本文整理汇总了C++中Genome::readRFPFile方法的典型用法代码示例。如果您正苦于以下问题：C++ Genome::readRFPFile方法的具体用法？C++ Genome::readRFPFile怎么用？C++ Genome::readRFPFile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Genome的用法示例。
在下文中一共展示了Genome::readRFPFile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: main
int main()
{
unsigned index;
bool fromRestart = false;
std::string modelToRun = "FONSE";
bool withPhi = false;
std::cout << "Initializing MCMCAlgorithm object---------------" << std::endl;
int samples = 100;
int thinning = 10;
int useSamples = 100;
unsigned numMixtures = 1;
std::cout << "\t# Samples: " << samples << "\n";
std::cout << "\tThinning: " << thinning << "\n";
std::cout << "\t # Samples used: " << useSamples << "\n";
MCMCAlgorithm mcmc = MCMCAlgorithm(samples, thinning, 10, true, true, false);
mcmc.setRestartFileSettings("RestartFile.txt", 20, true);
std::cout << "Done!-------------------------------\n\n\n";
if (modelToRun == "FONSE") {
std::cout << "initialize Genome object--------------------------" << std::endl;
Genome genome;
std::cout << "Reading fasta file\n";
genome.readFasta("C:/Users/Alan/Documents/GitHub/RibModelDev/data/FONSE/nse2000.fasta");
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "Initializing shared parameter variables---------------\n";
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
std::vector<double> sphi_init(numMixtures, 1);
/* For 1 mixture */
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = 0u;
}
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
std::cout << "Done!------------------------\n\n\n";
//ROCParameter parameter;
FONSEParameter parameter;
std::cout << "initialize Parameter object" << std::endl;
std::string mixDef = Parameter::allUnique;
if (fromRestart)
{
FONSEParameter tmp("C:/Users/Alan/Documents/GitHub/RibModelDev/DevRScripts/10restartfile.rst");
parameter = tmp;
}
else
{
//ROCParameter tmp(sphi_init, nu/mMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
FONSEParameter tmp(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
for (unsigned i = 0u; i < numMixtures; i++)
{
unsigned selectionCategry = tmp.getSelectionCategory(i);
std::cout << "Sphi_init for selection category " << selectionCategry << ": " << sphi_init[selectionCategry] << std::endl;
}
std::cout << "\t# mixtures: " << numMixtures << "\n";
std::cout << "\tmixture definition: " << mixDef << "\n";
//std::vector<std::string> files(1);
//files[0] = std::string("C:/Users/Jeremy/Documents/GitHub/RibModelDev/data/FONSE/Scereviciae.mut.csv");
//tmp.initMutationCategories(files, tmp.getNumMutationCategories());
//tmp.InitializeSynthesisRate(genome, sphi_init[0]);
std::vector<double> phiVals = parameter.readPhiValues("C:/Users/Alan/Documents/GitHub/RibModelDev/data/FONSE/nse2000.phi.csv");
tmp.InitializeSynthesisRate(phiVals);
parameter = tmp;
}
std::cout << "done initialize Parameter object" << std::endl;
std::cout << "Initializing Model object\n";
bool withPhi = true;
FONSEModel model;
//ROCModel model(withPhi);
model.setParameter(parameter);
std::cout << "starting MCMC for FONSE" << std::endl;
mcmc.run(genome, model, 1, 0);
std::cout << std::endl << "Finished MCMC for FONSE" << std::endl;
}
else if (modelToRun == "RFP")
{
std::cout << "Initializing Genome object--------------------------" << std::endl;
Genome genome;
genome.readRFPFile("C:/Users/Jeremy/Documents/GitHub/RibModelDev/data/rfp/rfp.counts.by.codon.and.gene.GSE63789.wt.csv");
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "Initializing shared parameter variables---------------\n";
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
std::vector<double> sphi_init(numMixtures, 1);
if (numMixtures == 1)
//.........这里部分代码省略.........