void Liftover::liftInterval()
{
PositionMap posCacheMap;
_colIt = _srcSequence->getColumnIterator(&_tgtSet, 0, _inStart, _inEnd - 1);
while (true)
{
const ColumnMap* cMap = _colIt->getColumnMap();
for (ColumnMap::const_iterator i = cMap->begin(); i != cMap->end(); ++i)
{
if (i->first->getGenome() == _tgtGenome)
{
const DNASet* dSet = i->second;
const Sequence* seq = i->first;
// if we're not adding the column, don't bother keeping track
hal_size_t paralogyFactor = _addDupeColumn ? dSet->size() : 0;
SeqIndex seqIdx(seq, paralogyFactor);
for (DNASet::const_iterator j = dSet->begin(); j != dSet->end(); ++j)
{
pair<PositionMap::iterator, bool> res =
posCacheMap.insert(pair<SeqIndex, PositionCache*>(seqIdx, NULL));
if (res.second == true)
{
res.first->second = new PositionCache();
}
res.first->second->insert((*j)->getArrayIndex());
}
}
}
if (_colIt->lastColumn() == true)
{
break;
}
_colIt->toRight();
}
PositionMap::iterator pcmIt;
for (pcmIt = posCacheMap.begin(); pcmIt != posCacheMap.end(); ++pcmIt)
{
const Sequence* seq = pcmIt->first.first;
_outParalogy = pcmIt->first.second;
hal_size_t seqStart = seq->getStartPosition();
PositionCache* posCache = pcmIt->second;
const IntervalSet* iSet = posCache->getIntervalSet();
_outName = seq->getName();
for (IntervalSet::const_iterator k = iSet->begin(); k != iSet->end(); ++k)
{
_outStart = k->second - seqStart;
_outEnd = k->first + 1 - seqStart;
writeBedLine();
}
delete posCache;
}
}
void ColumnLiftover::liftInterval(BedList& mappedBedLines)
{
PositionMap posCacheMap;
PositionMap revCacheMap;
_colIt = _srcSequence->getColumnIterator(&_tgtSet, 0, _bedLine._start,
_bedLine._end - 1,
!_traverseDupes,
false,
_bedLine._strand == '-');
while (true)
{
const ColumnMap* cMap = _colIt->getColumnMap();
for (ColumnMap::const_iterator i = cMap->begin(); i != cMap->end(); ++i)
{
if (i->first->getGenome() == _tgtGenome)
{
const DNASet* dSet = i->second;
const Sequence* seq = i->first;
// if we're not adding the column, don't bother keeping track
SeqIndex seqIdx(seq, 0);
for (DNASet::const_iterator j = dSet->begin(); j != dSet->end(); ++j)
{
pair<PositionMap::iterator, bool> res;
if ((*j)->getReversed() == false)
{
res =
posCacheMap.insert(pair<SeqIndex, PositionCache*>(seqIdx, NULL));
}
else
{
res =
revCacheMap.insert(pair<SeqIndex, PositionCache*>(seqIdx, NULL));
}
if (res.second == true)
{
res.first->second = new PositionCache();
}
res.first->second->insert((*j)->getArrayIndex());
}
}
}
if (_colIt->lastColumn() == true)
{
break;
}
_colIt->toRight();
}
PositionMap::iterator pcmIt;
for (pcmIt = posCacheMap.begin(); pcmIt != posCacheMap.end(); ++pcmIt)
{
const Sequence* seq = pcmIt->first.first;
_outParalogy = pcmIt->first.second;
hal_size_t seqStart = seq->getStartPosition();
PositionCache* posCache = pcmIt->second;
const IntervalSet* iSet = posCache->getIntervalSet();
for (IntervalSet::const_iterator k = iSet->begin(); k != iSet->end(); ++k)
{
mappedBedLines.push_back(_bedLine);
BedLine& outBedLine = mappedBedLines.back();
outBedLine._blocks.clear();
outBedLine._chrName = seq->getName();
outBedLine._start = k->second - seqStart;
outBedLine._end = k->first + 1 - seqStart;
outBedLine._strand = _bedLine._strand == '.' ? '.' : '+';
outBedLine._srcStart = NULL_INDEX; // not available from posMap
}
delete posCache;
}
for (pcmIt = revCacheMap.begin(); pcmIt != revCacheMap.end(); ++pcmIt)
{
const Sequence* seq = pcmIt->first.first;
_outParalogy = pcmIt->first.second;
hal_size_t seqStart = seq->getStartPosition();
PositionCache* posCache = pcmIt->second;
const IntervalSet* iSet = posCache->getIntervalSet();
for (IntervalSet::const_iterator k = iSet->begin(); k != iSet->end(); ++k)
{
mappedBedLines.push_back(_bedLine);
BedLine& outBedLine = mappedBedLines.back();
outBedLine._blocks.clear();
outBedLine._chrName = seq->getName();
outBedLine._start = k->second - seqStart;
outBedLine._end = k->first + 1 - seqStart;
outBedLine._strand = _bedLine._strand == '.' ? '.' : '-';
outBedLine._srcStart = NULL_INDEX; // not available from posMap
}
delete posCache;
}
}
void csMeshGenerator::GeneratePositions (int cidx, csMGCell& cell,
csMGPositionBlock* block)
{
random.Initialize ((unsigned int)cidx); // @@@ Consider using a better seed?
