1 | // ============================================================ // |
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2 | // // |
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3 | // File : awti_imp_local.hxx // |
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4 | // Purpose : local definitions for import // |
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5 | // // |
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6 | // Institute of Microbiology (Technical University Munich) // |
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7 | // www.arb-home.de // |
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8 | // // |
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9 | // ============================================================ // |
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10 | |
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11 | #ifndef AWTI_IMP_LOCAL_HXX |
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12 | #define AWTI_IMP_LOCAL_HXX |
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13 | |
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14 | #ifndef _GLIBCXX_STRING |
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15 | #include <string> |
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16 | #endif |
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17 | |
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18 | #ifndef ARBDBT_H |
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19 | #include <arbdbt.h> |
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20 | #endif |
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21 | #ifndef AWTI_IMPORT_HXX |
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22 | #include <awti_import.hxx> |
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23 | #endif |
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24 | #ifndef ARB_STRARRAY_H |
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25 | #include <arb_strarray.h> |
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26 | #endif |
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27 | |
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28 | #define awti_assert(cond) arb_assert(cond) |
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29 | |
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30 | // more awars defined at awti_import.hxx@AWAR_IMPORT |
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31 | #define AWAR_IMPORT_FILEBASE AWAR_IMPORT_TMP_PREFIX "pattern" |
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32 | #define AWAR_IMPORT_FILENAME AWAR_IMPORT_FILEBASE "/file_name" |
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33 | |
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34 | #define AWAR_IMPORT_FORMATBASE AWAR_IMPORT_TMP_PREFIX "form" |
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35 | #define AWAR_IMPORT_FORMATNAME AWAR_IMPORT_FORMATBASE "/file_name" |
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36 | #define AWAR_IMPORT_FORMATFILTER AWAR_IMPORT_FORMATBASE "/filter" |
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37 | #define AWAR_IMPORT_FORMATDIR AWAR_IMPORT_FORMATBASE "/directory" |
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38 | |
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39 | #define AWAR_IMPORT_FORMAT_DESC AWAR_IMPORT_TMP_PREFIX "description" |
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40 | #define AWAR_IMPORT_ALI AWAR_IMPORT_TMP_PREFIX "alignment" |
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41 | #define AWAR_IMPORT_ALI_TYPE AWAR_IMPORT_TMP_PREFIX "alignment_type" |
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42 | #define AWAR_IMPORT_ALI_PROTECTION AWAR_IMPORT_TMP_PREFIX "alignment_protection" |
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43 | |
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44 | #define AWTI_IMPORT_CHECK_BUFFER_SIZE 10000 |
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45 | |
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46 | |
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47 | struct import_match : virtual Noncopyable { |
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48 | // one for each "MATCH" section of the import format |
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49 | |
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50 | char *match; |
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51 | |
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52 | // variables get expanded when one of the following variables is used: |
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53 | // (search for 'expandSetVariables') |
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54 | char *aci; |
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55 | char *srt; |
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56 | char *mtag; |
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57 | char *append; |
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58 | char *write; |
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59 | // -------------------- |
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60 | |
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61 | char *setvar; |
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62 | GB_TYPES type; |
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63 | char *defined_at; // where was match defined |
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64 | |
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65 | import_match *next; |
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66 | |
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67 | import_match *reverse(import_match *to_append) { |
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68 | import_match *rest = next; |
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69 | next = to_append; |
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70 | return rest ? rest->reverse(this) : this; |
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71 | } |
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72 | |
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73 | import_match(); |
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74 | ~import_match(); |
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75 | }; |
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76 | |
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77 | #define IFS_VARIABLES 26 // 'a'-'z' |
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78 | |
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79 | class SetVariables { |
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80 | typedef SmartPtr<std::string> StringPtr; |
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81 | StringPtr value[IFS_VARIABLES]; |
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82 | |
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83 | public: |
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84 | SetVariables() {} |
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85 | |
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86 | void set(char c, const char *s) { |
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87 | awti_assert(c >= 'a' && c <= 'z'); |
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88 | value[c-'a'] = new std::string(s); |
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89 | } |
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90 | const std::string *get(char c) const { |
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91 | awti_assert(c >= 'a' && c <= 'z'); |
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92 | StringPtr v = value[c-'a']; |
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93 | return v.isNull() ? NULp : &*v; |
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94 | } |
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95 | }; |
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96 | |
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97 | |
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98 | struct import_format : virtual Noncopyable { |
