1 | /* |
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2 | * Definition of all objects belonging to this version of |
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3 | * the valid names text file |
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4 | * |
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5 | * 29. November 2002 |
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6 | * |
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7 | * coded by Lothar Richter |
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8 | * |
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9 | * Copyright (C) 2002 Department of Microbiology (Technical University Munich) |
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10 | */ |
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11 | |
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12 | #if defined(DEVEL_LOTHAR) |
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13 | #define DUMP |
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14 | #endif // DEVEL_LOTHAR |
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15 | |
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16 | #include "nt_validNameParser.hxx" |
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17 | |
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18 | #include <arb_assert.h> |
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19 | |
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20 | #include <cstdlib> |
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21 | #include <cstdlib> |
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22 | #include <iostream> |
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23 | #include <fstream> |
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24 | |
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25 | using namespace std; |
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26 | |
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27 | #define nt_assert(bed) arb_assert(bed) |
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28 | |
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29 | namespace validNames { |
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30 | |
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31 | |
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32 | TokLPtr tokenize(const string& description, TokLPtr tokenLP) |
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33 | { |
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34 | size_t tokenEnd = 0; |
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35 | size_t tokenBegin = 0; |
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36 | |
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37 | while (tokenEnd != description.size()) { // CC : warning: comparison between signed and unsigned (tokenEnd sollte nicht 'int' sondern 'unsigned' sein) |
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38 | tokenEnd = description.find_first_of(' ', tokenBegin); |
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39 | if (tokenEnd == string::npos) tokenEnd = description.size(); |
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40 | int tokLength = tokenEnd - tokenBegin; |
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41 | if (tokLength != 0) { |
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42 | tokenLP->push_back(description.substr(tokenBegin, tokenEnd - tokenBegin)); |
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43 | } |
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44 | tokenBegin = tokenEnd + 1; |
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45 | |
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46 | } |
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47 | return tokenLP; |
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48 | } |
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49 | |
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50 | |
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51 | |
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52 | |
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53 | |
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54 | Desco determineType(const string& descriptionString) |
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55 | { // begin determineType |
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56 | |
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57 | DESCT actType = NOTYPE; |
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58 | TokLPtr tokenLP = new TokL; |
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59 | tokenLP = tokenize(descriptionString, tokenLP); |
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60 | // remove all tokens in parentheses |
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61 | { |
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62 | TokL::iterator it = tokenLP->begin(); |
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63 | while (it != tokenLP->end()) { |
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64 | if (((*it).at(0) == '(') && *it != string("(corrig.)")) it = tokenLP->erase(it); |
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65 | else ++it; |
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66 | } |
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67 | } |
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68 | |
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69 | // check first word for upper case letters |
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70 | string descNames[6]; // first the valid genus, species, subsp. then the other names |
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71 | // stores occurrence of subsp. which is needed to retrieve the right tokens later on and status flags |
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72 | int sspPos[2] = { 0, 0 }; // token subsp. occurs maximum twice |
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73 | int ssp = 0; |
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74 | bool isValid = true; |
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75 | bool isRenamed = false; |
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76 | bool isHetero = false; |
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77 | bool isHomo = false; |
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78 | bool isGenus = false; |
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79 | // bool isSee = false; |
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80 | bool isCorr = false; |
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81 | |
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82 | |
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83 | |
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84 | for (TokL::iterator it = tokenLP->begin(); it != tokenLP->end(); it ++, ssp++) |
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85 | { |
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86 | if (isUpperCase(*it)) { |
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87 | isGenus = true; |
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88 | #if defined(DUMP) |
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89 | std::cout << "genus detected" << std::endl; |
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90 | #endif // DUMP |
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91 | } |
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92 | |
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93 | |
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94 | else { // begin operators |
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95 | if (*it == string("->")) { |
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96 | nt_assert(!isHetero); |
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97 | nt_assert(!isHomo); |
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98 | nt_assert(isValid); // only one operator per line allowed |
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99 | isRenamed = true; |
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100 | isValid = false; |
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101 | #if defined(DUMP) |
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102 | std::cout << "renaming detected" << std::endl; |
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103 | #endif // DUMP |
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104 | } |
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105 | else { |
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106 | if (*it == string("=>")) { |
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107 | nt_assert(!isRenamed); |
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108 | nt_assert(!isHomo); |
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109 | nt_assert(isValid); |
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110 | isHetero = true; |
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111 | isValid = false; |
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112 | #if defined(DUMP) |
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113 | std::cout << "heteronym detected" << std::endl; |
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114 | #endif // DUMP |
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115 | } |
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116 | else { |
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117 | if (*it == string("=")) { |
