void TopSegmentStruct::applyTo(TopSegmentIteratorPtr it) const {
TopSegment *seg = it->getTopSegment();
seg->setCoordinates(_startPosition, _length);
seg->setNextParalogyIndex(_nextParalogyIndex);
seg->setParentIndex(_parentIndex);
seg->setParentReversed(_parentReversed);
seg->setBottomParseIndex(_bottomParseIndex);
}
void Genome::fixParseInfo()
{
if (getParent() == NULL || getNumChildren() == 0)
{
return;
}
// copied from CactusHalConverter::updateRootParseInfo() in
// cactus2hal/src/cactusHalConverter.cpp
BottomSegmentIteratorPtr bottomIterator =
getBottomSegmentIterator();
TopSegmentIteratorPtr topIterator = getTopSegmentIterator();
BottomSegmentIteratorConstPtr bend = getBottomSegmentEndIterator();
TopSegmentIteratorConstPtr tend = getTopSegmentEndIterator();
int top = 0, bot = 0;
while (bottomIterator != bend && topIterator != tend)
{
bool bright = false;
bool tright = false;
BottomSegment* bseg = bottomIterator->getBottomSegment();
TopSegment* tseg = topIterator->getTopSegment();
hal_index_t bstart = bseg->getStartPosition();
hal_index_t bendidx = bstart + (hal_index_t)bseg->getLength();
hal_index_t tstart = tseg->getStartPosition();
hal_index_t tendidx = tstart + (hal_index_t)tseg->getLength();
if (bstart >= tstart && bstart < tendidx)
{
bseg->setTopParseIndex(tseg->getArrayIndex());
}
if (bendidx <= tendidx || bstart == bendidx)
{
bright = true;
}
if (tstart >= bstart && tstart < bendidx)
{
tseg->setBottomParseIndex(bseg->getArrayIndex());
}
if (tendidx <= bendidx || tstart == tendidx)
{
tright = true;
}
assert(bright || tright);
if (bright == true)
{
bot += 1;
bottomIterator->toRight();
}
if (tright == true)
{
top += 1;
topIterator->toRight();
}
}
}