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comparison egglib/egglib-2.1.5/include/egglib-cpp/Population.hpp @ 1:420b57c3c185 draft

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author dereeper
date Fri, 10 Jul 2015 04:39:30 -0400
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0:3e19d0dfcf3e 1:420b57c3c185
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_POPULATION_HPP
21 #define EGGLIB_POPULATION_HPP
22
23
24 #include "Edge.hpp"
25
26 namespace egglib {
27
28 class Random;
29
30 /** \brief Handles a single population
31 *
32 * \ingroup coalesce
33 *
34 */
35 class Population {
36
37 public:
38
39 /** \brief Default constructor
40 *
41 * Generates an empty population.
42 *
43 */
44 Population();
45
46 /** \brief Copy constructor
47 *
48 */
49 Population(const Population& source);
50
51 /** \brief Assignment operator
52 *
53 */
54 Population& operator=(const Population& source);
55
56 /** \brief Destructor
57 *
58 * The object only cleans Edge objects currently stored in it.
59 *
60 */
61 ~Population();
62
63 /** \brief Standard constructor
64 *
65 * The Edge instances will be handled by address and they
66 * MUST be passed using the method set().
67 *
68 * \param numberOfSegments number of recombining segments.
69 *
70 * \param numberOfLineages the number of lineages contained
71 * in this population.
72 *
73 * \param firstIndex the absolute index (or ID) of the first
74 * lineage (the other will have consecutive incremented
75 * ID's).
76 *
77 */
78 Population(unsigned int numberOfSegments,
79 unsigned int numberOfLineages, unsigned firstIndex);
80
81 /** \brief Gets the number of lineages
82 *
83 */
84 unsigned int numberOfLineages() const;
85
86 /** \brief Gets the efficient number of lineages
87 *
88 * The number of lineages is multiplied by the number of
89 * covered segments of each lineages.
90 *
91 */
92 unsigned int efficientNumberOfLineages() const;
93
94 /** \brief Sets the Edge of a lineage
95 *
96 * \param index the index of the lineage within the
97 * population.
98 * \param edge the address of the Edge instance representing
99 * the lineage.
100 *
101 */
102 void set(unsigned int index, Edge* edge);
103
104 /** \brief Removes and returns a random lineage.
105 *
106 * \param random pointer to simulator's random generator
107 * instance.
108 *
109 */
110 Edge* extractRandomly(Random* random);
111
112 /** \brief Removes and returns a given lineage.
113 *
114 * \param index the relative index of the lineage.
115 *
116 */
117 Edge* extractByIndex(unsigned int index);
118
119 /** \brief Appends a lineage to the object
120 *
121 */
122 void push(Edge* edge);
123
124 /** \brief Gets coverage
125 *
126 */
127 unsigned int coverage(unsigned int edgeIndex) const;
128
129
130 private:
131
132 void copy(const Population& source);
133 void clear();
134 Edge* pick(unsigned int index);
135 void init();
136 unsigned int _numberOfLineages;
137 unsigned int _efficientNumberOfLineages;
138 Edge** lineages;
139 };
140
141 }
142
143 #endif