1 | // =============================================================== // |
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2 | // // |
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3 | // File : adGene.cxx // |
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4 | // Purpose : Basic gene access functions // |
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5 | // // |
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6 | // Coded by Ralf Westram (coder@reallysoft.de) in July 2002 // |
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7 | // Institute of Microbiology (Technical University Munich) // |
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8 | // http://www.arb-home.de/ // |
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9 | // // |
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10 | // =============================================================== // |
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11 | |
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12 | #include "gb_local.h" |
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13 | |
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14 | #include <adGene.h> |
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15 | #include <arbdbt.h> |
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16 | #include <arb_strbuf.h> |
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17 | #include <arb_strarray.h> |
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18 | |
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19 | |
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20 | bool GEN_is_genome_db(GBDATA *gb_main, int default_value) { |
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21 | // default_value == 0 -> default to normal database |
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22 | // == 1 -> default to GENOM database |
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23 | // == -1 -> assume that type is already defined |
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24 | GBDATA *gb_genom_db = GB_entry(gb_main, GENOM_DB_TYPE); |
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25 | |
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26 | if (!gb_genom_db) { // no DB-type entry -> create one with default |
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27 | GB_ERROR error = NULL; |
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28 | |
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29 | assert_or_exit(default_value != -1); // first call to GEN_is_genome_db has to provide a 'default_value' |
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30 | |
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31 | gb_genom_db = GB_create(gb_main, GENOM_DB_TYPE, GB_INT); |
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32 | if (!gb_genom_db) error = GB_await_error(); |
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33 | else error = GB_write_int(gb_genom_db, default_value); |
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34 | |
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35 | if (error) GBK_terminatef("Fatal in GEN_is_genome_db: %s", error); |
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36 | } |
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37 | |
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38 | return GB_read_int(gb_genom_db) != 0; |
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39 | } |
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40 | |
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41 | // -------------- |
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42 | // genes: |
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43 | |
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44 | GBDATA* GEN_findOrCreate_gene_data(GBDATA *gb_species) { |
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45 | GBDATA *gb_gene_data = GB_search(gb_species, "gene_data", GB_CREATE_CONTAINER); |
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46 | gb_assert(gb_gene_data); |
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47 | return gb_gene_data; |
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48 | } |
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49 | |
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50 | GBDATA* GEN_find_gene_data(GBDATA *gb_species) { |
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51 | return GB_search(gb_species, "gene_data", GB_FIND); |
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52 | } |
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53 | |
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54 | GBDATA* GEN_expect_gene_data(GBDATA *gb_species) { |
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55 | GBDATA *gb_gene_data = GB_search(gb_species, "gene_data", GB_FIND); |
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56 | gb_assert(gb_gene_data); |
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57 | return gb_gene_data; |
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58 | } |
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59 | |
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60 | GBDATA* GEN_find_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name) { |
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61 | GBDATA *gb_name = GB_find_string(gb_gene_data, "name", name, GB_IGNORE_CASE, SEARCH_GRANDCHILD); |
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62 | |
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63 | if (gb_name) return GB_get_father(gb_name); // found existing gene |
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64 | return 0; |
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65 | } |
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66 | |
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67 | GBDATA* GEN_find_gene(GBDATA *gb_species, const char *name) { |
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68 | // find existing gene. returns 0 if it does not exist. |
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69 | GBDATA *gb_gene_data = GEN_find_gene_data(gb_species); |
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70 | return gb_gene_data ? GEN_find_gene_rel_gene_data(gb_gene_data, name) : 0; |
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71 | } |
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72 | |
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73 | static GBDATA* GEN_create_nonexisting_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name) { |
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74 | GB_ERROR error = GB_push_transaction(gb_gene_data); |
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75 | GBDATA *gb_gene = 0; |
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76 | |
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77 | gb_assert(!GEN_find_gene_rel_gene_data(gb_gene_data, name)); // don't call this function if you are not sure that the gene does not exists! |
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78 | |
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79 | if (!error) { |
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80 | gb_gene = GB_create_container(gb_gene_data, "gene"); |
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81 | error = gb_gene ? GBT_write_string(gb_gene, "name", name) : GB_await_error(); |
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82 | } |
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83 | |
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84 | gb_assert(gb_gene || error); |