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99 | char *autodetect; |
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100 | char *system; |
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101 | char *new_format; |
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102 | size_t new_format_lineno; |
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103 | size_t tab; |
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104 | |
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105 | char *description; // (multiline) description of filter |
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106 | |
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107 | char *begin; |
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108 | |
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109 | char *sequencestart; |
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110 | int read_this_sequence_line_too; |
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111 | char *sequenceend; |
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112 | char *sequencesrt; |
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113 | char *sequenceaci; |
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114 | char *filetag; |
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115 | char *autotag; |
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116 | size_t sequencecolumn; |
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117 | int autocreateacc; |
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118 | int noautonames; |
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119 | |
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120 | char *end; |
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121 | |
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122 | SetVariables global_variables; // values of global variables |
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123 | SetVariables variable_errors; // user-defined errors (used when var not set) |
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124 | |
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125 | char *b1; |
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126 | char *b2; |
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127 | |
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128 | import_match *match; |
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129 | |
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130 | import_format(); |
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131 | ~import_format(); |
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132 | }; |
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133 | |
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134 | class ArbImporter : virtual Noncopyable { |
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135 | import_format *ifo; // main input format |
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136 | import_format *ifo2; // symlink to input format |
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137 | |
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138 | GBDATA *gb_import_main; // import database |
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139 | |
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140 | RootCallback after_import_cb; |
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141 | |
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142 | StrArray filenames; |
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143 | int current_file_idx; |
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144 | |
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145 | FILE *in; |
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146 | |
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147 | GBDATA *gb_main_4_nameserver; // main DB (needed to auto-select correct nameserver-settings) |
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148 | |
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149 | public: |
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150 | explicit ArbImporter(const RootCallback& after_import_cb_) |
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151 | : ifo(NULp), |
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152 | ifo2(NULp), |
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153 | gb_import_main(NULp), |
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154 | after_import_cb(after_import_cb_), |
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155 | current_file_idx(0), |
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156 | in(NULp), |
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157 | gb_main_4_nameserver(NULp) |
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158 | { |
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159 | gb_import_main = GB_open("noname.arb", "wc"); |
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160 | awti_assert(gb_import_main); |
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161 | } |
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162 | |
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163 | ~ArbImporter() { |
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164 | if (gb_import_main) GB_close(gb_import_main); |
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165 | delete ifo; |
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166 | delete ifo2; |
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167 | |
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168 | awti_assert(!in); |
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169 | } |
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170 | |
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171 | GB_ERROR read_format(const char *file); |
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172 | void detect_format(AW_root *root); |
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173 | const import_format *peek_format() const { return ifo; } |
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174 | |
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175 | int next_file(); |
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176 | char *read_line(int tab, char *sequencestart, char *sequenceend); |
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177 | GB_ERROR read_data(char *ali_name, int security_write); |
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178 | |
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179 | void set_db_4_nameserver(GBDATA *gb_main) { gb_main_4_nameserver = gb_main; } |
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180 | |
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181 | GB_ERROR import_data(AW_root *awr, const char *mask, bool keep_found_IDs); |
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182 | void import_and_continueOnSuccess(AW_window *aww); |
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183 | |
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184 | GBDATA *peekImportDB() { |
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185 | return gb_import_main; |
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186 | } |
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187 | GBDATA *takeImportDB() { |
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188 | GBDATA *gbm = gb_import_main; |
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189 | gb_import_main = NULp; |
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190 | return gbm; |
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191 | } |
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192 | }; |
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193 | |
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194 | |
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195 | #else |
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196 | #error awti_imp_local.hxx included twice |
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197 | #endif // AWTI_IMP_LOCAL_HXX |
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