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_ALI AWAR_IMPORT_TMP_PREFIX "alignment" |
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40 | #define AWAR_IMPORT_ALI_TYPE AWAR_IMPORT_TMP_PREFIX "alignment_type" |
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41 | #define AWAR_IMPORT_ALI_PROTECTION AWAR_IMPORT_TMP_PREFIX "alignment_protection" |
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42 | |
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43 | #define AWTI_IMPORT_CHECK_BUFFER_SIZE 10000 |
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44 | |
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45 | |
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46 | struct import_match : virtual Noncopyable { |
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47 | // one for each "MATCH" section of the import format |
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48 | |
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49 | char *match; |
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50 | |
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51 | // variables get expanded when one of the following variables is used: |
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52 | // (search for 'expandSetVariables') |
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53 | char *aci; |
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54 | char *srt; |
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55 | char *mtag; |
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56 | char *append; |
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57 | char *write; |
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58 | // -------------------- |
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59 | |
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60 | char *setvar; |
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61 | GB_TYPES type; |
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62 | char *defined_at; // where was match defined |
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63 | |
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64 | import_match *next; |
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65 | |
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66 | import_match *reverse(import_match *to_append) { |
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67 | import_match *rest = next; |
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68 | next = to_append; |
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69 | return rest ? rest->reverse(this) : this; |
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70 | } |
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71 | |
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72 | import_match(); |
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73 | ~import_match(); |
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74 | }; |
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75 | |
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76 | #define IFS_VARIABLES 26 // 'a'-'z' |
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77 | |
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78 | class SetVariables { |
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79 | typedef SmartPtr<std::string> StringPtr; |
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80 | StringPtr value[IFS_VARIABLES]; |
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81 | |
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82 | public: |
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83 | SetVariables() {} |
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84 | |
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85 | void set(char c, const char *s) { |
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86 | awti_assert(c >= 'a' && c <= 'z'); |
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87 | value[c-'a'] = new std::string(s); |
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88 | } |
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89 | const std::string *get(char c) const { |
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90 | awti_assert(c >= 'a' && c <= 'z'); |
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91 | StringPtr v = value[c-'a']; |
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92 | return v.isNull() ? NULL : &*v; |
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93 | } |
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94 | }; |
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95 | |
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96 | |
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97 | struct import_format : virtual Noncopyable { |
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98 | char *autodetect; |
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99 | char *system; |
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100 | char *new_format; |
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101 | size_t new_format_lineno; |
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102 | size_t tab; |
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103 | |
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104 | char *begin; |
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105 | |
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106 | char *sequencestart; |
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107 | int read_this_sequence_line_too; |
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108 | char *sequenceend; |
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109 | char *sequencesrt; |
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110 | char *sequenceaci; |
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111 | char *filetag; |
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112 | char *autotag; |
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113 | size_t sequencecolumn; |
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114 | int autocreateacc; |
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115 | int noautonames; |
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116 | |
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117 | char *end; |
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118 | |
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119 | SetVariables global_variables; // values of global variables |
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120 | SetVariables variable_errors; // user-defined errors (used when var not set) |
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121 | |
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122 | char *b1; |
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123 | char *b2; |
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124 | |
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125 | import_match *match; |
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126 | |
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127 | import_format(); |
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128 | ~import_format(); |
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129 | }; |
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130 | |
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131 | struct ArbImporter : virtual Noncopyable { |
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132 | import_format *ifo; // main input format |
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133 | import_format *ifo2; // symlink to input format |
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134 | |
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135 | GBDATA *gb_import_main; // import database |
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136 | |
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137 | RootCallback after_import_cb; |
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138 | |
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139 | StrArray filenames; |
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140 | int current_file_idx; |
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141 | |
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142 | FILE *in; |
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143 | bool doExit; // whether import window 'close' does exit // @@@ rename (meaning is: import from inside ARB or not) |
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144 | |
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145 | GBDATA *gb_main_4_nameserver; // main DB (needed to select nameserver-settings) |
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146 | |
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147 | ArbImporter(const RootCallback& after_import_cb_) |
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148 | : ifo(NULL), |
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149 | ifo2(NULL), |
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150 | gb_import_main(NULL), |
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151 | after_import_cb(after_import_cb_), |
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152 | current_file_idx(0), |
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153 | in(NULL), |
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154 | doExit(false), |
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155 | gb_main_4_nameserver(NULL) |
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156 | { |
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157 | } |
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158 | |
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159 | ~ArbImporter() { |
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160 | if (gb_import_main) GB_close(gb_import_main); |
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161 | delete ifo; |
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162 | delete ifo2; |
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163 | |
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164 | awti_assert(!in); |
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165 | } |
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166 | |
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167 | GB_ERROR read_format(const char *file); |
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168 | void detect_format(AW_root *root); |
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169 | |
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170 | int next_file(); |
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171 | char *read_line(int tab, char *sequencestart, char *sequenceend); |
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172 | GB_ERROR read_data(char *ali_name, int security_write); |
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173 | |
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174 | void go(AW_window *aww); |
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175 | |
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176 | GBDATA *peekImportDB() { |
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177 | return gb_import_main; |
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178 | } |
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179 | GBDATA *takeImportDB() { |
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180 | GBDATA *gbm = gb_import_main; |
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181 | gb_import_main = NULL; |
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182 | return gbm; |
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183 | } |
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184 | }; |
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185 | |
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186 | |
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187 | #else |
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188 | #error awti_imp_local.hxx included twice |
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189 | #endif // AWTI_IMP_LOCAL_HXX |
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