void LodExtract::writeUnsampledSequence(const Sequence* outSequence,
SegmentIteratorPtr outSegment)
{
outSegment->setCoordinates(outSequence->getStartPosition(),
outSequence->getSequenceLength());
if (outSegment->isTop())
{
assert(outSequence->getNumTopSegments() == 1);
TopSegmentIteratorPtr top = outSegment.downCast<TopSegmentIteratorPtr>();
top->setParentIndex(NULL_INDEX);
top->setParentReversed(false);
top->setNextParalogyIndex(NULL_INDEX);
top->setBottomParseIndex(NULL_INDEX);
}
else
{
assert(outSequence->getNumBottomSegments() == 1);
BottomSegmentIteratorPtr bottom =
outSegment.downCast<BottomSegmentIteratorPtr>();
hal_size_t numChildren = bottom->getNumChildren();
for (hal_size_t childNum = 0; childNum < numChildren; ++childNum)
{
bottom->setChildIndex(childNum, NULL_INDEX);
bottom->setChildReversed(childNum, false);
}
bottom->setTopParseIndex(NULL_INDEX);
}
}
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;
}
int MappedSegment::fastComp(const SegmentIteratorPtr &s1, const SegmentIteratorPtr &s2) {
// compare without accessing anything from disk (ie using only index
// and offset)
int res = 0;
assert(s1->getGenome() == s2->getGenome());
if (s1->isTop() != s2->isTop()) {
res = boundComp(s1, s2);
if (res == 0) {
res = slowComp(s1, s2);
}
} else {
if (s1->getArrayIndex() < s2->getArrayIndex()) {
res = -1;
} else if (s1->getArrayIndex() > s2->getArrayIndex()) {
res = 1;
} else {
hal_offset_t so1 = s1->getStartOffset();
hal_offset_t eo1 = s1->getEndOffset();
if (s1->getReversed()) {
swap(so1, eo1);
}
hal_offset_t so2 = s2->getStartOffset();
hal_offset_t eo2 = s2->getEndOffset();
if (s2->getReversed()) {
swap(so2, eo2);
}
if (so1 < so2) {
res = -1;
} else if (so1 > so2) {
res = 1;
} else if (eo1 > eo2) {
res = -1;
} else if (eo1 < eo2) {
res = 1;
}
}
}
assert(res == slowComp(s1, s2));
return res;
}
// note: takes smart pointer as it maybe added to the results
static hal_size_t mapSelf(MappedSegmentPtr mappedSeg, list<MappedSegmentPtr> &results, hal_size_t minLength) {
hal_size_t added = 0;
if (mappedSeg->isTop() == true) {
SegmentIteratorPtr target = mappedSeg->getTargetIteratorPtr();
SegmentIteratorPtr source = mappedSeg->getSourceIteratorPtr();
TopSegmentIteratorPtr top = std::dynamic_pointer_cast<TopSegmentIterator>(target);
TopSegmentIteratorPtr topCopy = top->clone();
do {
// FIXME: why isn't clone() polymorphic?
SegmentIteratorPtr newSource;
if (source->isTop()) {
newSource = std::dynamic_pointer_cast<TopSegmentIterator>(source)->clone();
} else {
newSource = std::dynamic_pointer_cast<BottomSegmentIterator>(source)->clone();
}
TopSegmentIteratorPtr newTop = topCopy->clone();
MappedSegmentPtr newMappedSeg(new MappedSegment(newSource, newTop));
assert(newMappedSeg->getGenome() == mappedSeg->getGenome());
assert(newMappedSeg->getSource()->getGenome() == mappedSeg->getSource()->getGenome());
results.push_back(newMappedSeg);
++added;
if (topCopy->tseg()->hasNextParalogy()) {
topCopy->toNextParalogy();
}
} while (topCopy->tseg()->hasNextParalogy() == true && topCopy->getLength() >= minLength &&
topCopy->getArrayIndex() != top->getArrayIndex());
} else if (mappedSeg->getGenome()->getParent() != NULL) {
hal_index_t rightCutoff = mappedSeg->getEndPosition();
BottomSegmentIteratorPtr bottom = mappedSeg->targetAsBottom();
hal_index_t startOffset = (hal_index_t)bottom->getStartOffset();
hal_index_t endOffset = (hal_index_t)bottom->getEndOffset();
TopSegmentIteratorPtr top = mappedSeg->getGenome()->getTopSegmentIterator();
top->toParseUp(bottom);
do {
TopSegmentIteratorPtr topNew = top->clone();
// we map the new target back to see how the offsets have
// changed. these changes are then applied to the source segment
// as deltas
BottomSegmentIteratorPtr bottomBack = bottom->clone();
bottomBack->toParseDown(topNew);
hal_index_t startBack = (hal_index_t)bottomBack->getStartOffset();
hal_index_t endBack = (hal_index_t)bottomBack->getEndOffset();
assert(startBack >= startOffset);
assert(endBack >= endOffset);
SegmentIteratorPtr newSource = mappedSeg->sourceClone();
hal_index_t startDelta = startBack - startOffset;
hal_index_t endDelta = endBack - endOffset;
assert((hal_index_t)newSource->getLength() > startDelta + endDelta);
newSource->slice(newSource->getStartOffset() + startDelta, newSource->getEndOffset() + endDelta);
MappedSegmentPtr newMappedSeg(new MappedSegment(newSource, topNew));
assert(newMappedSeg->isTop() == true);
assert(newMappedSeg->getSource()->getGenome() == mappedSeg->getSource()->getGenome());
added += mapSelf(newMappedSeg, results, minLength);
// stupid that we have to make this check but odn't want to
// make fundamental api change now
if (top->getEndPosition() != rightCutoff) {
top->toRight(rightCutoff);
} else {
break;
}
} while (true);
}
return added;
}