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85 | error = GB_end_transaction(gb_gene_data, error); |
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86 | if (error) GB_export_error(error); |
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87 | |
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88 | return gb_gene; |
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89 | } |
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90 | |
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91 | GBDATA* GEN_create_nonexisting_gene(GBDATA *gb_species, const char *name) { // needed by ../PERL_SCRIPTS/GENOME/GI.pm@create_nonexisting_gene |
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92 | return GEN_create_nonexisting_gene_rel_gene_data(GEN_findOrCreate_gene_data(gb_species), name); |
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93 | } |
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94 | |
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95 | GBDATA* GEN_find_or_create_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name) { |
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96 | GBDATA *gb_gene = 0; |
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97 | |
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98 | // Search for a gene, when gene does not exist create it |
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99 | if (!name || !name[0]) { |
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100 | GB_export_error("Missing gene name"); |
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101 | } |
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102 | else { |
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103 | GBDATA *gb_name = GB_find_string(gb_gene_data, "name", name, GB_IGNORE_CASE, SEARCH_GRANDCHILD); |
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104 | |
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105 | if (gb_name) { |
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106 | gb_gene = GB_get_father(gb_name); // found existing gene |
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107 | } |
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108 | else { |
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109 | GB_ERROR error = GB_push_transaction(gb_gene_data); |
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110 | |
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111 | if (!error) { |
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112 | gb_gene = GB_create_container(gb_gene_data, "gene"); |
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113 | error = GBT_write_string(gb_gene, "name", name); |
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114 | } |
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115 | error = GB_end_transaction(gb_gene_data, error); |
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116 | if (error) { |
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117 | gb_gene = NULL; |
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118 | GB_export_error(error); |
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119 | } |
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120 | } |
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121 | } |
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122 | return gb_gene; |
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123 | } |
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124 | |
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125 | GBDATA* GEN_first_gene(GBDATA *gb_species) { |
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126 | return GB_entry(GEN_expect_gene_data(gb_species), "gene"); |
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127 | } |
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128 | |
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129 | GBDATA* GEN_first_gene_rel_gene_data(GBDATA *gb_gene_data) { |
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130 | return GB_entry(gb_gene_data, "gene"); |
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131 | } |
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132 | |
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133 | GBDATA* GEN_next_gene(GBDATA *gb_gene) { |
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134 | gb_assert(GB_has_key(gb_gene, "gene")); |
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135 | return GB_nextEntry(gb_gene); |
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136 | } |
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137 | |
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138 | GBDATA *GEN_first_marked_gene(GBDATA *gb_species) { |
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139 | return GB_first_marked(GEN_expect_gene_data(gb_species), "gene"); |
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140 | } |
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141 | GBDATA *GEN_next_marked_gene(GBDATA *gb_gene) { |
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142 | return GB_next_marked(gb_gene, "gene"); |
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143 | } |
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144 | |
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145 | // ---------------------- |
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146 | // gene position |
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147 | |
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148 | static GEN_position *lastFreedPosition = 0; |
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149 | |
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150 | GEN_position *GEN_new_position(int parts, bool joinable) { |
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151 | GEN_position *pos; |
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152 | |
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153 | size_t pos_size = parts*sizeof(pos->start_pos[0]); |
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154 | size_t comp_size = parts*sizeof(pos->complement[0]); |
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155 | size_t data_size = 2*pos_size+3*comp_size; |
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156 | |
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157 | gb_assert(parts>0); |
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158 | |
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159 | if (lastFreedPosition && lastFreedPosition->parts == parts) { |
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160 | pos = lastFreedPosition; |
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161 | lastFreedPosition = 0; |
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162 | memset(pos->start_pos, 0, data_size); |
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163 | } |
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164 | else { |
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165 | ARB_calloc(pos, 1); |
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166 | pos->parts = parts; |
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167 | pos->start_pos = (size_t*)ARB_calloc<char>(data_size); |
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168 | pos->stop_pos = pos->start_pos+parts; |
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169 | pos->complement = (unsigned char*)(pos->stop_pos+parts); |
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170 | } |
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171 | |
