alphabet.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *    * Redistributions of source code must retain the above copyright
 *      notice, this list of conditions and the following disclaimer.
 *    * Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in the
 *      documentation and/or other materials provided with the distribution.
 *    * Neither the name of the NVIDIA CORPORATION nor the
 *      names of its contributors may be used to endorse or promote products
 *      derived from this software without specific prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

#include <nvbio/basic/types.h>
#include <nvbio/basic/transform_iterator.h>

namespace nvbio {



enum Alphabet
{
    DNA       = 0u,           
    DNA_N     = 1u,           
    DNA_IUPAC = 2u,           
    PROTEIN   = 3u,           
    RNA       = 4u,           
    RNA_N     = 5u,           
    ASCII     = 6u            
};

template <Alphabet ALPHABET> struct AlphabetTraits {};

template <> struct AlphabetTraits<DNA>
{
    static const uint32 SYMBOL_SIZE  = 2;
    static const uint32 SYMBOL_COUNT = 4;

    enum {
        A = 0,
        C = 1,
        G = 2,
        T = 3,
    };
};
template <> struct AlphabetTraits<DNA_N>
{
    static const uint32 SYMBOL_SIZE  = 4;
    static const uint32 SYMBOL_COUNT = 5;

    enum {
        A = 0,
        C = 1,
        G = 2,
        T = 3,
        N = 4,
    };
};
template <> struct AlphabetTraits<DNA_IUPAC>
{
    static const uint32 SYMBOL_SIZE  = 4;
    static const uint32 SYMBOL_COUNT = 16;

    enum {
        EQUAL = 0,
        A     = 1,
        C     = 2,
        M     = 3,
        G     = 4,
        R     = 5,
        S     = 6,
        V     = 7,
        T     = 8,
        W     = 9,
        Y     = 10,
        H     = 11,
        K     = 12,
        D     = 13,
        B     = 14,
        N     = 15,
    };
};
template <> struct AlphabetTraits<PROTEIN>
{
    static const uint32 SYMBOL_SIZE  = 8;
    static const uint32 SYMBOL_COUNT = 24;

    enum {
        A = 0,
        C = 1,
        D = 2,
        E = 3,
        F = 4,
        G = 5,
        H = 6,
        I = 7,
        K = 8,
        L = 9,
        M = 10,
        N = 11,
        O = 12,
        P = 13,
        Q = 14,
        R = 15,
        S = 16,
        T = 17,
        V = 18,
        W = 19,
        Y = 20,
        B = 21,
        Z = 22,
        X = 23,
    };
};
template <> struct AlphabetTraits<RNA>
{
    static const uint32 SYMBOL_SIZE  = 2;
    static const uint32 SYMBOL_COUNT = 4;

    enum {
        A = 0,
        C = 1,
        G = 2,
        U = 3,
    };
};
template <> struct AlphabetTraits<RNA_N>
{
    static const uint32 SYMBOL_SIZE  = 4;
    static const uint32 SYMBOL_COUNT = 5;

    enum {
         A = 0,
         C = 1,
         G = 2,
         U = 3,
         N = 4,
    };
};
template <> struct AlphabetTraits<ASCII>
{
    static const uint32 SYMBOL_SIZE  = 8;
    static const uint32 SYMBOL_COUNT = 256;
};

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
uint32 bits_per_symbol(const Alphabet alphabet)
{
    return alphabet == DNA       ? 2 :
           alphabet == DNA_N     ? 4 :
           alphabet == DNA_IUPAC ? 4 :
           alphabet == PROTEIN   ? 8 :
           alphabet == RNA       ? 2 :
           alphabet == RNA_N     ? 4 :
           alphabet == ASCII     ? 8 :
           8u;
}

template <Alphabet ALPHABET>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char to_char(const uint8 c);

template <Alphabet ALPHABET>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8 from_char(const char c);

template <Alphabet ALPHABET, typename SymbolIterator>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void to_string(
    const SymbolIterator begin,
    const uint32         n,
    char*                string);

template <Alphabet ALPHABET, typename SymbolIterator>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void to_string(
    const SymbolIterator begin,
    const SymbolIterator end,
    char*                string);

template <Alphabet ALPHABET, typename SymbolIterator>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void from_string(
    const char*             begin,
    const char*             end,
    SymbolIterator          symbols);

template <Alphabet ALPHABET, typename SymbolIterator>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void from_string(
    const char*             begin,
    SymbolIterator          symbols);

template <Alphabet ALPHABET>
struct to_char_functor
{
    typedef uint8 argument_type;
    typedef char  result_type;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char operator() (const uint8 c) const { return to_char<ALPHABET>( c ); }
};

template <Alphabet ALPHABET>
struct from_char_functor
{
    typedef char  argument_type;
    typedef uint8 result_type;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8 operator() (const char c) const { return from_char<ALPHABET>( c ); }
};

template <Alphabet ALPHABET, typename Iterator>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
transform_iterator< Iterator, to_char_functor<ALPHABET> > 
to_string(Iterator it)
{
    return make_transform_iterator( it, to_char_functor<ALPHABET>() );
}

template <Alphabet ALPHABET, typename Iterator>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
transform_iterator< Iterator, from_char_functor<ALPHABET> >
from_string(Iterator it)
{
    return make_transform_iterator( it, from_char_functor<ALPHABET>() );
}


} // namespace nvbio

#include <nvbio/strings/alphabet_inl.h>