split2.scala

case class Symbol()
case object Gap2 extends Symbol
case object A extends Symbol
case object G extends Symbol
case object C extends Symbol
case object T extends Symbol

def splitSimplePass2(seq: List[Symbol], gap: Symbol): List[List[Symbol]] = {
  def isMatch(inGapped: Boolean, c: Symbol) = {
    if (inGapped) 
      c == gap
    else
      c != gap
  }
  val isGap = (seq(0) == gap)
  val s = seq.takeWhile{ isMatch(isGap,_) }
  val tail = seq.takeRight(seq.length - s.length)
  tail match {
    case Nil => s :: Nil
    case _   => s :: splitSimplePass2(tail, gap)
  }
}