1 | // This file is a part of Framsticks SDK. http://www.framsticks.com/ |
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2 | // Copyright (C) 1999-2015 Maciej Komosinski and Szymon Ulatowski. |
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3 | // See LICENSE.txt for details. |
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4 | |
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5 | |
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6 | #include <vector> |
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7 | #include "frams/errmgr/stdouterr.h" |
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8 | #include "frams/_demos/genotypeloader.h" |
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9 | #include "frams/genetics/preconfigured.h" |
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10 | #include "frams/virtfile/stdiofile.h" |
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11 | #include "frams/model/similarity/simil_model.h" |
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12 | |
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13 | |
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14 | |
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15 | using namespace std; |
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16 | |
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17 | /** Computes a matrix of distances between all genotypes in the specified |
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18 | .gen file, using the matching and measure weights as specified in the |
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19 | command line. |
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20 | |
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21 | Command line parameters: [-names] <genotypesFile> <w_dP> <w_dDEG> <w_dNEU> <w_dGEO> |
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22 | |
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23 | Parameters: |
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24 | <genotypesFile> name of a file with genotypes (only f1 format) |
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25 | <w_dP> weight of the difference in the number of parts |
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26 | <w_dDEG> weight of the difference in degrees of matched parts |
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27 | <w_dNEU> weight of the difference in neurons of matched parts |
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28 | <w_dGEO> weight of the distance of matched parts |
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29 | |
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30 | Switches: |
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31 | -names specifies that the number and names of genotypes are to be printed to output |
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32 | before the distance matrix; by default the number and names are not printed |
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33 | |
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34 | Outputs a distance matrix in the format: |
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35 | <row_1> (columns in a row are separated by TABs) |
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36 | ... |
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37 | <row_n> |
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38 | |
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39 | Last modified: 2015-04-16 |
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40 | */ |
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41 | int main(int argc, char *argv[]) |
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42 | { |
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43 | //StdoutErrorHandler err; //?TODO |
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44 | typedef double *pDouble; |
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45 | int iCurrParam = 0; // index of the currently processed parameter |
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46 | char *szCurrParam = NULL; |
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47 | ModelSimil M; // similarity computing object |
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48 | bool bPrintNames = false; // specifies if names of genotypes are to be printed |
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49 | int nResult = 0; // a temporary result |
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50 | |
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51 | if (argc < 6) |
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52 | { |
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53 | // too few parameters |
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54 | printf("Too few parameters!\n"); |
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55 | printf("Command line: [-names] <genotypesFile> <matchType> <w_dP> <w_dDEG> <w_dNEU> <w_dGEO> <ifFUZZY>\n\n"); |
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56 | printf("Parameters:\n"); |
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57 | printf(" <genotypesFile> name of a file with genotypes (only f1 format is allowed)\n"); |
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58 | printf(" <w_dP> weight of the difference in the number of parts\n"); |
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59 | printf(" <w_dDEG> weight of the difference in degrees of matched parts\n"); |
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60 | printf(" <w_dNEU> weight of the difference in neurons of matched parts\n"); |
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61 | printf(" <w_dGEO> weight of the distance of matched parts\n\n"); |
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62 | printf("Switches:\n"); |
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63 | printf(" -names specifies that the number and names of genotypes are to be printed to output\n"); |
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64 | printf(" before the distance matrix; by default the number and names are not printed\n\n"); |
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65 | |
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66 | printf("Outputs a symmetric distance matrix in the format:\n"); |
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67 | printf(" <row_1> (columns in a row are separated by TABs)\n"); |
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68 | printf(" ...\n"); |
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69 | printf(" <row_n>\n"); |
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70 | |
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71 | return -1; |
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72 | } |
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73 | |
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74 | // prepare output parameters from .gen file |
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75 | vector<Geno *> *pvGenos = new vector<Geno *>(); |
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76 | vector<char *> *pvNames = new vector<char *>(); |
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77 | |
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78 | // check if there is a switch |
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79 | iCurrParam = 1; |
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80 | szCurrParam = argv[ iCurrParam ]; |
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81 | if (strcmp(szCurrParam, "-names") == 0) |
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82 | { |
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83 | // switch "-names" was given; print names also |
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84 | bPrintNames = true; |
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85 | // pass to the next parameter |
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86 | iCurrParam++; |
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87 | } |
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88 | |
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89 | // check the parameters |
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90 | // get <genotypesFile> name from command line |
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91 | char *szFileName = argv[ iCurrParam ]; |
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92 | |
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93 | // initially set measure components' weights to invalid values (negative) |
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94 | for (int i = 0; i < M.GetNOFactors(); i++) |
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95 | { |
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96 | M.m_adFactors[i] = -1.0; |
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97 | } |
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98 | |
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99 | const char *params[] = {"<w_dP>", "<w_dDEG>", "<w_dNEU>", "<w_dGEO>"}; |
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100 | for (int i = 0; i < M.GetNOFactors(); i++) |
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101 | { |
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102 | iCurrParam++; |
