void GCFramePlotAlgorithm::calculate(QVector<float>& res, U2SequenceObject* o, const U2Region& vr,
const GSequenceGraphWindowData* d, U2OpStatus &os)
{
assert(d!=NULL);
int nSteps = GSequenceGraphUtils::getNumSteps(vr, d->window, d->step);
res.reserve(nSteps);
const QByteArray &seq = getSequenceData(o, os);
CHECK_OP(os, );
int startPos = vr.startPos;
windowStrategyWithoutMemorize(res, seq, startPos, d, nSteps, os);
}
void EntropyGraphAlgorithm::calculate(QVector<float>& res, U2SequenceObject* o, const U2Region& vr,
const GSequenceGraphWindowData* d, U2OpStatus &os)
{
assert(d!=NULL);
int nSteps = GSequenceGraphUtils::getNumSteps(vr, d->window, d->step);
res.reserve(nSteps);
const QByteArray &seq = getSequenceData(o, os);
CHECK_OP(os, );
const DNAAlphabet* al = o->getAlphabet();
// prepare index -> TODO: make it once and cache!
IndexedMapping3To1<int> index(al->getAlphabetChars(), 0);
int* mapData = index.mapData();
int indexSize = index.getMapSize();
// algorithm
float log10_2 = log10(2.0);
const char* seqStr = seq.constData();
for (int i = 0; i < nSteps; i++) {
int start = vr.startPos + i * d->step;
int end = start + d->window;
for (int x = start; x < end-2; x++) {
int& val = index.mapNC(seqStr + x);
val++;
}
//derive entropy from triplets and zero them
float total = end-start-2;
float ent = 0;
for (int j = 0; j < indexSize; j++) {
CHECK_OP(os, );
int ifreq = mapData[j];
if (ifreq == 0) {
continue;
}
mapData[j] = 0; //zero triplets
float freq = ifreq / total;
ent -= freq*log10(freq)/log10_2;
}
res.append(ent);
}
}
