func (self *Multi) Flush(where int, fill alphabet.Letter) {
if self.IsFlush(where) {
return
}
if where&seq.Start != 0 {
start := self.Start()
for _, s := range self.S {
if s.Start()-start < 1 {
continue
}
if m, ok := s.(*Multi); ok {
m.Flush(where, fill)
continue
}
S := s.Raw()
switch S.(type) {
case *[]alphabet.Letter:
uS := S.(*[]alphabet.Letter)
*uS = append(fill.Repeat(s.Start()-start), *uS...)
case *[]alphabet.QLetter:
uS := S.(*[]alphabet.QLetter)
*uS = append(alphabet.QLetter{L: fill}.Repeat(s.Start()-start), *uS...)
case packed.Packing, *[]alphabet.QPack:
panic("not implemented") // and never will be
// packed.Seq cannot hold letters beyond the 4 letters in the
// alphabet so it cannot have gaps.
// Perhaps a bitmap of valid bases may be considered though
// I can't see any particularly strong argument for this.
// packed.QSeq could have gaps, by assigning 0 Qphred, but this
// opens up possibility for abuse unless a valid bitmap is also
// inlcuded for this type.
}
s.Offset(start)
}
}
if where&seq.End != 0 {
end := self.End()
for i := 0; i < self.Count(); i++ {
s := self.Get(i)
if end-s.End() < 1 {
continue
}
s.(seq.Appender).AppendQLetters(alphabet.QLetter{L: fill}.Repeat(end - s.End())...)
}
}
}
func (self *Multi) Flush(where int, fill alphabet.Letter) {
if self.IsFlush(where) {
return
}
if where&seq.Start != 0 {
start := self.Start()
for _, s := range self.S {
if s.Start()-start < 1 {
continue
}
if m, ok := s.(*Multi); ok {
m.Flush(where, fill)
continue
}
S := s.Raw()
switch S.(type) {
case *[]alphabet.Letter:
uS := S.(*[]alphabet.Letter)
*uS = append(fill.Repeat(s.Start()-start), *uS...)
case *[]alphabet.QLetter:
uS := S.(*[]alphabet.QLetter)
*uS = append(alphabet.QLetter{L: fill}.Repeat(s.Start()-start), *uS...)
}
s.Offset(start)
}
}
if where&seq.End != 0 {
end := self.End()
for i := 0; i < self.Count(); i++ {
s := self.Get(i)
if end-s.End() < 1 {
continue
}
s.(seq.Appender).AppendQLetters(alphabet.QLetter{L: fill}.Repeat(end - s.End())...)
}
}
}