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1
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1 /*
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2 Copyright 2008-2010 Stéphane De Mita, Mathieu Siol
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3
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4 This file is part of the EggLib library.
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5
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6 EggLib is free software: you can redistribute it and/or modify
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7 it under the terms of the GNU General Public License as published by
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8 the Free Software Foundation, either version 3 of the License, or
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9 (at your option) any later version.
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10
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11 EggLib is distributed in the hope that it will be useful,
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12 but WITHOUT ANY WARRANTY; without even the implied warranty of
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13 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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14 GNU General Public License for more details.
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15
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16 You should have received a copy of the GNU General Public License
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17 along with EggLib. If not, see <http://www.gnu.org/licenses/>.
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18 */
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19
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20 #ifndef EGGLIB_MICROSATELLITEDIVERSITY_HPP
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21 #define EGGLIB_MICROSATELLITEDIVERSITY_HPP
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22
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23 #include "DataMatrix.hpp"
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24 #include <cstdlib>
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25
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26 namespace egglib {
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27
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28 /** \brief Analyzes microsatellite data
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29 *
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30 * \ingroup polymorphism
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31 *
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32 * Use the load() method to analyze data. All sites will be analyzed
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33 * and accessors allow to access the value of a given statistics for
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34 * a given site. There is no out-of-bound checking implemented in
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35 * accessors.
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36 *
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37 */
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38 class MicrosatelliteDiversity {
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39
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40 public:
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41
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42 /** \brief Creates an object
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43 *
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44 */
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45 MicrosatelliteDiversity();
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46
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47
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48 /** \brief Destroys an object
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49 *
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50 */
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51 virtual ~MicrosatelliteDiversity();
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52
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53
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54 /** \brief Performs the analysis
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55 *
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56 * \param dataMatrix the object to analyze.
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57 *
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58 * \param missingData the integer identifying missing data.
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59 *
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60 * \param noMissingData if true, no allele will be
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61 * excluded (including the one identified by the argument
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62 * missingData).
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63 *
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64 */
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65 void load(const DataMatrix& dataMatrix,
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66 int missingData=999, bool noMissingData=false);
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67
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68
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69 /// Number of sites (or markers)
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70 unsigned int numberOfSites() const;
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71
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72 /// Heterozygosity
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73 double He(unsigned int siteIndex) const;
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74
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75 /// Number of alleles
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76 unsigned int numberOfAlleles(unsigned int siteIndex) const;
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77
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78 /// Variance of allele size
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79 double sizeVariance(unsigned int siteIndex) const;
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80
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81 /// IAM-based estimator of theta
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82 double thetaAssumingIAM(unsigned int siteIndex) const;
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83
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84 /// SMM-based estimator of theta, calculated from He
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85 double thetaAssumingSMMfromHe(unsigned int siteIndex) const;
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86
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87 /// SMM-based estimator of theta, calculated from VarSize
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88 double thetaAssumingSMMfromSizeVariance(unsigned int siteIndex) const;
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89
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90
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91 protected:
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92
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93 unsigned int v_numberOfSites;
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94 double *v_He;
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95 unsigned int *v_numberOfAlleles;
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96 double *v_sizeVariance;
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97 double *v_thetaAssumingIAM;
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98 double *v_thetaAssumingSMMfromHe;
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99 double *v_thetaAssumingSMMfromSizeVariance;
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100
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101 void init();
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102 void clear();
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103
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104
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105 private:
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106
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107
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108 /// No copy allowed
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109 MicrosatelliteDiversity(const MicrosatelliteDiversity& source) {
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110 }
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111
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112 /// No copy allowed
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113 MicrosatelliteDiversity& operator=(const MicrosatelliteDiversity& source) {
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114 return *this;
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115 }
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116
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117 };
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118 }
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119
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120 #endif
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