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172 | pos->joinable = joinable; |
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173 | pos->start_uncertain = 0; |
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174 | pos->stop_uncertain = 0; |
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175 | |
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176 | return pos; |
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177 | } |
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178 | |
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179 | void GEN_use_uncertainties(GEN_position *pos) { |
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180 | if (pos->start_uncertain == 0) { |
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181 | // space was already allocated in GEN_new_position |
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182 | pos->start_uncertain = pos->complement+pos->parts; |
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183 | pos->stop_uncertain = pos->start_uncertain+pos->parts; |
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184 | |
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185 | size_t comp_size = pos->parts*sizeof(pos->complement[0]); |
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186 | memset(pos->start_uncertain, '=', 2*comp_size); |
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187 | } |
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188 | } |
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189 | |
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190 | void GEN_free_position(GEN_position *pos) { |
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191 | if (pos) { |
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192 | if (lastFreedPosition) { |
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193 | free(lastFreedPosition->start_pos); // rest is allocated together with start_pos |
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194 | free(lastFreedPosition); |
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195 | } |
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196 | |
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197 | lastFreedPosition = pos; |
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198 | } |
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199 | } |
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200 | |
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201 | static struct GEN_position_mem_handler { |
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202 | ~GEN_position_mem_handler() { GEN_free_position(NULL); } |
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203 | } GEN_position_dealloc; |
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204 | |
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205 | |
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206 | static GB_ERROR parseCSV(GBDATA *gb_gene, const char *field_name, size_t parts_expected, ConstStrArray& parseTable) { |
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207 | // reads a field and splits the content at ',' |
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208 | // results are stored in parseTable |
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209 | |
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210 | GB_ERROR error = 0; |
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211 | GBDATA *gb_field = GB_entry(gb_gene, field_name); |
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212 | if (!gb_field) error = GBS_global_string("Expected entry '%s' missing", field_name); |
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213 | else { |
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214 | char *content = GB_read_string(gb_field); |
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215 | if (!content) error = GB_await_error(); |
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216 | else { |
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217 | parseTable.erase(); |
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218 | GBT_splitNdestroy_string(parseTable, content, ','); |
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219 | if (parseTable.size() != parts_expected) { |
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220 | error = GBS_global_string("Expected %zu CSV, found %zu", parts_expected, parseTable.size()); |
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221 | } |
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222 | } |
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223 | } |
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224 | return error; |
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225 | } |
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226 | |
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227 | static GB_ERROR parsePositions(GBDATA *gb_gene, const char *field_name, int parts_expected, size_t *results, ConstStrArray& parseTable) { |
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228 | GB_ERROR error = parseCSV(gb_gene, field_name, parts_expected, parseTable); |
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229 | if (!error) { |
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230 | int p; |
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231 | for (p = 0; p<parts_expected && !error; p++) { |
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232 | char *end; |
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233 | results[p] = strtol(parseTable[p], &end, 10); |
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234 | if (end == parseTable[p]) { // error |
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235 | error = GBS_global_string("can't convert '%s' to number", parseTable[p]); |
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236 | } |
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237 | } |
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238 | } |
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239 | if (error) { |
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240 | error = GBS_global_string("While parsing field '%s': %s", field_name, error); |
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241 | } |
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242 | return error; |
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243 | } |
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244 | |
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245 | GEN_position *GEN_read_position(GBDATA *gb_gene) { |
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246 | int parts = 1; |
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247 | bool joinable = false; |
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248 | GBDATA *gb_pos_joined = GB_entry(gb_gene, "pos_joined"); |
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249 | GEN_position *pos = 0; |
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250 | GB_ERROR error = 0; |
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251 | |
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252 | if (gb_pos_joined) { |
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253 | parts = GB_read_int(gb_pos_joined); |
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254 | if (parts != 1) { // split |
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255 | if (parts>1) joinable = true; |
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256 | else if (parts<-1) parts = -parts; // neg value means "not joinable" (comes from feature location 'order(...)') |
