int MappedSegment::boundComp(const SegmentIteratorPtr &s1, const SegmentIteratorPtr &s2) { int res = 0; bool flip = s2->getReversed(); if (flip) { s2->toReverse(); } if (s1->isTop() && !s2->isTop()) { BottomSegmentIteratorPtr bot = std::dynamic_pointer_cast<BottomSegmentIterator>(s2); hal_index_t lb = bot->bseg()->getTopParseIndex(); hal_index_t ub = lb; if ((hal_size_t)bot->getArrayIndex() < bot->getGenome()->getNumBottomSegments() - 1) { bot = bot->clone(); bot->slice(0, 0); bot->toRight(); ub = bot->bseg()->getTopParseIndex(); } if (s1->getArrayIndex() < lb) { res = -1; } else if (s1->getArrayIndex() > ub) { res = 1; } } else if (!s1->isTop() && s2->isTop()) { TopSegmentIteratorPtr top = std::dynamic_pointer_cast<TopSegmentIterator>(s2); hal_index_t lb = top->tseg()->getBottomParseIndex(); hal_index_t ub = lb; if ((hal_size_t)top->getArrayIndex() < top->getGenome()->getNumTopSegments() - 1) { top = top->clone(); top->slice(0, 0); top->toRight(); ub = top->tseg()->getBottomParseIndex(); } if (s1->getArrayIndex() < lb) { res = -1; } else if (s1->getArrayIndex() > ub) { res = 1; } } if (flip) { s2->toReverse(); } return res; }