Example #1
0
// Set the letter at position pos to l.
func (self *Seq) Set(pos seq.Position, l alphabet.QLetter) {
	if pos.Ind != 0 || pos.Pos < self.offset || pos.Pos >= self.End() {
		panic("packed: index out of range")
	}
	p := pos.Pos + int(self.S.LeftPad) - self.offset
	pIndex, pOffset := p/4, uint(p%4)
	self.S.Letters[pIndex] &^= 0x3 << (2 * pOffset)
	self.S.Letters[pIndex] |= alphabet.Pack(self.alphabet.IndexOf(l.L)) << (2 * pOffset)
}
Example #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
}
Example #3
0
// Append QLetters to the sequence.
func (self *Seq) AppendQLetters(a ...alphabet.QLetter) (err error) {
	defer func() {
		if r := recover(); r != nil {
			_, pos := self.alphabet.AllValidQLetter(a)
			err = bio.NewError(fmt.Sprintf("Encoding error: %s %q at position %d.", r, a[pos], pos), 1, a)
		}
	}()

	i := 0
	for ; self.S.RightPad > 0 && i < len(a); i, self.S.RightPad = i+1, self.S.RightPad-1 {
		if !self.alphabet.IsValid(a[i].L) {
			return bio.NewError(fmt.Sprintf("Invalid letter %q at position %d.", a[i], i), 0, nil)
		}
		self.S.Letters[len(self.S.Letters)-1] |= alphabet.Pack(self.alphabet.IndexOf(a[i].L)) << (4 - byte(self.S.RightPad))
	}
	self.S.Letters = append(self.S.Letters, PackQLetters(self.alphabet, a[i:]...).Letters...)

	return
}