// note: takes smart pointer as it maybe added to the results
static hal_size_t mapDown(MappedSegmentPtr mappedSeg, hal_size_t childIndex, list<MappedSegmentPtr> &results,
hal_size_t minLength) {
const Genome *child = mappedSeg->getGenome()->getChild(childIndex);
assert(child != NULL);
hal_size_t added = 0;
if (mappedSeg->isTop() == false) {
TopSegmentIteratorPtr topSegIt = child->getTopSegmentIterator();
SegmentIteratorPtr targetSegIt = mappedSeg->getTargetIteratorPtr();
BottomSegmentIteratorPtr botSegIt = std::dynamic_pointer_cast<BottomSegmentIterator>(targetSegIt);
if (botSegIt->bseg()->hasChild(childIndex) == true && botSegIt->getLength() >= minLength) {
topSegIt->toChild(botSegIt, childIndex);
mappedSeg->setTarget(std::dynamic_pointer_cast<SegmentIterator>(topSegIt));
results.push_back(MappedSegmentPtr(mappedSeg));
++added;
}
} else {
hal_index_t rightCutoff = mappedSeg->getEndPosition();
TopSegmentIteratorPtr topSegIt = mappedSeg->targetAsTop();
hal_index_t startOffset = (hal_index_t)topSegIt->getStartOffset();
hal_index_t endOffset = (hal_index_t)topSegIt->getEndOffset();
BottomSegmentIteratorPtr botSegIt = mappedSeg->getGenome()->getBottomSegmentIterator();
botSegIt->toParseDown(topSegIt);
do {
BottomSegmentIteratorPtr newBotSegIt = botSegIt->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
TopSegmentIteratorPtr backTopSegIt = topSegIt->clone();
backTopSegIt->toParseUp(newBotSegIt);
hal_index_t startBack = (hal_index_t)backTopSegIt->getStartOffset();
hal_index_t endBack = (hal_index_t)backTopSegIt->getEndOffset();
assert(startBack >= startOffset);
assert(endBack >= endOffset);
SegmentIteratorPtr newSourceSegIt = mappedSeg->sourceClone();
hal_index_t startDelta = startBack - startOffset;
hal_index_t endDelta = endBack - endOffset;
assert((hal_index_t)newSourceSegIt->getLength() > startDelta + endDelta);
newSourceSegIt->slice(newSourceSegIt->getStartOffset() + startDelta, newSourceSegIt->getEndOffset() + endDelta);
MappedSegmentPtr newMappedSeg(new MappedSegment(newSourceSegIt, newBotSegIt));
assert(newMappedSeg->isTop() == false);
assert(newMappedSeg->getSource()->getGenome() == mappedSeg->getSource()->getGenome());
added += mapDown(newMappedSeg, childIndex, results, minLength);
// stupid that we have to make this check but odn't want to
// make fundamental api change now
if (botSegIt->getEndPosition() != rightCutoff) {
botSegIt->toRight(rightCutoff);
} else {
break;
}
} while (true);
}
return added;
}
// note: takes smart pointer as it maybe added to the results
static hal_size_t mapUp(MappedSegmentPtr mappedSeg, list<MappedSegmentPtr> &results, bool doDupes, hal_size_t minLength) {
const Genome *parent = mappedSeg->getGenome()->getParent();
assert(parent != NULL);
hal_size_t added = 0;
if (mappedSeg->isTop() == true) {
BottomSegmentIteratorPtr botSegIt = parent->getBottomSegmentIterator();
TopSegmentIteratorPtr topSegIt = mappedSeg->targetAsTop();
if (topSegIt->tseg()->hasParent() == true && topSegIt->getLength() >= minLength &&
(doDupes == true || topSegIt->tseg()->isCanonicalParalog() == true)) {
botSegIt->toParent(topSegIt);
mappedSeg->setTarget(std::dynamic_pointer_cast<SegmentIterator>(botSegIt));
results.push_back(mappedSeg);
++added;
}
} else {
hal_index_t rightCutoff = mappedSeg->getEndPosition();
BottomSegmentIteratorPtr botSegIt = mappedSeg->targetAsBottom();
hal_index_t startOffset = (hal_index_t)botSegIt->getStartOffset();
hal_index_t endOffset = (hal_index_t)botSegIt->getEndOffset();
TopSegmentIteratorPtr topSegIt = mappedSeg->getGenome()->getTopSegmentIterator();
topSegIt->toParseUp(botSegIt);
do {
TopSegmentIteratorPtr newTopSegIt = topSegIt->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 backBotSegIt = botSegIt->clone();
backBotSegIt->toParseDown(newTopSegIt);
hal_index_t startBack = (hal_index_t)backBotSegIt->getStartOffset();
hal_index_t endBack = (hal_index_t)backBotSegIt->getEndOffset();
assert(startBack >= startOffset);
assert(endBack >= endOffset);
SegmentIteratorPtr newSourceSegIt = mappedSeg->sourceClone();
hal_index_t startDelta = startBack - startOffset;
hal_index_t endDelta = endBack - endOffset;
assert((hal_index_t)newSourceSegIt->getLength() > startDelta + endDelta);
newSourceSegIt->slice(newSourceSegIt->getStartOffset() + startDelta, newSourceSegIt->getEndOffset() + endDelta);
MappedSegmentPtr newMappedSeg(new MappedSegment(newSourceSegIt, newTopSegIt));
assert(newMappedSeg->isTop() == true);
assert(newMappedSeg->getSource()->getGenome() == mappedSeg->getSource()->getGenome());
added += mapUp(newMappedSeg, results, doDupes, minLength);
// stupid that we have to make this check but odn't want to
// make fundamental api change now
if (topSegIt->getEndPosition() != rightCutoff) {
topSegIt->toRight(rightCutoff);
} else {
break;
}
} while (true);
}
return added;
}
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;
}
// 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;
}