else
{
alignment[s].setSequence(alignment[s].getSequenceAsString() +
- mseq[s].getSequence());
+ mseq[s].getSequenceAsString());
if (mseq[s].getStart() <= mseq[s].getEnd())
{
alignment[s].setEnd(mseq[s].getEnd());
else
{
alignment[s].setSequence(alignment[s].getSequenceAsString() +
- oseq.getSequence());
+ oseq.getSequenceAsString());
if (oseq.getEnd() >= oseq.getStart())
{
alignment[s].setEnd(oseq.getEnd());
else
{
alignment[s].setSequence(alignment[s].getSequenceAsString() +
- hseq.getSequence());
+ hseq.getSequenceAsString());
if (hseq.getEnd() >= hseq.getStart())
{
alignment[s].setEnd(hseq.getEnd());
else
{
alignment[s].setSequence(alignment[s].getSequenceAsString() +
- mseq[s].getSequence());
+ mseq[s].getSequenceAsString());
if (mseq[s].getEnd() >= mseq[s].getStart())
{
alignment[s].setEnd(mseq[s].getEnd());
else
{
alignment[s].setSequence(alignment[s].getSequenceAsString() +
- oseq.getSequence());
+ oseq.getSequenceAsString());
if (oseq.getEnd() >= oseq.getStart())
{
alignment[s].setEnd(oseq.getEnd());