|
1
|
1 /*
|
|
|
2 Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
|
|
|
3
|
|
|
4 This file is part of the EggLib library.
|
|
|
5
|
|
|
6 EggLib is free software: you can redistribute it and/or modify
|
|
|
7 it under the terms of the GNU General Public License as published by
|
|
|
8 the Free Software Foundation, either version 3 of the License, or
|
|
|
9 (at your option) any later version.
|
|
|
10
|
|
|
11 EggLib is distributed in the hope that it will be useful,
|
|
|
12 but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
|
13 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
|
14 GNU General Public License for more details.
|
|
|
15
|
|
|
16 You should have received a copy of the GNU General Public License
|
|
|
17 along with EggLib. If not, see <http://www.gnu.org/licenses/>.
|
|
|
18 */
|
|
|
19
|
|
|
20 #ifndef EGGLIB_CONTROLLER_HPP
|
|
|
21 #define EGGLIB_CONTROLLER_HPP
|
|
|
22
|
|
|
23 #include "Current.hpp"
|
|
|
24 #include "Arg.hpp"
|
|
|
25 #include "ParamSet.hpp"
|
|
|
26
|
|
|
27 namespace egglib {
|
|
|
28
|
|
|
29 class Random;
|
|
|
30
|
|
|
31 /** \brief Controls a coalescent simulation
|
|
|
32 *
|
|
|
33 * \ingroup coalesce
|
|
|
34 *
|
|
|
35 * This class generates the gene genealogy, based on the parameters
|
|
|
36 * stocked in a ParamSet object.
|
|
|
37 *
|
|
|
38 */
|
|
|
39 class Controller {
|
|
|
40
|
|
|
41 public:
|
|
|
42
|
|
|
43 /** \brief Default constructor
|
|
|
44 *
|
|
|
45 * Uses a default ParamSet object that will not allow
|
|
|
46 * performing simulations.
|
|
|
47 *
|
|
|
48 */
|
|
|
49 Controller();
|
|
|
50
|
|
|
51 /** \brief Destructor
|
|
|
52 *
|
|
|
53 */
|
|
|
54 ~Controller();
|
|
|
55
|
|
|
56 /** \brief Standard constructor
|
|
|
57 *
|
|
|
58 * \param paramSet a ParamSet object containing run
|
|
|
59 * parameters (it is taken as a reference and stored as this
|
|
|
60 * so it must not be modified during simulations).
|
|
|
61 *
|
|
|
62 * \param random the address of the random number generator.
|
|
|
63 *
|
|
|
64 */
|
|
|
65 Controller(const ParamSet* paramSet, Random* random);
|
|
|
66
|
|
|
67 /** \brief Reset for a new simulation
|
|
|
68 *
|
|
|
69 * Object is reinitiliazed for a new simulation.
|
|
|
70 *
|
|
|
71 */
|
|
|
72 void reset();
|
|
|
73
|
|
|
74 /** \brief Increments the coalescent model
|
|
|
75 *
|
|
|
76 * \return The number of lineages.
|
|
|
77 *
|
|
|
78 */
|
|
|
79 unsigned int step();
|
|
|
80
|
|
|
81 /** \brief Gets the Ancestral Recombination Graph
|
|
|
82 *
|
|
|
83 * \return The address of the ARG contained in the object.
|
|
|
84 *
|
|
|
85 */
|
|
|
86 Arg* getArg();
|
|
|
87
|
|
|
88 /** \brief Applies a bottleneck to a given population
|
|
|
89 *
|
|
|
90 * The bottleneck is applied following Galtier, Depaulis and
|
|
|
91 * Barton (Genetics, 2000): the general time counter is
|
|
|
92 * stopped, and coalescence events are performed during a
|
|
|
93 * time (of normal coalescent process) given by the parameter
|
|
|
94 * strength. All coalescent events are instantaneous.
|
|
|
95 *
|
|
|
96 * \param populationIndex index of the population concerned
|
|
|
97 * by the event.
|
|
|
98 *
|
|
|
99 * \param strength strength of the bottleneck given by a
|
|
|
100 * number of time units (2N generations times the size of
|
|
|
101 * the population).
|
|
|
102 *
|
|
|
103 */
|
|
|
104 void bottleneck(unsigned int populationIndex, double strength);
|
|
|
105
|
|
|
106 /** \brief Migrate a complete population
|
|
|
107 *
|
|
|
108 * Takes all the lineages currently present in the population
|
|
|
109 * source to the population dest.
|
|
|
110 *
|
|
|
111 */
|
|
|
112 void moveAllLineages(unsigned int source, unsigned int dest);
|
|
|
113
|
|
|
114 /** \brief Migrate a complete population
|
|
|
115 *
|
|
|
116 * Takes all the lineages currently present in the population
|
|
|
117 * source to the population dest.
|
|
|
118 *
|
|
|
119 * \param source source population.
|
|
|
120 * \param dest destination population.
|
|
|
121 * \param probability the probability that a lineage of
|
|
|
122 * source migrates to dest.
|
|
|
123 *
|
|
|
124 */
|
|
|
125 void moveSomeLineages(unsigned int source, unsigned int dest, double probability);
|
|
|
126
|
|
|
127 /// Adds an empty population
|
|
|
128 void addPopulation();
|
|
|
129
|
|
|
130 private:
|
|
|
131
|
|
|
132 /// The copy constructor is disabled
|
|
|
133 Controller(const Controller& source) {}
|
|
|
134
|
|
|
135 /// The assignment operator is disabled
|
|
|
136 Controller& operator=(const Controller& source) {return *this;}
|
|
|
137
|
|
|
138 void diploids();
|
|
|
139 double getMigrationTime(double& migrationParameterDestination);
|
|
|
140 void getCoalescenceTime(double& destTime, unsigned int& destPopIndex);
|
|
|
141 double getCoalescenceTimeForPopulation(unsigned int populationIndex);
|
|
|
142 double getRecombinationTime() const;
|
|
|
143 void migrate(double migrationParameter);
|
|
|
144
|
|
|
145 const ParamSet* initialParamSet;
|
|
|
146 ParamSet paramSet;
|
|
|
147 Current current;
|
|
|
148 Arg arg;
|
|
|
149
|
|
|
150 Random* random;
|
|
|
151
|
|
|
152 };
|
|
|
153
|
|
|
154 }
|
|
|
155
|
|
|
156 #endif
|
