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Forward simulation of Recombination, Quantitative traits, and Selection
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RecombinationPositionGenerator.hpp
1 //
2 // RecombinationPositionGenerator.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 _RECOMBINATIONPOSITIONGENERATOR_HPP_
37 #define _RECOMBINATIONPOSITIONGENERATOR_HPP_
38 
39 
40 #include "RecombinationMap.hpp"
41 #include "Configurable.hpp"
42 #include "Random.hpp"
43 #include "shared_ptr.hpp"
44 #include <vector>
45 
46 
61 
62 
63 //
64 // RecombinationPositionGenerator
65 //
66 
70 
72 {
73  public:
74 
75  virtual std::vector<unsigned int> get_positions(size_t chromosome_pair_index = 0) const = 0;
77 
78  // Configurable interface
79 
80  virtual std::string class_name() const;
81  virtual Parameters parameters() const;
82  virtual void configure(const Parameters& parameters, const Registry& registry);
83 
84  protected:
85 
86  RecombinationPositionGenerator(const std::string& id) : Configurable(id) {}
87 };
88 
89 typedef shared_ptr<RecombinationPositionGenerator> RecombinationPositionGeneratorPtr;
90 
91 
92 //
93 // RecombinationPositionGenerator_Trivial
94 //
95 
105 
107 {
108  public:
109 
110  RecombinationPositionGenerator_Trivial(const std::string& id)
112  {}
113 
114  virtual std::vector<unsigned int> get_positions(size_t chromosome_pair_index) const;
115 
116  // Configurable interface
117 
118  virtual std::string class_name() const {return "RecombinationPositionGenerator_Trivial";}
119  virtual Parameters parameters() const;
120  virtual void configure(const Parameters& parameters, const Registry& registry);
121 };
122 
123 
124 //
125 // RecombinationPositionGenerator_SingleCrossover
126 //
127 
137 
138 
140 {
141  public:
142 
145  {}
146 
147  virtual std::vector<unsigned int> get_positions(size_t chromosome_pair_index) const;
148 
149  // Configurable interface
150 
151  virtual std::string class_name() const {return "RecombinationPositionGenerator_SingleCrossover";}
152  virtual Parameters parameters() const;
153  virtual void configure(const Parameters& parameters, const Registry& registry);
154  virtual void initialize(const SimulatorConfig& config);
155 
156  private:
157  std::vector<unsigned int> chromosome_lengths_;
158 };
159 
160 
161 //
162 // RecombinationPositionGenerator_Uniform
163 //
164 
181 
182 
184 {
185  public:
186 
188  {
189  size_t length;
190  double rate;
191  Random::DistributionPtr poisson;
192  ChromosomeInfo(size_t _length, double _rate = 1.0);
193  };
194 
195  RecombinationPositionGenerator_Uniform(const std::string& id,
196  std::vector<ChromosomeInfo> infos = std::vector<ChromosomeInfo>());
197 
198  virtual std::vector<unsigned int> get_positions(size_t chromosome_pair_index) const;
199 
200  // Configurable interface
201 
202  virtual std::string class_name() const {return "RecombinationPositionGenerator_Uniform";}
203  virtual Parameters parameters() const;
204  virtual void configure(const Parameters& parameters, const Registry& registry);
205  virtual void initialize(const SimulatorConfig& config);
206 
207  private:
208 
209  double common_rate_;
210  typedef std::vector<ChromosomeInfo> ChromosomeInfos;
211  ChromosomeInfos infos_;
212 };
213 
214 
215 //
216 // RecombinationPositionGenerator_RecombinationMap
217 //
218 
232 
233 
235 {
236  public:
237 
239  const std::vector<std::string>& filenames = std::vector<std::string>());
240 
241  virtual std::vector<unsigned int> get_positions(size_t chromosome_pair_index) const;
242 
243  // Configurable interface
244 
245  virtual std::string class_name() const {return "RecombinationPositionGenerator_RecombinationMap";}
246  virtual Parameters parameters() const;
247  virtual void configure(const Parameters& parameters, const Registry& registry);
248 
249  private:
250 
251  std::vector<std::string> filenames_;
252  std::vector< shared_ptr<RecombinationMap> > recombination_maps_;
253 
254  void initialize();
255 };
256 
257 
258 #endif // _RECOMBINATIONPOSITIONGENERATOR_HPP_
259