本文整理汇总了C++中Alphabet::getSize方法的典型用法代码示例。如果您正苦于以下问题：C++ Alphabet::getSize方法的具体用法？C++ Alphabet::getSize怎么用？C++ Alphabet::getSize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Alphabet的用法示例。
在下文中一共展示了Alphabet::getSize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(int args, char** argv)
{
cout << "******************************************************************" << endl;
cout << "* Bio++ Computation of site likelihoods inside mixed models *" << endl;
cout << "* Version 2.2.0. *" << endl;
cout << "* Author: L. Guéguen Last Modif.: 25/09/14 *" << endl;
cout << "******************************************************************" << endl;
cout << endl;
if (args == 1)
{
help();
return 0;
}
try
{
BppApplication bppmixedlikelihoods(args, argv, "BppMixedLikelihoods");
bppmixedlikelihoods.startTimer();
Alphabet* alphabet = SequenceApplicationTools::getAlphabet(bppmixedlikelihoods.getParams(), "", false);
auto_ptr<GeneticCode> gCode;
CodonAlphabet* codonAlphabet = dynamic_cast<CodonAlphabet*>(alphabet);
if (codonAlphabet) {
string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppmixedlikelihoods.getParams(), "Standard", "", true, true);
ApplicationTools::displayResult("Genetic Code", codeDesc);
gCode.reset(SequenceApplicationTools::getGeneticCode(codonAlphabet->getNucleicAlphabet(), codeDesc));
}
// get the data
VectorSiteContainer* allSites = SequenceApplicationTools::getSiteContainer(alphabet, bppmixedlikelihoods.getParams());
VectorSiteContainer* sites = SequenceApplicationTools::getSitesToAnalyse(*allSites, bppmixedlikelihoods.getParams(), "", true, false);
delete allSites;
ApplicationTools::displayResult("Number of sequences", TextTools::toString(sites->getNumberOfSequences()));
ApplicationTools::displayResult("Number of sites", TextTools::toString(sites->getNumberOfSites()));
// Get the tree
Tree* tree = PhylogeneticsApplicationTools::getTree(bppmixedlikelihoods.getParams());
ApplicationTools::displayResult("Number of leaves", TextTools::toString(tree->getNumberOfLeaves()));
AbstractDiscreteRatesAcrossSitesTreeLikelihood* tl;
string nhOpt = ApplicationTools::getStringParameter("nonhomogeneous", bppmixedlikelihoods.getParams(), "no", "", true, false);
ApplicationTools::displayResult("Heterogeneous model", nhOpt);
MixedSubstitutionModel* model = 0;
MixedSubstitutionModelSet* modelSet = 0;
DiscreteDistribution* rDist = 0;
if (nhOpt == "no")
{
model = dynamic_cast<MixedSubstitutionModel*>(PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, gCode.get(), sites, bppmixedlikelihoods.getParams()));
if (model == 0)
{
cout << "Model is not a Mixed model" << endl;
exit(0);
}
SiteContainerTools::changeGapsToUnknownCharacters(*sites);
if (model->getNumberOfStates() > model->getAlphabet()->getSize())
{
// Markov-modulated Markov model!
rDist = new ConstantRateDistribution();
}
else
{
rDist = PhylogeneticsApplicationTools::getRateDistribution(bppmixedlikelihoods.getParams());
}
tl = new RHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, true);
}
else if (nhOpt == "one_per_branch")
{
model = dynamic_cast<MixedSubstitutionModel*>(PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, gCode.get(), sites, bppmixedlikelihoods.getParams()));
if (model == 0)
{
cout << "Model is not a Mixed model" << endl;
exit(0);
}
SiteContainerTools::changeGapsToUnknownCharacters(*sites);
if (model->getNumberOfStates() > model->getAlphabet()->getSize())
{
// Markov-modulated Markov model!
rDist = new ConstantRateDistribution();
}
else
{
rDist = PhylogeneticsApplicationTools::getRateDistribution(bppmixedlikelihoods.getParams());
}
vector<double> rateFreqs;
if (model->getNumberOfStates() != alphabet->getSize())
{
// Markov-Modulated Markov Model...
unsigned int n = (unsigned int)(model->getNumberOfStates() / alphabet->getSize());
rateFreqs = vector<double>(n, 1. / (double)n); // Equal rates assumed for now, may be changed later (actually, in the most general case,
// we should assume a rate distribution for the root also!!!
//.........这里部分代码省略.........