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103 | szCurrParam = argv[ iCurrParam ]; |
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104 | nResult = sscanf(szCurrParam, " %lf ", & M.m_adFactors[ i ]); |
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105 | if (nResult != 1) |
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106 | { |
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107 | // <w_dP> is not a number -- error |
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108 | printf("%s", params[i]); |
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109 | printf(" should be a number\n"); |
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110 | return -1; |
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111 | } |
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112 | else |
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113 | { |
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114 | // <w_dP> is a number; check if nonnegative |
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115 | if (M.m_adFactors[ i ] < 0.0) |
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116 | { |
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117 | printf("%s", params[i]); |
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118 | printf(" should be a nonnegative number\n"); |
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119 | return -1; |
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120 | } |
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121 | } |
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122 | } |
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123 | |
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124 | // read the input file |
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125 | // prepare loading of genotypes from a .gen file |
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126 | // create some basic genotype converters |
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127 | PreconfiguredGenetics genetics; |
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128 | StdioFileSystem_autoselect stdiofilesys; |
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129 | |
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130 | long count = 0, totalsize = 0; |
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131 | MiniGenotypeLoader loader(szFileName); |
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132 | MiniGenotype *loaded; |
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133 | while (loaded = loader.loadNextGenotype()) |
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134 | { |
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135 | // while a valid genotype was loaded |
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136 | count++; |
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137 | totalsize += loaded->genotype.len(); |
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138 | // create a Geno object based on the MiniGenotype |
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139 | Geno *pNextGenotype = new Geno(loaded->genotype); |
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140 | if ((pNextGenotype != NULL) && (pNextGenotype->isValid())) |
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141 | { |
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142 | pvGenos->push_back(pNextGenotype); |
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143 | char *szNewName = new char [ loaded->name.len() + 1]; |
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144 | strcpy(szNewName, loaded->name.c_str()); |
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145 | pvNames->push_back(szNewName); |
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146 | } |
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147 | else |
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148 | { |
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149 | printf("Genotype %2li is not valid\n", count); |
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150 | } |
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151 | } |
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152 | if (loader.getStatus() == MiniGenotypeLoader::OnError) |
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153 | { |
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154 | printf("Error: %s", loader.getError().c_str()); |
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155 | } |
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156 | |
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157 | double dSimilarity = 0.0; |
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158 | double **aaSimil = NULL; // array of similarities |
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159 | |
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160 | // create the empty array of similarities |
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161 | aaSimil = new pDouble [pvGenos->size()]; |
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162 | for (int k = 0; k < (int) pvGenos->size(); k++) |
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163 | { |
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164 | aaSimil[k] = new double [pvGenos->size()]; |
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165 | for (int l = 0; l < (int) pvGenos->size(); l++) |
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166 | aaSimil[k][l] = 0.0; |
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167 | } |
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168 | |
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169 | // compute and remember similarities |
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170 | int i, j; |
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171 | for (i = 0; i < (int) pvGenos->size(); i++) |
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172 | { |
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173 | for (j = 0; j < (int) pvGenos->size(); j++) |
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174 | { |
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175 | dSimilarity = M.EvaluateDistance(pvGenos->operator[](i), pvGenos->operator[](j)); |
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176 | aaSimil[i][j] = dSimilarity; |
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177 | } |
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178 | } |
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179 | |
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180 | if (bPrintNames) |
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181 | { |
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182 | // if "-names" switch was given, |
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183 | // print the number of genotypes and their names |
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184 | printf("%li\n", pvGenos->size()); |
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185 | int iGen; |
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186 | for (iGen = 0; iGen < (int) pvNames->size(); iGen++) |
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187 | { |
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188 | printf("%s\n", pvNames->at(iGen)); |
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189 | } |
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190 | } // if (bPrintNames) |
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191 | |
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192 | // print out the matrix of similarities |
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193 | for (i = 0; i < (int) pvGenos->size(); i++) |
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194 | { |
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195 | for (j = 0; j < (int) pvGenos->size(); j++) |
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196 | { |
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197 | printf("%.2lf\t", aaSimil[i][j]); |
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198 | } |
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199 | printf("\n"); |
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200 | } |
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201 | |
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202 | // delete vectors and arrays |
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203 | for (i = 0; i < (int) pvGenos->size(); i++) |
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204 | { |
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205 | delete pvGenos->operator[](i); |
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206 | delete [] pvNames->operator[](i); |
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207 | delete [] aaSimil[i]; |
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208 | } |
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209 | |
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210 | delete pvGenos; |
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211 | delete pvNames; |
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212 | delete [] aaSimil; |
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213 | |
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214 | return 0; |
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215 | } |
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