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257 | else error = GBS_global_string("Illegal value %i in 'pos_joined'", parts); |
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258 | } |
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259 | } |
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260 | |
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261 | if (!error) { |
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262 | pos = GEN_new_position(parts, joinable); |
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263 | |
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264 | ConstStrArray parseTable; |
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265 | parseTable.reserve(parts); |
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266 | |
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267 | error = parsePositions(gb_gene, "pos_start", parts, pos->start_pos, parseTable); |
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268 | if (!error) error = parsePositions(gb_gene, "pos_stop", parts, pos->stop_pos, parseTable); |
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269 | |
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270 | int p; |
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271 | if (!error) { |
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272 | error = parseCSV(gb_gene, "pos_complement", parts, parseTable); |
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273 | for (p = 0; p<parts && !error; p++) { |
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274 | const char *val = parseTable[p]; |
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275 | if ((val[0] != '0' && val[0] != '1') || val[1] != 0) { |
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276 | error = GBS_global_string("Invalid content '%s' in 'pos_complement' (expected: \"01\")", val); |
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277 | } |
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278 | else { |
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279 | pos->complement[p] = (unsigned char)atoi(val); |
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280 | } |
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281 | } |
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282 | } |
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283 | |
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284 | if (!error) { |
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285 | GBDATA *gb_pos_certain = GB_entry(gb_gene, "pos_certain"); |
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286 | |
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287 | if (gb_pos_certain) { |
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288 | error = parseCSV(gb_gene, "pos_certain", parts, parseTable); |
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289 | GEN_use_uncertainties(pos); |
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290 | for (p = 0; p<parts && !error; p++) { |
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291 | const unsigned char *val = (unsigned char *)(parseTable[p]); |
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292 | int vp; |
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293 | |
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294 | for (vp = 0; vp<2; vp++) { |
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295 | unsigned char c = val[vp]; |
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296 | if (c != '<' && c != '=' && c != '>' && (c != "+-"[vp])) { |
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297 | error = GBS_global_string("Invalid content '%s' in 'pos_certain' (expected 2 from \"<=>\")", val); |
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298 | } |
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299 | } |
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300 | if (!error) { |
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301 | pos->start_uncertain[p] = val[0]; |
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302 | pos->stop_uncertain[p] = val[1]; |
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303 | } |
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304 | } |
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305 | } |
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306 | } |
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307 | } |
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308 | |
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309 | gb_assert(error || pos); |
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310 | if (error) { |
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311 | GB_export_error(error); |
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312 | if (pos) { |
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313 | GEN_free_position(pos); |
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314 | pos = 0; |
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315 | } |
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316 | } |
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317 | return pos; |
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318 | } |
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319 | |
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320 | GB_ERROR GEN_write_position(GBDATA *gb_gene, const GEN_position *pos, long seqLength) { |
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321 | // if 'seqLength' is != 0, it is used to check the correctness of 'pos' |
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322 | // (otherwise this function reads the genome-sequence to detect its length) |
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323 | |
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324 | GB_ERROR error = 0; |
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325 | GBDATA *gb_pos_joined = GB_entry(gb_gene, "pos_joined"); |
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326 | GBDATA *gb_pos_certain = GB_entry(gb_gene, "pos_certain"); |
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327 | GBDATA *gb_pos_start; |
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328 | GBDATA *gb_pos_stop; |
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329 | GBDATA *gb_pos_complement; |
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330 | int p; |
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331 | |
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332 | gb_assert(pos); |
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333 | |
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334 | gb_pos_start = GB_search(gb_gene, "pos_start", GB_STRING); |
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335 | if (!gb_pos_start) error = GB_await_error(); |
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336 | |
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337 | if (!error) { |
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338 | gb_pos_stop = GB_search(gb_gene, "pos_stop", GB_STRING); |
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339 | if (!gb_pos_stop) error = GB_await_error(); |
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340 | } |
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341 | if (!error) { |
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342 | gb_pos_complement = GB_search(gb_gene, "pos_complement", GB_STRING); |
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343 | if (!gb_pos_complement) error = GB_await_error(); |
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344 | } |
