forqs module reference
Forward simulation of Recombination, Quantitative traits, and Selection
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Locus.hpp
1 //
2 // Locus.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 _LOCUS_HPP_
37 #define _LOCUS_HPP_
38 
39 
40 #include "Configurable.hpp"
41 
42 
48 
49 
50 //
51 // Locus
52 //
53 
54 
67 
68 
69 struct Locus : public Configurable
70 {
71  size_t chromosome_pair_index;
72  unsigned int position;
73 
74  Locus(const std::string& id, size_t _chromosome_pair_index = 0, unsigned int _position = 0)
75  : Configurable(id), chromosome_pair_index(_chromosome_pair_index), position(_position)
76  {}
77 
78  // Configurable interface
79 
80  virtual std::string class_name() const {return "Locus";}
81  virtual Parameters parameters() const;
82  virtual void configure(const Parameters& parameters, const Registry& registry);
83 };
84 
85 
86 typedef shared_ptr<Locus> LocusPtr;
87 typedef std::set<Locus> Loci;
88 
89 
90 bool operator<(const Locus& a, const Locus& b);
91 bool operator==(const Locus& a, const Locus& b);
92 bool operator!=(const Locus& a, const Locus& b);
93 std::ostream& operator<<(std::ostream& os, const Locus& locus);
94 
95 
96 //
97 // LocusList
98 //
99 
100 
124 
125 
126 class LocusList : public std::vector<Locus>, public Configurable
127 {
128  public:
129 
130  LocusList(const std::string& id) : Configurable(id) {}
131 
132  // Configurable interface
133 
134  virtual std::string class_name() const {return "LocusList";}
135  virtual Parameters parameters() const;
136  virtual void configure(const Parameters& parameters, const Registry& registry);
137  virtual void write_child_configurations(std::ostream& os, std::set<std::string>& ids_written) const;
138 
139  protected:
140 
141  std::string generate_locus_id(size_t index) const;
142 };
143 
144 
145 typedef shared_ptr<LocusList> LocusListPtr;
146 typedef std::vector<LocusListPtr> LocusListPtrs;
147 
148 
149 //
150 // LocusList_Random
151 //
152 
153 
165 
166 
168 {
169  public:
170 
171  LocusList_Random(const std::string& id) : LocusList(id), locus_count_(0) {}
172 
173  // Configurable interface
174 
175  virtual std::string class_name() const {return "LocusList_Random";}
176  virtual Parameters parameters() const;
177  virtual void configure(const Parameters& parameters, const Registry& registry);
178  virtual void initialize(const SimulatorConfig& config);
179  virtual void write_child_configurations(std::ostream& os, std::set<std::string>& ids_written) const {}
180 
181  private:
182 
183  size_t locus_count_;
184 };
185 
186 
187 #endif // _LOCUS_HPP_
188