RewardMappingTools.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef _REWARDMAPPINGTOOLS_H_
#define _REWARDMAPPINGTOOLS_H_
 
#include "ProbabilisticRewardMapping.h"
#include "../../Mapping/Reward.h"
 
#include "../Likelihood/DRTreeLikelihood.h"
 
namespace bpp
{
class LegacyRewardMappingTools
{
public:
  LegacyRewardMappingTools() {}
  virtual ~LegacyRewardMappingTools() {}
 
public:
  static std::unique_ptr<LegacyProbabilisticRewardMapping> computeRewardVectors(
      std::shared_ptr<const DRTreeLikelihoodInterface> drtl,
      const std::vector<int>& nodeIds,
      std::shared_ptr<Reward> reward,
      bool verbose = true);
 
 
  static void writeToStream(
      const LegacyProbabilisticRewardMapping& rewards,
      const SiteContainerInterface& sites,
      std::ostream& out);
 
 
  static void readFromStream(std::istream& in, LegacyProbabilisticRewardMapping& rewards);
 
 
  static double computeSumForBranch(const LegacyRewardMappingInterface& smap, size_t branchIndex);
 
 
  static double computeSumForSite(const LegacyRewardMappingInterface& smap, size_t siteIndex);
};
} // end of namespace bpp.
 
#endif // _REWARDMAPPINGTOOLS_H_