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345 | |
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346 | if (!error) { |
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347 | if (pos->start_uncertain) { |
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348 | if (!gb_pos_certain) { |
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349 | gb_pos_certain = GB_search(gb_gene, "pos_certain", GB_STRING); |
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350 | if (!gb_pos_certain) error = GB_await_error(); |
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351 | } |
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352 | } |
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353 | else { |
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354 | if (gb_pos_certain) { |
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355 | error = GB_delete(gb_pos_certain); |
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356 | gb_pos_certain = 0; |
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357 | } |
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358 | } |
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359 | } |
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360 | |
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361 | // test data |
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362 | if (!error) { |
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363 | size_t length; |
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364 | |
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365 | if (seqLength) { |
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366 | length = seqLength; |
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367 | } |
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368 | else { // unknown -> autodetect |
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369 | GBDATA *gb_organism = GB_get_grandfather(gb_gene); |
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370 | GBDATA *gb_genome = GBT_find_sequence(gb_organism, GENOM_ALIGNMENT); |
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371 | |
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372 | length = GB_read_count(gb_genome); |
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373 | } |
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374 | |
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375 | for (p = 0; p<pos->parts && !error; ++p) { |
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376 | char c; |
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377 | |
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378 | c = pos->complement[p]; gb_assert(c == 0 || c == 1); |
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379 | if (c<0 || c>1) { |
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380 | error = GBS_global_string("Illegal value %i in complement", int(c)); |
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381 | } |
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382 | else { |
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383 | if (pos->start_pos[p]>pos->stop_pos[p]) { |
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384 | error = GBS_global_string("Illegal positions (%zu>%zu)", pos->start_pos[p], pos->stop_pos[p]); |
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385 | } |
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386 | else if (pos->start_pos[p] == 0) { |
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387 | error = GBS_global_string("Illegal start position %zu", pos->start_pos[p]); |
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388 | } |
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389 | else if (pos->stop_pos[p] > length) { |
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390 | error = GBS_global_string("Illegal stop position %zu (>length(=%zu))", pos->stop_pos[p], length); |
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391 | } |
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392 | else { |
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393 | if (pos->start_uncertain) { |
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394 | c = pos->start_uncertain[p]; |
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395 | char c2 = pos->stop_uncertain[p]; |
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396 | |
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397 | if (!c || strchr("<=>+", c) == 0) error = GBS_global_string("Invalid uncertainty '%c'", c); |
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398 | else if (!c2 || strchr("<=>-", c2) == 0) error = GBS_global_string("Invalid uncertainty '%c'", c2); |
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399 | else { |
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400 | if (c == '+' || c2 == '-') { |
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401 | if (c == '+' && c2 == '-') { |
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402 | if (pos->start_pos[p] != pos->stop_pos[p]-1) { |
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403 | error = GBS_global_string("Invalid positions %zu^%zu for uncertainties +-", pos->start_pos[p], pos->stop_pos[p]); |
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404 | } |
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405 | } |
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406 | else { |
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407 | error = "uncertainties '+' and '-' can only be used together"; |
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408 | } |
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409 | } |
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410 | } |
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411 | } |
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412 | } |
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413 | } |
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414 | } |
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415 | } |
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416 | |
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417 | if (!error) { |
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418 | if (pos->parts == 1) { |
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419 | if (gb_pos_joined) error = GB_delete(gb_pos_joined); |
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420 | |
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421 | if (!error) error = GB_write_string(gb_pos_start, GBS_global_string("%zu", pos->start_pos[0])); |
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422 | if (!error) error = GB_write_string(gb_pos_stop, GBS_global_string("%zu", pos->stop_pos[0])); |
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423 | if (!error) error = GB_write_string(gb_pos_complement, GBS_global_string("%c", pos->complement[0]+'0')); |
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424 | |
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425 | if (!error && gb_pos_certain) { |
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426 | error = GB_write_string(gb_pos_certain, GBS_global_string("%c%c", pos->start_uncertain[0], pos->stop_uncertain[0])); |
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427 | } |
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428 | } |
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429 | else { |
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430 | if (!gb_pos_joined) { |
