void TopSegmentSimpleIteratorTest::checkCallBack(const Alignment *alignment) {
const Genome *ancGenome = alignment->openGenome("Anc0");
CuAssertTrue(_testCase, ancGenome->getNumTopSegments() == _topSegments.size());
TopSegmentIteratorPtr tsIt = ancGenome->getTopSegmentIterator(0);
for (size_t i = 0; i < ancGenome->getNumTopSegments(); ++i) {
CuAssertTrue(_testCase, (size_t)tsIt->getTopSegment()->getArrayIndex() == i);
_topSegments[i].compareTo(tsIt, _testCase);
tsIt->toRight();
}
tsIt = ancGenome->getTopSegmentIterator(ancGenome->getNumTopSegments() - 1);
for (hal_index_t i = ancGenome->getNumTopSegments() - 1; i >= 0; --i) {
CuAssertTrue(_testCase, tsIt->getTopSegment()->getArrayIndex() == i);
_topSegments[i].compareTo(tsIt, _testCase);
tsIt->toLeft();
}
tsIt = ancGenome->getTopSegmentIterator(0);
tsIt->slice(0, tsIt->getLength() - 1);
for (hal_index_t i = 0; i < (hal_index_t)ancGenome->getSequenceLength(); ++i) {
CuAssertTrue(_testCase, tsIt->getLength() == 1);
CuAssertTrue(_testCase, tsIt->getStartPosition() == i);
tsIt->toRight(tsIt->getStartPosition() + 1);
}
tsIt = ancGenome->getTopSegmentIterator(ancGenome->getNumTopSegments() - 1);
tsIt->slice(tsIt->getLength() - 1, 0);
for (hal_index_t i = ancGenome->getSequenceLength() - 1; i >= 0; --i) {
CuAssertTrue(_testCase, tsIt->getLength() == 1);
CuAssertTrue(_testCase, tsIt->getStartPosition() == i);
tsIt->toLeft(tsIt->getStartPosition() - 1);
}
tsIt = ancGenome->getTopSegmentIterator(0);
tsIt->toReverse();
CuAssertTrue(_testCase, tsIt->getReversed() == true);
tsIt->slice(tsIt->getLength() - 1, 0);
for (hal_index_t i = 0; i < (hal_index_t)ancGenome->getSequenceLength(); ++i) {
CuAssertTrue(_testCase, tsIt->getLength() == 1);
CuAssertTrue(_testCase, tsIt->getStartPosition() == i);
tsIt->toLeft(tsIt->getStartPosition() + 1);
}
tsIt = ancGenome->getTopSegmentIterator(ancGenome->getNumTopSegments() - 1);
tsIt->toReverse();
tsIt->slice(0, tsIt->getLength() - 1);
for (hal_index_t i = ancGenome->getSequenceLength() - 1; i >= 0; --i) {
CuAssertTrue(_testCase, tsIt->getLength() == 1);
CuAssertTrue(_testCase, tsIt->getStartPosition() == i);
tsIt->toRight(tsIt->getStartPosition() - 1);
}
}
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;
}