code: public static Alignment<NucleotideSequence> alignGlobal(final AlignmentScoring<NucleotideSequence> scoring,
                                                              final NucleotideSequence seq1, final NucleotideSequence seq2,
                                                              final int offset1, final int length1,
                                                              final int offset2, final int length2,
                                                              final int width) {
          if (scoring instanceof AffineGapAlignmentScoring)
              return BandedAffineAligner.align((AffineGapAlignmentScoring<NucleotideSequence>) scoring, seq1, seq2, offset1, length1, offset2, length2, width);
          else
              return BandedLinearAligner.align((LinearGapAlignmentScoring<NucleotideSequence>) scoring, seq1, seq2, offset1, length1, offset2, length2, width);
      }
docs: Classical Banded Alignment.
  
  Both sequences must be highly similar.
  
  Align 2 sequence completely (i.e. while first sequence will be aligned against whole second sequence).
  
  @param scoring scoring system
  @param seq1    first sequence
  @param seq2    second sequence
  @param offset1 offset in first sequence
  @param length1 length of first sequence's part to be aligned
  @param offset2 offset in second sequence
  @param length2 length of second sequence's part to be aligned
  @param width   width of banded alignment matrix. In other terms max allowed number of indels