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431 | gb_pos_joined = GB_search(gb_gene, "pos_joined", GB_INT); |
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432 | if (!gb_pos_joined) error = GB_await_error(); |
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433 | } |
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434 | if (!error) error = GB_write_int(gb_pos_joined, pos->parts * (pos->joinable ? 1 : -1)); // neg. parts means not joinable |
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435 | |
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436 | if (!error) { |
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437 | GBS_strstruct *start = GBS_stropen(12*pos->parts); |
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438 | GBS_strstruct *stop = GBS_stropen(12*pos->parts); |
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439 | GBS_strstruct *complement = GBS_stropen(2*pos->parts); |
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440 | GBS_strstruct *uncertain = GBS_stropen(3*pos->parts); |
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441 | |
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442 | for (p = 0; p<pos->parts; ++p) { |
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443 | if (p>0) { |
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444 | GBS_chrcat(start, ','); |
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445 | GBS_chrcat(stop, ','); |
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446 | GBS_chrcat(complement, ','); |
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447 | GBS_chrcat(uncertain, ','); |
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448 | } |
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449 | GBS_strcat(start, GBS_global_string("%zu", pos->start_pos[p])); |
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450 | GBS_strcat(stop, GBS_global_string("%zu", pos->stop_pos[p])); |
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451 | GBS_chrcat(complement, pos->complement[p]+'0'); |
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452 | if (gb_pos_certain) { |
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453 | GBS_chrcat(uncertain, pos->start_uncertain[p]); |
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454 | GBS_chrcat(uncertain, pos->stop_uncertain[p]); |
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455 | } |
---|
456 | } |
---|
457 | |
---|
458 | char *sstart = GBS_strclose(start); |
---|
459 | char *sstop = GBS_strclose(stop); |
---|
460 | char *scomplement = GBS_strclose(complement); |
---|
461 | char *suncertain = GBS_strclose(uncertain); |
---|
462 | |
---|
463 | error = GB_write_string(gb_pos_start, sstart); |
---|
464 | if (!error) error = GB_write_string(gb_pos_stop, sstop); |
---|
465 | if (!error) error = GB_write_string(gb_pos_complement, scomplement); |
---|
466 | if (!error && gb_pos_certain) error = GB_write_string(gb_pos_certain, suncertain); |
---|
467 | |
---|
468 | free(suncertain); |
---|
469 | free(scomplement); |
---|
470 | free(sstop); |
---|
471 | free(sstart); |
---|
472 | } |
---|
473 | } |
---|
474 | } |
---|
475 | |
---|
476 | return error; |
---|
477 | } |
---|
478 | |
---|
479 | static GEN_position *location2sort = 0; |
---|
480 | |
---|
481 | static int cmp_location_parts(const void *v1, const void *v2) { |
---|
482 | int i1 = *(int*)v1; |
---|
483 | int i2 = *(int*)v2; |
---|
484 | |
---|
485 | int cmp = location2sort->start_pos[i1]-location2sort->start_pos[i2]; |
---|
486 | if (!cmp) { |
---|
487 | cmp = location2sort->stop_pos[i1]-location2sort->stop_pos[i2]; |
---|
488 | } |
---|
489 | return cmp; |
---|
490 | } |
---|
491 | |
---|
492 | void GEN_sortAndMergeLocationParts(GEN_position *location) { |
---|
493 | // Note: makes location partly invalid (only start_pos + stop_pos are valid afterwards) |
---|
494 | int parts = location->parts; |
---|
495 | int *idx = ARB_alloc<int>(parts); // idx[newpos] = oldpos |
---|
496 | int i, p; |
---|
497 | |
---|
498 | for (p = 0; p<parts; ++p) idx[p] = p; |
---|
499 | |
---|
500 | location2sort = location; |
---|
501 | qsort(idx, parts, sizeof(*idx), cmp_location_parts); |
---|
502 | location2sort = 0; |
---|
503 | |
---|
504 | for (p = 0; p<parts; ++p) { |
---|
505 | i = idx[p]; |
---|
506 | |
---|
507 | #define swap(a, b, type) do { type tmp = (a); (a) = (b); (b) = (tmp); } while (0) |
---|
508 | |
---|
509 | if (i != p) { |
---|
510 | swap(location->start_pos[i], location->start_pos[p], size_t); |
---|
511 | swap(location->stop_pos[i], location->stop_pos[p], size_t); |
---|
512 | swap(idx[i], idx[p], int); |
---|
513 | } |
---|
514 | } |
---|
515 | |
---|
516 | #if defined(DEBUG) && 0 |
---|
517 | printf("Locations sorted:\n"); |
---|
518 | for (p = 0; p<parts; ++p) { |
---|
519 | printf(" [%i] %i - %i %i\n", p, location->start_pos[p], location->stop_pos[p], (int)(location->complement[p])); |
---|
520 | } |
---|
521 | #endif // DEBUG |
---|
522 | |
---|
523 | i = 0; |
---|
524 | for (p = 1; p<parts; p++) { |
---|
525 | if ((location->stop_pos[i]+1) >= location->start_pos[p]) { |
---|
526 | // parts overlap or are directly consecutive |
---|
527 | |
---|
528 | location->stop_pos[i] = location->stop_pos[p]; |
---|
529 | } |
---|
530 | else { |
---|
531 | i++; |
---|
532 | location->start_pos[i] = location->start_pos[p]; |
---|
533 | location->stop_pos[i] = location->stop_pos[p]; |
---|
534 | } |
---|
535 | } |
---|
536 | location->parts = i+1; |
---|
537 | |
---|
538 | #if defined(DEBUG) && 0 |
---|
539 | parts = location->parts; |
---|
540 | printf("Locations merged:\n"); |
---|
541 | for (p = 0; p<parts; ++p) { |
---|
542 | printf(" [%i] %i - %i %i\n", p, location->start_pos[p], location->stop_pos[p], (int)(location->complement[p])); |
---|
543 | } |
---|
544 | #endif // DEBUG |
---|
545 | |
---|
546 | free(idx); |
---|
547 | } |
---|
548 | |
---|
549 | |
---|
550 | |
---|
551 | // ----------------------------------------- |
---|
552 | // test if species is pseudo-species |
---|
553 | |
---|
554 | const char *GEN_origin_organism(GBDATA *gb_pseudo) { |
---|
555 | GBDATA *gb_origin = GB_entry(gb_pseudo, "ARB_origin_species"); |
---|
556 | return gb_origin ? GB_read_char_pntr(gb_origin) : 0; |
---|
557 | } |
---|
558 | const char *GEN_origin_gene(GBDATA *gb_pseudo) { |
---|
559 | GBDATA *gb_origin = GB_entry(gb_pseudo, "ARB_origin_gene"); |
---|
560 | return gb_origin ? GB_read_char_pntr(gb_origin) : 0; |
---|
561 | } |
---|
562 | |
---|
563 | bool GEN_is_pseudo_gene_species(GBDATA *gb_species) { |
---|
564 | return GEN_origin_organism(gb_species) != 0; |
---|
565 | } |
---|
566 | |
---|
567 | // ------------------------------------------------ |
---|
568 | // find organism or gene for pseudo-species |
---|
569 | |
---|
570 | GB_ERROR GEN_organism_not_found(GBDATA *gb_pseudo) { |
---|
571 | gb_assert(GEN_is_pseudo_gene_species(gb_pseudo)); |
---|
572 | gb_assert(GEN_find_origin_organism(gb_pseudo, 0) == 0); |
---|
573 | |
---|
574 | return GB_export_errorf("The gene-species '%s' refers to an unknown organism (%s)\n" |
---|
575 | "This occurs if you rename or delete the organism or change the entry\n" |
---|
576 | "'ARB_origin_species' and will most likely cause serious problems.", |
---|
577 | GBT_read_name(gb_pseudo), |
---|
578 | GEN_origin_organism(gb_pseudo)); |
---|
579 | } |
---|
580 | |
---|
581 | // @@@ FIXME: missing: GEN_gene_not_found (like GEN_organism_not_found) |
---|
582 | |
---|
583 | // ------------------------------ |
---|
584 | // search pseudo species |
---|
585 | |
---|
586 | static const char *pseudo_species_hash_key(const char *organism_name, const char *gene_name) { |