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118 | nt_assert(!isRenamed); |
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119 | nt_assert(!isHetero); |
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120 | nt_assert(isValid); |
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121 | isHomo = true; |
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122 | isValid = false; |
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123 | #if defined(DUMP) |
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124 | std::cout << "homonym detected" << std::endl; |
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125 | #endif // DUMP |
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126 | } |
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127 | else { |
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128 | if (*it == string("(corrig.)")) { |
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129 | isCorr = true; |
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130 | #if defined(DUMP) |
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131 | std::cout << "correction" << std::endl; |
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132 | #endif // DUMP |
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133 | } |
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134 | else { |
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135 | if (*it == string("see:")) { |
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136 | // isSee = true; |
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137 | isValid = false; |
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138 | #if defined(DUMP) |
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139 | std::cout << "reference" << std::endl; |
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140 | #endif // DUMP |
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141 | } |
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142 | else { |
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143 | if (*it == string("subsp.")) { |
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144 | #if defined(DUMP) |
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145 | std::cout << "subspecies detected at position: >>>" << ssp << "<<<" << std::endl; |
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146 | #endif // DUMP |
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147 | ssp == 2 ? sspPos[0] = ssp : sspPos[1] = ssp; |
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148 | // max. one subsp. on each operator side |
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149 | #if defined(DUMP) |
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150 | std::cout << "position of subsp.: " << sspPos[0] << "\tand: " << sspPos[1] << std::endl; |
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151 | #endif // DUMP |
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152 | } |
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153 | } |
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154 | } |
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155 | } |
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156 | } |
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157 | } |
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158 | } |
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159 | } |
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160 | |
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161 | |
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162 | |
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163 | if (isGenus) { |
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164 | #if defined(DUMP) |
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165 | std::cout << " GENUS description found " << std::endl; |
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166 | #endif // DUMP |
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167 | if (isValid) { |
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168 | descNames[0] = (*tokenLP)[0]; |
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169 | actType = VALGEN; |
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170 | #if defined(DUMP) |
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171 | std::cout << "VALIDGEN type set to: " << actType << std::endl; |
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172 | #endif// DUMP |
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173 | } |
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174 | else { |
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175 | if (isHetero) { |
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176 | descNames[0] = (*tokenLP)[2]; |
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177 | descNames[3] = (*tokenLP)[0]; |
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178 | actType = HETGEN; |
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179 | #if defined(DUMP) |
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180 | std::cout << "HETERONYMGEN type set to: " << actType << std::endl; |
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181 | #endif // DUMP |
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182 | } |
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183 | else { |
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184 | if (isHomo) { |
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185 | descNames[0] = (*tokenLP)[2]; |
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186 | descNames[3] = (*tokenLP)[0]; |
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187 | actType = HOMGEN; |
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188 | #if defined(DUMP) |
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189 | std::cout << "HOMONYMGEN type set to: " << actType << std::endl; |
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190 | #endif // DUMP |
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191 | |
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192 | } |
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193 | else { |
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194 | |
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195 | if (isRenamed) { |
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196 | descNames[0] = (*tokenLP)[2]; |
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197 | descNames[3] = (*tokenLP)[0]; |
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198 | actType = RENGEN; |
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199 | #if defined(DUMP) |
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200 | std::cout << "RENAMEDGEN type set to: " << actType << std::endl; |
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201 | #endif // DUMP |
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202 | } |
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203 | else { |
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204 | #if defined(DUMP) |
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205 | std::cout << "no meaningful combination of conditions reached" << std::endl |
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206 | << "for line: " << descriptionString << std::endl; |
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207 | std::cout << "description type is set to NOTYPE: " << NOTYPE << std::endl; |
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208 | #endif // DUMP |
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209 | isValid = false; |
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210 | #if defined(DUMP) |
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211 | std::cout << "isValid set to false " << std::endl; |
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212 | #endif // DUMP |
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213 | actType = NOTYPE; |
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214 | } |
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215 | } |
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216 | } |
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217 | } |
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218 | } |
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219 | else { |
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220 | |
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221 | // just fancy experimental , maybe not 100% correct but looks good |
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222 | if (!(((sspPos[0] == 0) || (sspPos[0] == 2)) && (((sspPos[1] > 4)&&(sspPos[1]< 9))||(sspPos[1]==0)))) |
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223 | { |
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224 | #if defined(DUMP) |
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225 | std::cout << "subsp. at strange position found in line:" << std::endl << descriptionString << endl; |
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226 | std::cout << "description type is set to NOTYPE: " << NOTYPE << std::endl; |
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227 | #endif // DUMP |
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228 | isValid = false; |
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229 | #if defined(DUMP) |
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230 | std::cout << "isValid set to false " << std::endl; |
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231 | #endif // DUMP |
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232 | actType = NOTYPE; |
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233 | } |
