本文整理汇总了C++中Spectrum::initializeHypergeometricNK方法的典型用法代码示例。如果您正苦于以下问题：C++ Spectrum::initializeHypergeometricNK方法的具体用法？C++ Spectrum::initializeHypergeometricNK怎么用？C++ Spectrum::initializeHypergeometricNK使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Spectrum的用法示例。
在下文中一共展示了Spectrum::initializeHypergeometricNK方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: sortAndPrepareSpectra
void Spectra::sortAndPrepareSpectra(){
long totskippedpeaks = 0;
long totlen = 0;
long totlenB = 0;
//sort by parent mass
sort(spectra.begin(), spectra.end(), SpectrumComparator()); //greater<Spectrum*>());
//rearrange spectra
if(se1->rearrangespectra == true){
if(se1->writespecpos == true) writeSpectrumPositionsInMemory(se1->getOutFileName("specposfirst"));
if(se1->outputlevel > 2) cout << "\nRearranging spectra in memory to increase performance for long-running searches. This may take seconds to minutes." << flush;
//rearrange spectra in memory
Spectrum *src, *destinationspectrum;
vector<Spectrum*> spectraold;
for(int i = 0; i < spectra.size(); i++){
src = spectra[i];
destinationspectrum = new Spectrum(src);
spectra[i] = destinationspectrum;
spectraold.push_back(src);
}
for(int i = 0; i < spectraold.size(); i++){
delete spectraold[i];
}
spectraold.clear();
if(se1->writespecpos == true) writeSpectrumPositionsInMemory(se1->getOutFileName("specposafter"));
}
//initialize BestMatches, index them for writing results later on
for(int i = 0; i < spectra.size(); i++){
spectra[i]->initializeBestMatches();
//spectra[i]->bestmatches1->i = i;
}
//collect spectrum statistics
for(int i = 0; i < spectra.size(); i++){
parentmasses.push_back(spectra[i]->parentmassMH);
totlen += spectra[i]->lengthgood;
if (se1->outputlevel >2 ) cout << spectra[i] -> lengthgood << endl;
totlenB += spectra[i]->lengthB;
totskippedpeaks += spectra[i]->skippedpeaks;
if(se1->outputlevel > 5) cout << "\nSpectra::sortSpectraAndExtractPM: pointer " << (long)spectra[i] << " parent mass " << spectra[i]->parentmassMH;
}
//initialize spectrum parameters for hypergeometric score
unreachablebins1->initialize();
for(int i = 0; i < spectra.size(); i++){
Spectrum *spec = spectra[i];
spec->initializeHypergeometricNK(); //naive estimation for N and K
//reestimation for N
spec->N = spec->parentmassMHB - unreachablebins1->getTotal(se1->trypticendsrequired) - se1->blockedbins;
//reestimation for K
spec->K = unreachablebins1->estimateK(spec->binaryB, spec->parentmassMHB, se1->trypticendsrequired);
//avoid exceptions in hypergeometric calculations
if(spec->N < spec->K) spec->N = spec->K;
}
//set parent mass limits for tuple generation
if(parentmasses.size() > 0) se1->setMinMaxPM(parentmasses[0], parentmasses[spectra.size() - 1]);
//progressreport statistics
double sf = se1->dnaAA1->scaling_factor;
if(se1->outputlevel > 2){
if(spectra.size() > 0){
cout << "\nSpectra::sortSpectraAndExtractPM:";
cout << "\nThere are " << spectra.size() << " spectra which were sorted according to their parent mass.";
cout << "\nA spectrum contains on average " << (double)totlen / (double)spectra.size() << " correct peaks.";
cout << "\nAfter preprocessing, the spectrum contains on average " << (double)totlenB / (double)spectra.size() << " peaks.";
cout << "\nA spectrum contains on average " << (double)totskippedpeaks / (double) spectra.size() << " peaks of m/z < 0 or m/z > parentmass. Those were skipped.";
cout << "\nLowest parent mass in spectra : " << parentmasses[0]/sf << " Lowest theoretical parent mass considered: " << se1->min_monoparentmassMH / sf;
cout << "\nHighest parent mass in spectra: " << parentmasses[spectra.size() - 1] / sf << " Highest theoretical parent mass considered: " << se1->max_monoparentmassMH / sf;
}else{
cout << "\nSpectra::sortSpectraAndExtractPM: No spectra were parsed!";
}
}
}