---|
587 | return GBS_global_string("%s*%s", organism_name, gene_name); |
---|
588 | } |
---|
589 | |
---|
590 | static GBDATA *GEN_read_pseudo_species_from_hash(const GB_HASH *pseudo_hash, const char *organism_name, const char *gene_name) { |
---|
591 | return (GBDATA*)GBS_read_hash(pseudo_hash, pseudo_species_hash_key(organism_name, gene_name)); |
---|
592 | } |
---|
593 | |
---|
594 | void GEN_add_pseudo_species_to_hash(GBDATA *gb_pseudo, GB_HASH *pseudo_hash) { |
---|
595 | const char *organism_name = GEN_origin_organism(gb_pseudo); |
---|
596 | const char *gene_name = GEN_origin_gene(gb_pseudo); |
---|
597 | |
---|
598 | gb_assert(organism_name); |
---|
599 | gb_assert(gene_name); |
---|
600 | |
---|
601 | GBS_write_hash(pseudo_hash, pseudo_species_hash_key(organism_name, gene_name), (long)gb_pseudo); |
---|
602 | } |
---|
603 | |
---|
604 | GB_HASH *GEN_create_pseudo_species_hash(GBDATA *gb_main, int additionalSize) { |
---|
605 | GB_HASH *pseudo_hash = GBS_create_hash(GBT_get_species_count(gb_main)+additionalSize, GB_IGNORE_CASE); |
---|
606 | GBDATA *gb_pseudo; |
---|
607 | |
---|
608 | for (gb_pseudo = GEN_first_pseudo_species(gb_main); |
---|
609 | gb_pseudo; |
---|
610 | gb_pseudo = GEN_next_pseudo_species(gb_pseudo)) |
---|
611 | { |
---|
612 | GEN_add_pseudo_species_to_hash(gb_pseudo, pseudo_hash); |
---|
613 | } |
---|
614 | |
---|
615 | return pseudo_hash; |
---|
616 | } |
---|
617 | |
---|
618 | GBDATA *GEN_find_pseudo_species(GBDATA *gb_main, const char *organism_name, const char *gene_name, const GB_HASH *pseudo_hash) { |
---|
619 | // parameter pseudo_hash : |
---|
620 | // 0 -> use slow direct search [if you only search one] |
---|
621 | // otherwise it shall be a hash generated by GEN_create_pseudo_species_hash() [if you search several times] |
---|
622 | // Note : use GEN_add_pseudo_species_to_hash to keep hash up-to-date |
---|
623 | GBDATA *gb_pseudo; |
---|
624 | |
---|
625 | if (pseudo_hash) { |
---|
626 | gb_pseudo = GEN_read_pseudo_species_from_hash(pseudo_hash, organism_name, gene_name); |
---|
627 | } |
---|
628 | else { |
---|
629 | for (gb_pseudo = GEN_first_pseudo_species(gb_main); |
---|
630 | gb_pseudo; |
---|
631 | gb_pseudo = GEN_next_pseudo_species(gb_pseudo)) |
---|
632 | { |
---|
633 | const char *origin_gene_name = GEN_origin_gene(gb_pseudo); |
---|
634 | if (strcmp(gene_name, origin_gene_name) == 0) { |
---|
635 | const char *origin_species_name = GEN_origin_organism(gb_pseudo); |
---|
636 | if (strcmp(organism_name, origin_species_name) == 0) { |
---|
637 | break; // found pseudo species |
---|
638 | } |
---|
639 | } |
---|
640 | } |
---|
641 | } |
---|
642 | return gb_pseudo; |
---|
643 | } |
---|
644 | |
---|
645 | // ----------------------- |
---|
646 | // search origins |
---|
647 | |
---|
648 | GBDATA *GEN_find_origin_organism(GBDATA *gb_pseudo, const GB_HASH *organism_hash) { |
---|
649 | // parameter organism_hash: |
---|
650 | // 0 -> use slow direct search [if you only search one or two] |
---|
651 | // otherwise it shall be a hash generated by GBT_create_organism_hash() [if you search several times] |
---|
652 | // Note : use GBT_add_item_to_hash() to keep hash up-to-date |
---|
653 | |
---|
654 | const char *origin_species_name; |
---|
655 | GBDATA *gb_organism = 0; |
---|
656 | gb_assert(GEN_is_pseudo_gene_species(gb_pseudo)); |
---|
657 | |
---|
658 | origin_species_name = GEN_origin_organism(gb_pseudo); |
---|
659 | if (origin_species_name) { |
---|
660 | if (organism_hash) { |
---|
661 | gb_organism = (GBDATA*)GBS_read_hash(organism_hash, origin_species_name); |
---|
662 | } |
---|
663 | else { |
---|
664 | gb_organism = GBT_find_species_rel_species_data(GB_get_father(gb_pseudo), origin_species_name); |
---|
665 | } |
---|
666 | } |
---|
667 | |
---|
668 | return gb_organism; |
---|
669 | } |
---|
670 | |
---|
671 | GBDATA *GEN_find_origin_gene(GBDATA *gb_pseudo, const GB_HASH *organism_hash) { |
---|
672 | const char *origin_gene_name; |
---|
673 | |
---|
674 | gb_assert(GEN_is_pseudo_gene_species(gb_pseudo)); |
---|
675 | |
---|
676 | origin_gene_name = GEN_origin_gene(gb_pseudo); |
---|
677 | if (origin_gene_name) { |
---|
678 | GBDATA *gb_organism = GEN_find_origin_organism(gb_pseudo, organism_hash); |
---|
679 | gb_assert(gb_organism); |
---|
680 | |
---|
681 | return GEN_find_gene(gb_organism, origin_gene_name); |
---|
682 | } |
---|
683 | return 0; |
---|
684 | } |
---|
685 | |
---|
686 | // -------------------------------- |
---|
687 | // find pseudo-species |
---|
688 | |
---|
689 | GBDATA* GEN_first_pseudo_species(GBDATA *gb_main) { |
---|
690 | GBDATA *gb_species = GBT_first_species(gb_main); |
---|
691 | |
---|
692 | if (!gb_species || GEN_is_pseudo_gene_species(gb_species)) return gb_species; |
---|
693 | return GEN_next_pseudo_species(gb_species); |
---|
694 | } |
---|
695 | |
---|
696 | GBDATA* GEN_next_pseudo_species(GBDATA *gb_species) { |
---|
697 | if (gb_species) { |
---|
698 | while (1) { |
---|
699 | gb_species = GBT_next_species(gb_species); |
---|
700 | if (!gb_species || GEN_is_pseudo_gene_species(gb_species)) break; |
---|
701 | } |
---|
702 | } |
---|
703 | return gb_species; |
---|
704 | } |
---|
705 | |
---|
706 | static GBDATA* GEN_next_marked_pseudo_species(GBDATA *gb_species) { |
---|
707 | if (gb_species) { |
---|
708 | while (1) { |
---|
709 | gb_species = GBT_next_marked_species(gb_species); |
---|
710 | if (!gb_species || GEN_is_pseudo_gene_species(gb_species)) break; |
---|
711 | } |
---|
712 | } |
---|
713 | return gb_species; |
---|
714 | } |
---|
715 | |
---|
716 | GBDATA *GEN_first_marked_pseudo_species(GBDATA *gb_main) { |
---|
717 | GBDATA *gb_species = GBT_first_marked_species(gb_main); |
---|
718 | |
---|
719 | if (!gb_species || GEN_is_pseudo_gene_species(gb_species)) return gb_species; |
---|
720 | return GEN_next_marked_pseudo_species(gb_species); |
---|
721 | } |
---|
722 | |
---|
723 | // ------------------ |
---|
724 | // organisms |
---|
725 | |
---|
726 | bool GEN_is_organism(GBDATA *gb_species) { |
---|
727 | gb_assert(GEN_is_genome_db(GB_get_root(gb_species), -1)); // assert this is a genome db |
---|
728 | // otherwise it is an error to use GEN_is_organism (or its callers)!!!! |
---|
729 | |
---|
730 | return GB_entry(gb_species, GENOM_ALIGNMENT) != 0; |
---|
731 | } |
---|
732 | |
---|
733 | GBDATA *GEN_find_organism(GBDATA *gb_main, const char *name) { |
---|
734 | GBDATA *gb_orga = GBT_find_species(gb_main, name); |
---|
735 | if (gb_orga) { |
---|
736 | if (!GEN_is_organism(gb_orga)) { |
---|
737 | fprintf(stderr, "ARBDB-warning: found unspecific species named '%s', but expected an 'organism' with that name\n", name); |
---|
738 | gb_orga = 0; |
---|
739 | } |
---|
740 | } |
---|
741 | return gb_orga; |
---|
742 | } |
---|
743 | |
---|
744 | GBDATA *GEN_first_organism(GBDATA *gb_main) { |
---|
745 | GBDATA *gb_organism = GBT_first_species(gb_main); |
---|
746 | |
---|
747 | if (!gb_organism || GEN_is_organism(gb_organism)) return gb_organism; |
---|
748 | return GEN_next_organism(gb_organism); |
---|
749 | } |
---|
750 | GBDATA *GEN_next_organism(GBDATA *gb_organism) { |
---|
751 | if (gb_organism) { |
---|
752 | while (1) { |
---|
753 | gb_organism = GBT_next_species(gb_organism); |
---|
754 | if (!gb_organism || GEN_is_organism(gb_organism)) break; |
---|
755 | } |
---|
756 | } |
---|
757 | return gb_organism; |
---|
758 | |
---|
759 | } |
---|
760 | |
---|
761 | long GEN_get_organism_count(GBDATA *gb_main) { |
---|
762 | long count = 0; |
---|
763 | GBDATA *gb_organism = GEN_first_organism(gb_main); |
---|
764 | while (gb_organism) { |
---|
