RewardMappingTools.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_REWARDMAPPINGTOOLS_H
#define BPP_PHYL_MAPPING_REWARDMAPPINGTOOLS_H
 
 
#include "../Likelihood/DataFlow/LikelihoodCalculationSingleProcess.h"
#include "ProbabilisticRewardMapping.h"
#include "Reward.h"
#include "SubstitutionMappingTools.h"
 
namespace bpp
{
class RewardMappingTools
{
public:
  RewardMappingTools() {}
  virtual ~RewardMappingTools() {}
 
public:
  static std::unique_ptr<ProbabilisticRewardMapping> computeRewardVectors(
      LikelihoodCalculationSingleProcess& rltc,
      const std::vector<uint>& edgeIds,
      Reward& reward,
      short unresolvedOption = SubstitutionMappingTools::UNRESOLVED_ZERO,
      bool verbose = true);
 
 
  static void writeToStream(
      const ProbabilisticRewardMapping& rewards,
      const AlignmentDataInterface& sites,
      std::ostream& out);
 
 
  static void readFromStream(std::istream& in, ProbabilisticRewardMapping& rewards);
 
  static double computeSumForBranch(const ProbabilisticRewardMapping& smap, size_t branchIndex);
 
  static double computeSumForSite(const ProbabilisticRewardMapping& smap, size_t siteIndex);
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_REWARDMAPPINGTOOLS_H