Exemple #1
0
func checkPackedAlpha(alpha alphabet.Nucleic) error {
	if alpha.Len() != 4 {
		return bio.NewError("Cannot create packed sequence with alphabet length != 4", 0, alpha)
	}
	for _, v := range alphabet.BytesToLetters([]byte(alpha.String())) {
		if c, ok := alpha.Complement(v); ok && alpha.IndexOf(v) != alpha.IndexOf(c)^0x3 {
			// TODO: Resolution to the following problem:
			// Normal nucleotide alphabets (ACGT/ACGU) are safe with this in either case sensitive or
			// insensitive. Other alphabets may not be, in this case specify case sensitive.
			return bio.NewError("alphabet order not consistent with bit operations for packed.", 0, alpha)
		}
	}

	return nil
}
Exemple #2
0
// Pack bytes that conform to a into a slice of alphabet.Pack. Panics if a byte in s does not conform.
func PackLetters(a alphabet.Nucleic, s ...alphabet.Letter) (p *Packing) {
	p = &Packing{
		Letters:  make([]alphabet.Pack, (len(s)+3)/4),
		RightPad: int8(4-len(s)&3) & 3,
	}

	for i, c := range s {
		if !a.IsValid(c) {
			panic("packed: invalid letter")
		}
		p.Letters[i/4] <<= 2
		p.Letters[i/4] |= alphabet.Pack(a.IndexOf(c))
	}
	if sc := uint(len(s)) & 3; sc != 0 {
		p.Letters[len(p.Letters)-1] <<= (4 - sc) << 1
	}

	return
}