code: public static <S extends Sequence<C>, C extends Compound> SequencePair<S, C> getPairwiseAlignment(
  			S query, S target, PairwiseSequenceAlignerType type, GapPenalty gapPenalty,
  			SubstitutionMatrix<C> subMatrix) {
  		return getPairwiseAligner(query, target, type, gapPenalty, subMatrix).getPair();
  	}
docs: Factory method which computes a sequence alignment for the given {@link Sequence} pair.
  
  @param <S> each {@link Sequence} of the pair is of type S
  @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
  @param query the first {@link Sequence}s to align
  @param target the second {@link Sequence}s to align
  @param type chosen type from list of pairwise sequence alignment routines
  @param gapPenalty the gap penalties used during alignment
  @param subMatrix the set of substitution scores used during alignment
  @return sequence alignment pair