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234 | |
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235 | if (isValid) { |
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236 | descNames[0] = (*tokenLP)[0]; |
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237 | descNames[1] = (*tokenLP)[1]; |
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238 | if (sspPos[0] != 0) { descNames[2] = (*tokenLP)[sspPos[0]+1]; } // only if subsp. exists |
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239 | actType = VALSPEC; |
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240 | } |
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241 | else { // begin else isHetero |
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242 | if (isHetero) { |
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243 | descNames[0] = (*tokenLP)[3 + sspPos[0]]; |
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244 | descNames[1] = (*tokenLP)[4 + sspPos[0]]; |
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245 | if (sspPos[1]!=0) { descNames[2]=(*tokenLP)[6 + sspPos[0]]; } // only if subsp. exists |
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246 | |
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247 | descNames[3] = (*tokenLP)[0]; |
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248 | descNames[4] = (*tokenLP)[1]; |
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249 | if (sspPos[0]!=0) { descNames[5]=(*tokenLP)[sspPos[0]+1]; } // only if subsp. exists |
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250 | |
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251 | actType = HETSPEC; |
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252 | } |
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253 | else { |
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254 | if (isHomo) { |
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255 | descNames[0] = (*tokenLP)[3 + sspPos[0]]; |
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256 | descNames[1] = (*tokenLP)[4 + sspPos[0]]; |
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257 | if (sspPos[1]!=0) { descNames[2]=(*tokenLP)[6 + sspPos[0]]; } // only if subsp. exists |
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258 | |
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259 | descNames[3] = (*tokenLP)[0]; |
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260 | descNames[4] = (*tokenLP)[1]; |
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261 | if (sspPos[0]!=0) { descNames[5]=(*tokenLP)[sspPos[0]+1]; } // only if subsp. exists |
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262 | |
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263 | actType = HOMSPEC; |
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264 | |
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265 | } |
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266 | else { // else branch isHomo |
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267 | if (isRenamed) { |
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268 | descNames[0] = (*tokenLP)[3 + sspPos[0]]; |
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269 | descNames[1] = (*tokenLP)[4 + sspPos[0]]; |
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270 | if (sspPos[1]!=0) { descNames[2]=(*tokenLP)[6 + sspPos[0]]; } // only if subsp. exists |
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271 | |
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272 | descNames[3] = (*tokenLP)[0]; |
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273 | descNames[4] = (*tokenLP)[1]; |
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274 | if (sspPos[0]!=0) { descNames[5]=(*tokenLP)[sspPos[0]+1]; } // only if subsp. exists |
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275 | |
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276 | actType = RENSPEC; |
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277 | |
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278 | } |
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279 | else { // species remaining cases |
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280 | #if defined(DUMP) |
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281 | std::cout << "not a valid description line detected" << std::endl; |
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282 | std::cout << "isValid: " << isValid << std::endl; |
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283 | std::cout << "isRenamed: " << isRenamed << std::endl; |
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284 | std::cout << "isHetero: " << isHetero << std::endl; |
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285 | std::cout << "isHomo: " << isHomo << std::endl; |
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286 | std::cout << "isGenus: " << isGenus << std::endl; |
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287 | std::cout << "isSee: " << isSee << std::endl; |
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288 | std::cout << "isCorr: " << isCorr << std::endl; |
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289 | std::cout << "sspPos: " << sspPos[0] << " and " << sspPos[1] << std::endl; |
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290 | std::cout << descriptionString << std::endl; |
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291 | #endif // DUMP |
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292 | actType = NOTYPE; |
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293 | } |
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294 | |
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295 | } |
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296 | } |
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297 | } |
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298 | } |
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299 | |
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300 | |
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301 | #if defined(DUMP) |
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302 | std::cout << descriptionString << std::endl; |
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303 | std::cout << "classified as " << actType << std::endl; |
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304 | #endif // DUMP |
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305 | |
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306 | Desco actDesc(actType, isCorr, descNames[0], descNames[1], descNames[2], descNames[3], descNames[4], descNames[5]); |
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307 | delete tokenLP; |
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308 | return actDesc; |
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309 | } |
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310 | |
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311 | |
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312 | string Desco::getFirstName() { |
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313 | string tmp = firstgen; |
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314 | if (!firstspec.empty()) { |
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315 | tmp = tmp + " " + firstspec; |
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316 | if (!firstsub.empty()) { |
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317 | tmp = tmp + " " + "subsp." + " " + firstsub; |
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318 | } |
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319 | } |
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320 | |
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321 | |
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322 | return tmp; |
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323 | } |
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324 | |
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325 | string Desco::getSecondName() { |
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326 | string tmp = secondgen; |
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327 | if (!secondspec.empty()) { |
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328 | tmp = tmp + " " + firstspec; |
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329 | if (!secondsub.empty()) { |
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330 | tmp = tmp + " " + "subsp." + " " + secondsub; |
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331 | } |
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332 | } |
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333 | return tmp; |
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334 | } |
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335 | |
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336 | |
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337 | bool isUpperCase(const string& input) |
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338 | { |
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339 | for (size_t i=0; i<input.length(); ++i) |
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340 | { |
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341 | if (input[i]<'A' || input[i]>'Z') { return false; } |
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342 | } |
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343 | return true; |
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344 | } |
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345 | } |
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