765 | count++; |
---|
766 | gb_organism = GEN_next_organism(gb_organism); |
---|
767 | } |
---|
768 | return count; |
---|
769 | } |
---|
770 | |
---|
771 | |
---|
772 | GBDATA *GEN_first_marked_organism(GBDATA *gb_main) { |
---|
773 | GBDATA *gb_organism = GBT_first_marked_species(gb_main); |
---|
774 | |
---|
775 | if (!gb_organism || GEN_is_organism(gb_organism)) return gb_organism; |
---|
776 | return GEN_next_marked_organism(gb_organism); |
---|
777 | } |
---|
778 | GBDATA *GEN_next_marked_organism(GBDATA *gb_organism) { |
---|
779 | if (gb_organism) { |
---|
780 | while (1) { |
---|
781 | gb_organism = GBT_next_marked_species(gb_organism); |
---|
782 | if (!gb_organism || GEN_is_organism(gb_organism)) break; |
---|
783 | } |
---|
784 | } |
---|
785 | return gb_organism; |
---|
786 | } |
---|
787 | |
---|
788 | char *GEN_global_gene_identifier(GBDATA *gb_gene, GBDATA *gb_organism) { |
---|
789 | if (!gb_organism) { |
---|
790 | gb_organism = GB_get_grandfather(gb_gene); |
---|
791 | gb_assert(gb_organism); |
---|
792 | } |
---|
793 | |
---|
794 | return GBS_global_string_copy("%s/%s", GBT_read_name(gb_organism), GBT_read_name(gb_gene)); |
---|
795 | } |
---|
796 | |
---|
797 | // -------------------------------------------------------------------------------- |
---|
798 | |
---|
799 | #ifdef UNIT_TESTS |
---|
800 | #include <test_unit.h> |
---|
801 | #include <arb_unit_test.h> |
---|
802 | #include <arb_defs.h> |
---|
803 | |
---|
804 | static struct arb_unit_test::test_alignment_data TestAlignmentData_Genome[] = { |
---|
805 | { 0, "spec", "AUCUCCUAAACCCAACCGUAGUUCGAAUUGAG" }, |
---|
806 | }; |
---|
807 | |
---|
808 | #define TEST_EXPECT_MEMBER_EQUAL(s1,s2,member) TEST_EXPECT_EQUAL((s1)->member, (s2)->member) |
---|
809 | |
---|
810 | #define TEST_EXPECT_GENPOS_EQUAL(p1,p2) do { \ |
---|
811 | TEST_EXPECT_MEMBER_EQUAL(p1, p2, parts); \ |
---|
812 | TEST_EXPECT_MEMBER_EQUAL(p1, p2, joinable); \ |
---|
813 | for (int p = 0; p<(p1)->parts; ++p) { \ |
---|
814 | TEST_EXPECT_MEMBER_EQUAL(p1, p2, start_pos[p]); \ |
---|
815 | TEST_EXPECT_MEMBER_EQUAL(p1, p2, stop_pos[p]); \ |
---|
816 | TEST_EXPECT_MEMBER_EQUAL(p1, p2, complement[p]); \ |
---|
817 | if ((p1)->start_uncertain) { \ |
---|
818 | TEST_EXPECT_MEMBER_EQUAL(p1, p2, start_uncertain[p]); \ |
---|
819 | TEST_EXPECT_MEMBER_EQUAL(p1, p2, stop_uncertain[p]); \ |
---|
820 | } \ |
---|
821 | } \ |
---|
822 | } while(0) |
---|
823 | |
---|
824 | #define TEST_WRITE_READ_GEN_POSITION(pos) \ |
---|
825 | do { \ |
---|
826 | error = GEN_write_position(gb_gene, (pos), 0); \ |
---|
827 | if (!error) { \ |
---|
828 | GEN_position *rpos = GEN_read_position(gb_gene); \ |
---|
829 | if (!rpos) { \ |
---|
830 | error = GB_await_error(); \ |
---|
831 | } \ |
---|
832 | else { \ |
---|
833 | TEST_EXPECT_GENPOS_EQUAL((pos), rpos); \ |
---|
834 | GEN_free_position(rpos); \ |
---|
835 | } \ |
---|
836 | } \ |
---|
837 | TEST_EXPECT_NULL(error.deliver()); \ |
---|
838 | } while(0) |
---|
839 | |
---|
840 | #define TEST_WRITE_GEN_POSITION_ERROR(pos,exp_error) do { \ |
---|
841 | error = GEN_write_position(gb_gene, &*(pos), 0); \ |
---|
842 | TEST_EXPECT_EQUAL(error.deliver(), exp_error); \ |
---|
843 | } while(0) |
---|
844 | |
---|
845 | #define TEST_GENPOS_FIELD(field,value) do { \ |
---|
846 | GBDATA *gb_field = GB_entry(gb_gene, (field)); \ |
---|
847 | if ((value)) { \ |
---|
848 | TEST_REJECT_NULL(gb_field); \ |
---|
849 | TEST_EXPECT_EQUAL(GB_read_char_pntr(gb_field), (value)); \ |
---|
850 | } \ |
---|
851 | else { \ |
---|
852 | TEST_EXPECT_NULL(gb_field); \ |
---|
853 | } \ |
---|
854 | } while(0) |
---|
855 | |
---|
856 | #define TEST_GENPOS_FIELDS(start,stop,complement,certain) do { \ |
---|
857 | TEST_GENPOS_FIELD("pos_start", start); \ |
---|
858 | TEST_GENPOS_FIELD("pos_stop", stop); \ |
---|
859 | TEST_GENPOS_FIELD("pos_complement", complement); \ |
---|
860 | TEST_GENPOS_FIELD("pos_certain", certain); \ |
---|
861 | } while(0) |
---|
862 | |
---|
863 | #define TEST_GENE_SEQ_AND_LENGTH(werr,wseq,wlen) do { \ |
---|
864 | size_t len; \ |
---|
865 | char *seq = GBT_read_gene_sequence_and_length(gb_gene, true, '-', &len); \ |
---|
866 | TEST_EXPECT_EQUAL(GB_have_error(), werr); \ |
---|
867 | if (seq) { \ |
---|
868 | TEST_EXPECT_EQUAL(len, (size_t)(wlen)); \ |
---|
869 | TEST_EXPECT_EQUAL(seq, (wseq)); \ |
---|
870 | free(seq); \ |
---|
871 | } \ |
---|
872 | else { \ |
---|
873 | GB_clear_error(); \ |
---|
874 | } \ |
---|
875 | } while(0) |
---|
876 | |
---|
877 | void TEST_GEN_position() { |
---|
878 | // see also ../GENOM_IMPORT/Location.cxx@TEST_gene_location |
---|
879 | |
---|
880 | GB_shell shell; |
---|
881 | ARB_ERROR error; |
---|
882 | GBDATA *gb_main = TEST_CREATE_DB(error, "ali_genom", TestAlignmentData_Genome, false); |
---|
883 | |
---|
884 | TEST_EXPECT_NULL(error.deliver()); |
---|
885 | |
---|
886 | { |
---|
887 | GB_transaction ta(gb_main); |
---|
888 | |
---|
889 | GBDATA *gb_organism = GBT_find_species(gb_main, "spec"); TEST_REJECT_NULL(gb_organism); |
---|
890 | GBDATA *gb_gene_data = GEN_findOrCreate_gene_data(gb_organism); TEST_REJECT_NULL(gb_gene_data); |
---|
891 | GBDATA *gb_gene = GEN_create_nonexisting_gene_rel_gene_data(gb_gene_data, "gene"); TEST_REJECT_NULL(gb_gene); |
---|
892 | |
---|
893 | typedef SmartCustomPtr(GEN_position, GEN_free_position) GEN_position_Ptr; |
---|
894 | GEN_position_Ptr pos; |
---|
895 | |
---|
896 | pos = GEN_new_position(1, false); |
---|
897 | |
---|
898 | TEST_WRITE_GEN_POSITION_ERROR(pos, "Illegal start position 0"); |
---|
899 | |
---|
900 | pos->start_pos[0] = 5; |
---|
901 | pos->stop_pos[0] = 10; |
---|
902 | pos->complement[0] = 1; |
---|
903 | |
---|
904 | GEN_use_uncertainties(&*pos); |
---|
905 | |
---|
906 | TEST_WRITE_READ_GEN_POSITION(&*pos); |
---|
907 | TEST_GENPOS_FIELDS("5", "10", "1", "=="); |
---|
908 | |
---|
909 | TEST_GENE_SEQ_AND_LENGTH(false, "TTTAGG", 6); |
---|
910 | |
---|
911 | // ---------- |
---|
912 | |
---|
913 | pos = GEN_new_position(3, false); |
---|
914 | |
---|
915 | TEST_WRITE_GEN_POSITION_ERROR(pos, "Illegal start position 0"); |
---|
916 | |
---|
917 | GEN_use_uncertainties(&*pos); |
---|
918 | |
---|
919 | pos->start_pos[0] = 5; pos->start_pos[1] = 10; pos->start_pos[2] = 25; |
---|
920 | pos->stop_pos[0] = 15; pos->stop_pos[1] = 20; pos->stop_pos[2] = 25; |
---|
921 | pos->complement[0] = 0; pos->complement[1] = 1; pos->complement[2] = 0; |
---|
922 | |
---|
923 | pos->start_uncertain[0] = '<'; |
---|
924 | pos->stop_uncertain[2] = '>'; |
---|
925 | |
---|
926 | TEST_WRITE_READ_GEN_POSITION(&*pos); |
---|
927 | TEST_GENPOS_FIELDS("5,10,25", "15,20,25", "0,1,0", "<=,==,=>"); |
---|
928 | |
---|
929 | TEST_GENE_SEQ_AND_LENGTH(false, "CCUAAACCCAA-TACGGTTGGGT-G", 25); |
---|
930 | |
---|
931 | pos->stop_uncertain[2] = 'x'; |
---|
932 | TEST_WRITE_GEN_POSITION_ERROR(pos, "Invalid uncertainty 'x'"); |
---|
933 | |
---|
934 | pos->stop_uncertain[2] = '+'; |
---|
935 | TEST_WRITE_GEN_POSITION_ERROR(pos, "Invalid uncertainty '+'"); // invalid for stop |
---|
936 | |
---|
937 | pos->start_uncertain[2] = '+'; |
---|
938 | pos->stop_uncertain[2] = '-'; |
---|
939 | TEST_WRITE_GEN_POSITION_ERROR(pos, "Invalid positions 25^25 for uncertainties +-"); |
---|
940 | |
---|
941 | pos->stop_pos[2] = 26; |
---|
942 | TEST_WRITE_GEN_POSITION_ERROR(pos, (void*)NULL); |
---|
943 | |
---|
944 | pos->stop_pos[0] = 100; |
---|
945 | TEST_WRITE_GEN_POSITION_ERROR(pos, "Illegal stop position 100 (>length(=32))"); |
---|
946 | } |
---|
947 | |
---|
948 | GB_close(gb_main); |
---|
949 | } |
---|
950 | |
---|
951 | #endif // UNIT_TESTS |
---|
952 | |
---|