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1 /*
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2 Copyright 2009-2010 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_DATAMATRIX_HPP
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21 #define EGGLIB_DATAMATRIX_HPP
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22
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23
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24 #include "CharMatrix.hpp"
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25
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26
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27 namespace egglib {
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28
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29 /** \brief Data table
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30 *
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31 * \ingroup core
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32 *
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33 * Holds a data matrix representing genotype data from simulations.
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34 * Data are stored as integers, to each site is associated a
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35 * position, and to each sequence is associated a group index (any
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36 * integer labelling, for example, a subpopulation). Supports the
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37 * CharMatrix interface with the condition that allele genotype
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38 * datum is >=0 and <=9.
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39 *
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40 */
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41 class DataMatrix : public CharMatrix {
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42
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43 public:
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44
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45 /** \brief Default constructor
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46 *
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47 * The data table default dimensions are {0,0}
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48 *
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49 */
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50 DataMatrix();
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51
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52
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53 /** \brief Standard constructor
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54 *
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55 * The data table dimensions must be given.
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56 * Each cell default default is 0, and each site position is 0..
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57 *
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58 * \param numberOfSequences number of lines of the data table.
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59 * \param numberOfSites number of columns of the data table.
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60 *
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61 */
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62 DataMatrix(unsigned int numberOfSequences, unsigned int numberOfSites);
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63
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64
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65 /** \brief Copy constructor
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66 *
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67 */
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68 DataMatrix(const DataMatrix&);
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69
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70
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71 /** \brief Copy constructor
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72 *
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73 */
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74 DataMatrix(const CharMatrix&);
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75
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76
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77 /** \brief Assignment operator
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78 *
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79 */
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80 virtual DataMatrix& operator=(const DataMatrix&);
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81
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82
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83 /** \brief Assignment operator
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84 *
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85 */
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86 virtual DataMatrix& operator=(const CharMatrix&);
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87
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88
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89 /** \brief Destructor
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90 *
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91 */
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92 virtual ~DataMatrix();
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93
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94
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95 /** \brief Gets number of sites
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96 *
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97 */
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98 unsigned int numberOfSites() const;
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99
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100
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101 /** \brief Gets number of sequences
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102 *
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103 */
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104 unsigned int numberOfSequences() const;
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105
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106
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107 /** \brief Sets a value of the data table
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108 *
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109 */
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110 void set(unsigned int sequence, unsigned int site, int value);
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111
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112
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113 /** \brief Gets a value from the data table
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114 *
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115 */
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116 int get(unsigned int sequence, unsigned int site) const;
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117
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118
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119 /** \brief Faster and unsecure version of get
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120 *
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121 */
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122 inline int fget(unsigned int sequence, unsigned int site) const {
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123 return dataMatrix[sequence][site];
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124 }
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125
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126
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127 /** \brief Sets the position of a site
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128 *
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129 */
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130 void sitePosition(unsigned int site, double value);
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131
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132
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133 /** \brief Gets the position of a site
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134 *
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135 */
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136 double sitePosition(unsigned int site) const;
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137
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138
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139 /** \brief Sets the group label of a sequence
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140 *
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141 */
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142 void populationLabel(unsigned int sequence, unsigned int value);
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143
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144
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145 /** \brief Gets the group label of a sequence
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146 *
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147 */
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148 unsigned int populationLabel(unsigned int sequence) const;
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149
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150
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151 /** \brief Removes all information from the object
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152 *
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153 */
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154 void clear();
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155
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156
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157 /** \brief Resizes the data matrix
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158 *
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159 * \param newNumberOfSequences number of sequences (rows)
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160 * \param newNumberOfSites number of sites (columns)
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161 *
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162 * If new values are larger, data already set is left unchanged.
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163 * New data are set to zero.
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164 *
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165 */
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166 void resize(unsigned int newNumberOfSequences, unsigned int newNumberOfSites);
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167
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168
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169 /** \brief Shifts allele value
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170 *
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171 * \param minimum the minimum allele value.
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172 *
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173 * Shifts all alleles at all sites to ensure that alleles alleles
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174 * are equal to or larger than minimum. The shifting is specific
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175 * to each site.
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176 *
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177 */
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178 void shift(int minimum);
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179
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180 /** \brief Gets the character at a given position
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181 *
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182 * An exception is generated if the allele value at this
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183 * position is not >=0 and <=9. Not out-of-bound check is
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184 * performed.
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185 *
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186 */
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187 char character(unsigned int sequence, unsigned int site) const;
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188
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189
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190
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191 private:
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192
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193 // Initializes to default values (for empty object)
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194 void init();
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195
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196 // Copies from a source object
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197 virtual void copy(const CharMatrix&);
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198
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199 // Copies from a source object
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200 virtual void copy(const DataMatrix&);
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201
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202 // Number of lines of the data matrix
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203 unsigned int _numberOfSequences;
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204
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205 // Number of columns of the data matrix
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206 unsigned int _numberOfSites;
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207
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208 // Data matrix
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209 int **dataMatrix;
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210
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211 // Vector of site positions
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212 double *positions;
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213
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214 // Vector of group indices
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215 unsigned int *groups;
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216 };
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217 }
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218
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219 #endif
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