void SandCMapABF::CalculateForces( int stepNum, double *masses, double *positions, double *forces )
{
/* Change the masses and positions array to the STL vectors */
vector<double> vMasses (masses , masses +_nAtoms);
vector<double> vPositions(positions, positions+_hdim );
/* Compute the CV value of the current configuration and its related Jacobian */
try
{
_bDistance ? _sandcv->CalculateCVdist(vPositions) : _sandcv->CalculateCV(vPositions);
/* Calculate the Abf forces and return it */
vector<double> forceABF( _abf->CalculateForce( stepNum, vMasses, vPositions, _sandcv->GetValue(), _sandcv->GetJacobian() ) );
/* Copy the calculated forces to pass to the MD engine */
copy( forceABF.begin(), forceABF.end(), forces );
}
catch (const runtime_error &e)
{
fill( forces, forces+_hdim, 0.0 );
cout<<"NO FORCE is applied because "<<e.what()<<endl;
}
}
/**
* @brief Run the analysis.
*/
void CNAnalysisMethodMosaicism::run()
{
Verbose::out(1, "CNAnalysisMethodMosaicism::run(...) start");
isSetup();
determineLocalProbeSets();
m_vSegments.deleteAll();
vector<int> vChromosomes = getChromosomes(getProbeSets());
int iLastChromosome = vChromosomes[vChromosomes.size() - 1];
Verbose::progressBegin(1,"CNAnalysisMethodMosaicism::run(...) ", iLastChromosome, 1, iLastChromosome);
for (int i = 0; (i < vChromosomes.size()); i++)
{
int iChromosome = vChromosomes[i];
if (iChromosome == 255) {continue;}
if (iChromosome == m_iYChromosome && !m_bRunYChromosome) {
continue;
}
int iProbeSetCount = getProbeSetCount(iChromosome, getProbeSets());
if (iProbeSetCount == 0) continue; // probably 23 or Y
Verbose::progressStep(1);
// debug: for later use
m_current_experiment=getExperiment()->getExperimentName();
m_current_chr=ToStr(vChromosomes[i]);
std::vector<int> vPositions(iProbeSetCount);
double* pLog2Ratios = new double[iProbeSetCount];
int iStartChromosome = getChrBounds(iChromosome, getProbeSets()).first;
m_iStartIndex = 0;
m_iEndIndex = (iProbeSetCount - 1);
CNProbeSetArray* psets = getProbeSets();
for (int j = 0; (j < iProbeSetCount); j++)
{
vPositions[j] = psets->at(iStartChromosome + j)->getPosition();
pLog2Ratios[j] = psets->at(iStartChromosome + j)->getLog2Ratio();
}
double* pRunMean = new double[iProbeSetCount];
int iMarkerBandwidth = Min(iProbeSetCount, m_iMarkerBandwidth);
runmean(pLog2Ratios, pRunMean, &iProbeSetCount, &iMarkerBandwidth);
// debug - this has been ruled out.
#ifdef MOSAICISM_DEBUG_MEANS
writeRunningMeans(m_current_experiment+".chr"+m_current_chr+".means.tsv",
iProbeSetCount,
pLog2Ratios,
pRunMean);
#endif
CNSegmentArray vSegments;
newSegments((unsigned char)iChromosome, pRunMean, iProbeSetCount, vPositions, vSegments);
// dont need this anymore.
delete[] pRunMean;
// debug
#ifdef MOSAICISM_DEBUG
vSegments.writeToTsv(m_current_experiment+"-chr"+m_current_chr+".newseg1.tsv");
#endif
//
cleanSegments(vSegments);
// Set marker count and median marker distance.
for (int iSegmentIndex = 0; (iSegmentIndex < vSegments.getCount()); iSegmentIndex++)
{
CNSegment* p = vSegments.getAt(iSegmentIndex);
p->setStartPosition(vPositions[p->getStartIndex()]);
p->setEndPosition(vPositions[p->getEndIndex()]);
calculateSegmentConfidence(pLog2Ratios, p);
int iMarkerCount = 0;
for (unsigned int iProbeSetIndex = 0; (iProbeSetIndex < vPositions.size()); iProbeSetIndex++)
{
if ((vPositions[iProbeSetIndex] >= p->getStartPosition()) && (vPositions[iProbeSetIndex] <= p->getEndPosition()))
{
iMarkerCount++;
}
}
if (iMarkerCount < 2)
{
p->setMarkerCount(iMarkerCount);
p->setMeanMarkerDistance(0);
}
else
{
AffxMultiDimensionalArray<int> vMarkerDistances(iMarkerCount - 1);
int iIndex = 0;
for (unsigned int iProbeSetIndex = 1; (iProbeSetIndex < vPositions.size()); iProbeSetIndex++)
{
int iPrevPosition = vPositions[iProbeSetIndex - 1];
int iNextPosition = vPositions[iProbeSetIndex];
if ((iPrevPosition >= p->getStartPosition()) && (iNextPosition <= p->getEndPosition()))
{
getProbeSets()->getAt(iStartChromosome + iProbeSetIndex - 1)->setMosaicismMixture(p->getMixtureAsDouble());
getProbeSets()->getAt(iStartChromosome + iProbeSetIndex)->setMosaicismMixture(p->getMixtureAsDouble());
vMarkerDistances.set(iIndex, (iNextPosition - iPrevPosition));
iIndex++;
}
}
p->setMarkerCount(iMarkerCount);
p->setMeanMarkerDistance(vMarkerDistances.mean());
}
// transfer of ownership from vSegments to m_vSegments
m_vSegments.add(p);
}
#ifdef MOSAICISM_DEBUG
vSegments.writeToTsv(m_current_experiment+"-chr"+m_current_chr+".seg2.tsv");
#endif
// why "nullAll()" instead of "deleteAll()"?
// because the pointers were copied to m_vSegments above and
// AffxArray will delete the pointers in vSegments when it goes out of scope.
vSegments.nullAll();
delete[] pLog2Ratios;
}
Verbose::progressEnd(1, "Done");
Verbose::out(1, "CNAnalysisMethodMosaicism::run(...) end");
}
