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// Copyright 2014-2015 Johannes Köster, Peer Aramillo Irizar.
// Licensed under the MIT license (http://opensource.org/licenses/MIT)
// This file may not be copied, modified, or distributed
// except according to those terms.

//! Implementation of the DNA alphabet.
//!
//! # Example
//!
//! ```
//! use bio::alphabets;
//! let alphabet = alphabets::dna::alphabet();
//! assert!(alphabet.is_word(b"GATTACA"));
//! assert!(alphabet.is_word(b"gattaca"));
//! assert!(!alphabet.is_word(b"ACGU"));
//! ```

use alphabets::Alphabet;
use utils::IntoTextIterator;


/// The DNA alphabet (uppercase and lowercase).
pub fn alphabet() -> Alphabet {
    Alphabet::new(b"ACGTacgt")
}


/// The DNA alphabet including N (uppercase and lowercase).
pub fn n_alphabet() -> Alphabet {
    Alphabet::new(b"ACGTNacgtn")
}


/// The IUPAC DNA alphabet (uppercase and lowercase).
pub fn iupac_alphabet() -> Alphabet {
    Alphabet::new(b"ACGTURYSWKMBDHVNacgturyswkmbdhvn")
}


lazy_static! {
    static ref COMPLEMENT: Vec<u8> = {
        let mut comp = Vec::new();
        comp.resize(256, 0);
        for (v, mut a) in comp.iter_mut().enumerate() {
            *a = v as u8;
        }
        for (&a, &b) in b"AGCTYRWSKMDVHBN".iter().zip(b"TCGARYWSMKHBDVN".iter()) {
            comp[a as usize] = b;
            comp[a as usize + 32] = b + 32;  // lowercase variants
        }
        comp
    };
}


/// Return complement of given DNA alphabet character (IUPAC alphabet supported).
pub fn complement(a: u8) -> u8 {
    COMPLEMENT[a as usize]
}


/// Calculate reverse complement of given text (IUPAC alphabet supported).
pub fn revcomp<'a, T: IntoTextIterator<'a>>(text: T) -> Vec<u8> where
    T::IntoIter: DoubleEndedIterator {
    text.into_iter().rev().map(|&a| complement(a)).collect()
}