block->positions.Empty ();
cell.needPositions = false;
const csBox2& box = cell.box;
float box_area = box.Area ();
CS_ALLOC_STACK_ARRAY(float, geoRadii, geometries.GetSize ());
for (size_t i = 0 ; i < geometries.GetSize () ; i++)
geoRadii[i] = geometries[i]->GetRadius();
PositionMap positionMap (geoRadii, geometries.GetSize (),
box, cidx);
if(minRadius < 0.0f)
{
for (size_t i = 0 ; i < geometries.GetSize () ; i++)
{
if(geometries[i]->GetRadius() < minRadius || minRadius < 0.0f)
{
minRadius = geometries[i]->GetRadius();
}
}
}
size_t i, j;
for (size_t g = 0 ; g < geometries.GetSize () ; g++)
{
csMGPosition pos;
pos.geom_type = g;
size_t mpos_count = geometries[g]->GetManualPositionCount (cidx);
float density = geometries[g]->GetDensity () * default_density_factor;
size_t count = (mpos_count > 0)? mpos_count : size_t (density * box_area);
/* Estimation of actual number of generated positions
* Count how many of the generated positions have actually caused a mesh
* to be placed (densities < 1 will cause some position to be rejected...).
* After generating minSamples positions, estimate the total number
* of actually used positions, and break if that is reached. */
size_t minSamples = ceil (sqrtf (count));
size_t positionsUsed = 0;
const csArray<csMGDensityMaterialFactor>& mftable
= geometries[g]->GetDensityMaterialFactors ();
float default_material_factor
= geometries[g]->GetDefaultDensityMaterialFactor ();
bool do_material = mftable.GetSize () > 0;
for (j = 0 ; j < count ; j++)
{
float pos_factor;
float r = geometries[g]->csMeshGeneratorGeometry::GetRadius();
float x;
float z;
PositionMap::AreaID area;
if (mpos_count == 0)
{
if(!positionMap.GetRandomPosition (r, x, z, area))
{
// Ran out of room in this cell.
return;
}
geometries[g]->GetDensityMapFactor (x, z, pos_factor);
}
else
{
csVector2 mpos = geometries[g]->GetManualPosition (cidx,j);
x = mpos.x;
z = mpos.y;
pos_factor = 1.0f;
}
if (!((pos_factor < 0.0001) ||
(pos_factor < 0.9999 && random.Get () > pos_factor)))
{
csVector3 start (x, samplebox.MaxY (), z);
csVector3 end = start;
end.y = samplebox.MinY ();
bool hit = false;
iMaterialWrapper* hit_material = 0;
for (i = 0 ; i < cell.meshes.GetSize () ; i++)
{
csHitBeamResult rc = cell.meshes[i]->HitBeam (start, end,
do_material);
if (rc.hit)
{
pos.position = rc.isect;
end.y = rc.isect.y + 0.0001;
hit_material = rc.material;
hit = true;
}
}
if (hit)
{
if (do_material)
{
// We use material density tables.
float factor = default_material_factor;
for (size_t mi = 0 ; mi < mftable.GetSize () ; mi++)
{
if (mftable[mi].material == hit_material)
{
factor = mftable[mi].factor;
break;
}
}
if (factor < 0.0001 || (factor < 0.9999 && random.Get () > factor))
{
hit = false;
}
}
if (hit)
{
int rot = int (random.Get (CS_GEOM_MAX_ROTATIONS));
if (rot < 0) rot = 0;
else if (rot >= CS_GEOM_MAX_ROTATIONS) rot = CS_GEOM_MAX_ROTATIONS-1;
pos.rotation = rot;
block->positions.Push (new csMGPosition (pos));
positionsUsed++;
if (mpos_count == 0)
positionMap.MarkAreaUsed (area, r, x, z);
}
}
}
/* Estimate how many positions will actually be used based on the
* running count of used positions. */
size_t estimatedCount = ceil (count * (float (positionsUsed) / (j+1)));
// If enough samples have been collected...
if (j >= minSamples)
{
// ... and the estimated count has been hit, exit early.
if (positionsUsed >= estimatedCount)
break;
}
}
}
}
