );
void initCaseConversions( unsigned codeEnd );
void makeComplement();
};
std::ostream& operator<<( std::ostream& s, const Alphabet& a );
std::istream& operator>>( std::istream& s, Alphabet& a );
}
#endif
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