PairedSiteLikelihoods.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LEGACY_LIKELIHOOD_PAIREDSITELIKELIHOODS_H
#define BPP_PHYL_LEGACY_LIKELIHOOD_PAIREDSITELIKELIHOODS_H
 
 
// From the STL:
#include <vector>
#include <string>
 
// From Bio++
#include "TreeLikelihood.h"
#include <Bpp/Exceptions.h>
 
namespace bpp
{
class PairedSiteLikelihoods
{
private:
  std::vector<std::vector<double>> logLikelihoods_;
  std::vector<std::string> modelNames_;
 
public:
  PairedSiteLikelihoods();
 
  PairedSiteLikelihoods(
      const std::vector<std::vector<double>>& siteLogLikelihoods,
      const std::vector<std::string>& modelNames = std::vector<std::string>()
      );
 
  ~PairedSiteLikelihoods() {}
 
  void appendModel(
      const std::vector<double>& siteLogLikelihoods,
      const std::string& modelName = "");
 
  void appendModel(const bpp::TreeLikelihoodInterface& treelikelihood);
 
  void appendModels(const PairedSiteLikelihoods& psl);
 
  const std::vector<std::vector<double>>& getLikelihoods() const
  {
    return logLikelihoods_;
  }
 
  const std::vector<std::string>& getModelNames() const
  {
    return modelNames_;
  }
 
  size_t getNumberOfModels() const
  {
    return logLikelihoods_.size();
  }
 
  std::size_t getNumberOfSites() const
  {
    try
    {
      return logLikelihoods_.at(0).size();
    }
    catch (std::out_of_range&)
    {
      throw Exception("PairedSiteLikelihoods::nsites: The container is empty, there isn't a number of sites.");
    }
  }
 
  void setName(std::size_t pos, std::string& name)
  {
    modelNames_.at(pos) = name;
  }
 
  std::pair< std::vector<std::string>, std::vector<double>> computeExpectedLikelihoodWeights(int replicates = 10000) const;
 
  static std::vector<int> bootstrap(std::size_t length, double scaling = 1);
};
} // namespace bpp.
#endif // BPP_PHYL_LEGACY_LIKELIHOOD_PAIREDSITELIKELIHOODS_H