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

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1 /*
2 Copyright 2008-2009 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
21 #ifndef EGGLIB_SITEPOLYMORPHISM_HPP
22 #define EGGLIB_SITEPOLYMORPHISM_HPP
23
24
25
26 namespace egglib {
27
28
29 /** \brief Implements diversity analysis at the site level
30 *
31 * \ingroup polymorphism
32 *
33 * Data are loaded along with a population index. It is necessary to
34 * set the number of populations prior to use.
35 *
36 * Outgroup sequence must be loaded separetedly. There can be any
37 * number of outgroups, but they must be all consistent otherwise the
38 * site will be considered as not orientable.
39 *
40 */
41 class SitePolymorphism {
42
43 public:
44
45 /** \brief Builds an object
46 *
47 */
48 SitePolymorphism();
49
50
51 /** \brief Builds an object
52 *
53 * \param npop number of populations
54 *
55 */
56 SitePolymorphism(unsigned int npop);
57
58
59 /** \brief Destroys an object
60 *
61 */
62 virtual ~SitePolymorphism();
63
64
65 /** \brief Copy constructor
66 *
67 */
68 SitePolymorphism(const SitePolymorphism& source);
69
70
71 /** \brief Assignment operator
72 *
73 */
74 SitePolymorphism& operator=(const SitePolymorphism& source);
75
76
77 /** \brief Sets the number of populations
78 *
79 * NOTE THAT all previous data is lost.
80 *
81 */
82 void numberOfPopulations(unsigned int npop);
83
84
85 /** \brief Adds a character
86 *
87 * \param populationIndex the index of the population from
88 * which is sampled this character (do not use "population
89 * label").
90 *
91 * \param character the character value (it is assumed it
92 * represents a valid character.
93 *
94 */
95 void load(unsigned int populationIndex, char character);
96
97
98 /** \brief Loads outgroup state
99 *
100 * There can be any number of outgroup states. Only
101 * characters that are considered as valid (whatever the list
102 * is) should be loaded.
103 *
104 */
105 void outgroup(char state);
106
107
108 /** \brief Number of different alleles
109 *
110 */
111 unsigned int numberOfAlleles() const;
112
113
114 /** \brief Gets an allele (unsecure)
115 *
116 * Assumes that the index provided lies in the valid range
117 *
118 */
119 char allele(unsigned int index) const;
120
121
122 /** \brief Gets a frequency (unsecure)
123 *
124 * The sum of of frequencies of the allele over populations
125 * is computed. Not out-of-bounds check is performed.
126 *
127 */
128 unsigned int alleleFrequency(unsigned int alleleIndex) const;
129
130
131 /** \brief Gets the frequency of an allele in one pop (unsecure)
132 *
133 * The frequency of the allele in the given population is
134 * returned. Not out-of-bounds check is performed.
135 *
136 */
137 unsigned int alleleFrequency(unsigned int popIndex, unsigned int alleleIndex) const;
138
139
140 /** \brief Sums the frequency of derived allele(s)
141 *
142 * This method assumes that the site is orientable. It will
143 * use as outgroup the first outgroup character entered,
144 * assuming at least one was entered and that all (if more
145 * than one) were identical.
146 *
147 */
148 unsigned int derivedAlleleFrequency() const;
149
150
151 /** \brief Number of sequences that were analyzed
152 *
153 */
154 unsigned int ns() const;
155
156
157 /** \brief Gets the number of analyzed sequences for a population
158 *
159 * No out-of-bound check is performed
160 *
161 */
162 unsigned int ns(unsigned int popIndex) const;
163
164
165 /** \brief Checks if the site can be oriented
166 *
167 * Returns true if at least one outgroup datum has been
168 * loaded, if all outgroup data are identical (regardless of
169 * their value) and if the outgroup allele is one of the
170 * allele in the sample.
171 *
172 */
173 bool isOrientable() const;
174
175 bool isPolymorphic(unsigned int popIndex) const;
176 bool hasSpecificAllele(unsigned int popIndex, bool restrictToDerived) const;
177 bool haveFixedDifference(unsigned int pop1, unsigned int pop2) const;
178 bool haveCommonAllele(unsigned int pop1, unsigned int pop2) const;
179 bool haveSharedAllele(unsigned int pop1, unsigned int pop2) const;
180
181
182
183
184 protected:
185
186 // helpers
187 void init();
188 void clear();
189 void copy(const SitePolymorphism& site);
190
191
192 // data
193 unsigned int m_numberOfPopulations;
194 unsigned int m_numberOfStates;
195 char * m_states;
196 unsigned int ** m_frequencies;
197 unsigned int m_numberOfOutgroups;
198 char * m_outgroups;
199 unsigned int m_ns;
200 unsigned int * m_pop_ns;
201
202 bool m_cache_orientable;
203
204 };
205 }
206
207 #endif