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Forward simulation of Recombination, Quantitative traits, and Selection
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MutationGenerator.hpp
1 //
2 // MutationGenerator.hpp
3 //
4 // Created by Darren Kessner with John Novembre
5 //
6 // Copyright (c) 2013 Regents of the University of California
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34 
35 
36 #ifndef _MUTATIONGENERATOR_HPP_
37 #define _MUTATIONGENERATOR_HPP_
38 
39 
40 #include "Locus.hpp"
41 #include "Population.hpp"
42 #include "shared_ptr.hpp"
43 
44 
45 //
46 // MutationGenerator
47 //
48 
52 
54 {
55  public:
56 
57  struct MutationInfo
58  {
59  size_t individual_index;
60  Locus locus;
61  int which; // 0 == chromosome_pair.first, 1 == chromosome_pair.second
62  unsigned int value; // new value to be returned by VariantIndicator
63 
64  MutationInfo()
65  : individual_index(0), locus("id_dummy"), which(0), value(0)
66  {}
67  };
68 
69  typedef std::vector<MutationInfo> MutationInfos;
70 
71  MutationGenerator(const std::string& id) : Configurable(id) {}
72 
73  virtual MutationInfos generate_mutations(const Population& population,
74  size_t generation_index,
75  size_t population_index) const {return MutationInfos();}
76  // Configurable interface
77 
78  virtual std::string class_name() const {return "MutationGenerator";}
79  virtual Parameters parameters() const {return Parameters();}
80  virtual void configure(const Parameters& parameters, const Registry& registry) {}
81 
82  virtual ~MutationGenerator() {}
83 };
84 
85 
86 typedef shared_ptr<MutationGenerator> MutationGeneratorPtr;
87 
88 
89 std::ostream& operator<<(std::ostream& os, const MutationGenerator::MutationInfo& mutation_info);
90 
91 
92 #endif // _MUTATIONGENERATOR_HPP_
93