MappedSegment *MappedSegment::clone() const {
// FIXME: having both sourceCpySegIt and sourceSegIt seems pointless, same for target.
SegmentIteratorPtr sourceCpySegIt;
if (_source->isTop()) {
sourceCpySegIt = std::dynamic_pointer_cast<TopSegmentIterator>(_source)->clone();
} else {
sourceCpySegIt = std::dynamic_pointer_cast<BottomSegmentIterator>(_source)->clone();
}
SegmentIteratorPtr sourceSegIt = std::dynamic_pointer_cast<SegmentIterator>(sourceCpySegIt);
SegmentIteratorPtr targetCopySegIt;
if (_target->isTop()) {
targetCopySegIt = std::dynamic_pointer_cast<TopSegmentIterator>(_target)->clone();
} else {
targetCopySegIt = std::dynamic_pointer_cast<BottomSegmentIterator>(_target)->clone();
}
SegmentIteratorPtr targetSegIt = std::static_pointer_cast<SegmentIterator>(targetCopySegIt);
assert(sourceSegIt->getStartPosition() == _source->getStartPosition() &&
sourceSegIt->getEndPosition() == _source->getEndPosition());
assert(targetSegIt->getStartPosition() == _target->getStartPosition() &&
targetSegIt->getEndPosition() == _target->getEndPosition());
assert(_source->getLength() == _target->getLength());
assert(sourceSegIt->getLength() == targetSegIt->getLength());
MappedSegment *newSeg = new MappedSegment(sourceSegIt, targetSegIt);
assert(newSeg->getStartPosition() == getStartPosition() && newSeg->getEndPosition() == getEndPosition() &&
newSeg->_source->getStartPosition() == _source->getStartPosition() &&
newSeg->_source->getEndPosition() == _source->getEndPosition());
assert(newSeg->_source.get() != _source.get() && newSeg->_target.get() != _target.get());
return newSeg;
}
int MappedSegment::slowComp(const SegmentIteratorPtr &s1, const SegmentIteratorPtr &s2) {
assert(s1->getGenome() == s2->getGenome());
int res = 0;
hal_index_t sp1 = s1->getStartPosition();
hal_index_t ep1 = s1->getEndPosition();
hal_index_t sp2 = s2->getStartPosition();
hal_index_t ep2 = s2->getEndPosition();
if (s1->getReversed()) {
swap(sp1, ep1);
}
if (s2->getReversed()) {
swap(sp2, ep2);
}
if (sp1 < sp2) {
res = -1;
} else if (sp1 > sp2) {
res = 1;
} else if (ep1 < ep2) {
res = -1;
} else if (ep1 > ep2) {
res = 1;
}
return res;
}
