// 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)
}
// 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
}
// 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
}