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#include <alignment/datastructures/anchoring/WeightedInterval.hpp>
WeightedInterval::WeightedInterval() {}
void WeightedInterval::Init(int _size, int _start, int _end, int _readIndex, float _pValue)
{
size = _size;
start = _start;
end = _end;
readIndex = _readIndex;
pValue = _pValue;
qStart = 0;
qEnd = 0;
nAnchors = 0;
totalAnchorSize = 0;
pValueVariance = 0;
pValueNStdDev = 0;
sizeVariance = 0;
sizeNStdDev = 0;
}
WeightedInterval::WeightedInterval(int _size, int _start, int _end, int _readIndex, float _pValue)
{
Init(_size, _start, _end, _readIndex, _pValue);
}
WeightedInterval::WeightedInterval(int _size, int _start, int _end, int _readIndex, float _pValue,
int _qStart, int _qEnd)
{
Init(_size, _start, _end, _readIndex, _pValue);
qStart = _qStart;
qEnd = _qEnd;
}
WeightedInterval::WeightedInterval(int _size, unsigned int _nAnchors, unsigned int _totalAnchorSize,
int _start, int _end, int _readIndex, float _pValue, int _qStart,
int _qEnd, std::vector<ChainedMatchPos> &_matches)
{
Init(_size, _start, _end, _readIndex, _pValue);
qStart = _qStart;
qEnd = _qEnd;
matches = _matches;
nAnchors = _nAnchors;
totalAnchorSize = _totalAnchorSize;
}
float WeightedInterval::PValue() const { return pValue; }
int WeightedInterval::Size() const { return size; }
int WeightedInterval::GetStrandIndex() const { return readIndex; }
void WeightedInterval::SetPValueVariance(float v) { pValueVariance = v; }
void WeightedInterval::SetPValueNStdDev(float v) { pValueNStdDev = v; }
void WeightedInterval::SetSizeVariance(float v) { sizeVariance = v; }
void WeightedInterval::SetSizeNStdDev(float v) { sizeNStdDev = v; }
int WeightedInterval::operator<(const WeightedInterval &intv) const
{
if (size == intv.size) {
return start > intv.start;
} else {
return size < intv.size;
}
}
int WeightedInterval::operator==(const WeightedInterval &intv) const { return size == intv.size; }
// Functions of class CompareWeightedIntervalByPValue
int CompareWeightedIntervalByPValue::operator()(const WeightedInterval &a,
const WeightedInterval &b) const
{
if (a.PValue() != b.PValue()) {
return a.PValue() < b.PValue();
} else {
return a.start < b.start;
}
}
// Functions of class WeightedIntervalSet
WeightedIntervalSet::WeightedIntervalSet() : maxSize(0) {}
WeightedIntervalSet::WeightedIntervalSet(const size_t maxSizeP) : maxSize(maxSizeP) {}
bool WeightedIntervalSet::insert(WeightedInterval &intv)
{
intv.isOverlapping = false;
//
// Make sure this interval is not contained inside any other
// weighted intervals.
//
WeightedIntervalSet::iterator it = (*this).begin();
WeightedIntervalSet::iterator endit = (*this).end();
bool isContained = false;
while (it != endit and isContained == false) {
if (intv.qStart >= (*it).qStart and intv.qEnd <= (*it).qEnd and
intv.start >= (*it).start and intv.end <= (*it).end and
intv.readIndex == (*it).readIndex and intv.pValue >= (*it).pValue) {
//
// This already overlaps an existing interval, don't bother
// trying to add it.
//
isContained = true;
intv.isOverlapping = true;
} else if ((*it).start >= intv.start and (*it).end <= intv.end and
(*it).qStart >= intv.qStart and (*it).qEnd <= intv.qEnd and
(*it).readIndex == intv.readIndex and (*it).pValue >= intv.pValue) {
WeightedIntervalSet::iterator next = it;
++next;
this->erase(it);
it = next;
} else {
++it;
}
}
//
// Take a peek to see if this interval is too low of a score to
// bother attempting to add at all.
//
if (size() >= maxSize and maxSize > 0) {
WeightedIntervalSet::iterator last = (*this).end();
last--;
if (last->pValue < intv.pValue) {
return false;
}
}
if (isContained == false) {
bool addInsert = false;
if (size() == 0) {
addInsert = true;
} else {
it = end();
--it;
if (size() < maxSize or (*it).pValue > intv.pValue) {
addInsert = true;
//
// Keep the size of the stack the same if it is at the limit.
//
if (maxSize != 0 and size() >= maxSize and size() > 0) {
erase(it);
}
}
}
if (addInsert) {
((T_WeightedIntervalMultiSet *)this)->insert(intv);
}
return true;
}
return false;
}
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