1 | #include "GDE_extglob.h" |
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2 | |
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3 | static void StripSpecial(char *string) { |
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4 | int j, len; |
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5 | |
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6 | len = strlen(string); |
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7 | for (j=0; j<len; j++) |
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8 | { |
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9 | if (string[j] == '"') |
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10 | string[j] = '`'; |
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11 | else if (string[j] == '{') |
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12 | string[j] = '('; |
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13 | else if (string[j] == '}') |
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14 | string[j] = ')'; |
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15 | } |
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16 | } |
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17 | |
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18 | static void RemoveQuotes(char *string) |
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19 | { |
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20 | int i, j, len; |
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21 | |
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22 | len = strlen(string); |
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23 | for (j=0; j<len; j++) { |
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24 | if (string[j] == '"') string[j] = ' '; |
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25 | } |
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26 | |
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27 | for (j=0; string[j]==' ' && j<(int)strlen(string); j++) ; |
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28 | |
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29 | len = strlen(string); |
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30 | for (i=0; i<len - j; i++) string[i] = string[i+j]; |
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31 | |
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32 | for (j=strlen(string)-1; j>=0 && (string[j]=='\n'||string[j]==' '); j--) { |
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33 | string[j] = '\0'; |
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34 | } |
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35 | |
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36 | } |
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37 | |
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38 | int WriteGDE(NA_Alignment& aln, char *filename, int method) { |
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39 | FILE *file = fopen(filename, "w"); |
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40 | if (file == NULL) |
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41 | { |
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42 | Warning("Cannot open file for output"); |
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43 | return (1); |
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44 | } |
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45 | |
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46 | for (size_t j=0; j<aln.numelements; j++) |
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47 | { |
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48 | if (method == ALL) |
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49 | { |
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50 | NA_Sequence *this_elem = &(aln.element[j]); |
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51 | // @@@ code below should be in method of NA_Sequence (far too many 'this_elem->') |
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52 | fprintf(file, "{\n"); |
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53 | if (this_elem->short_name[0]) |
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54 | fprintf(file, "name \"%s\"\n", this_elem->short_name); |
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55 | switch (this_elem->elementtype) |
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56 | { |
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57 | case DNA: |
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58 | fprintf(file, "type \"DNA\"\n"); |
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59 | break; |
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60 | case RNA: |
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61 | fprintf(file, "type \"RNA\"\n"); |
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62 | break; |
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63 | case PROTEIN: |
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64 | fprintf(file, "type \"PROTEIN\"\n"); |
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65 | break; |
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66 | case MASK: |
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67 | fprintf(file, "type \"MASK\"\n"); |
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68 | break; |
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69 | case TEXT: |
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70 | fprintf(file, "type \"TEXT\"\n"); |
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71 | break; |
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72 | } |
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73 | if (this_elem->seq_name[0]) |
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74 | fprintf(file, "longname %s\n", this_elem->seq_name); |
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75 | |
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76 | if (this_elem->id[0]) |
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77 | fprintf(file, "sequence-ID \"%s\"\n", this_elem->id); |
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78 | RemoveQuotes(this_elem->barcode); |
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79 | RemoveQuotes(this_elem->contig); |
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80 | |
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81 | if (this_elem->barcode[0]) |
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82 | fprintf(file, "barcode \"%s\"\n", this_elem->barcode); |
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83 | if (this_elem->membrane[0]) |
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84 | fprintf(file, "membrane \"%s\"\n", this_elem->membrane); |
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85 | if (this_elem->contig[0]) |
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86 | fprintf(file, "contig \"%s\"\n", this_elem->contig); |
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87 | if (this_elem->description[0]) |
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88 | fprintf(file, "descrip \"%s\"\n", this_elem->description); |
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89 | if (this_elem->authority[0]) |
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90 | fprintf(file, "creator \"%s\"\n", this_elem->authority); |
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91 | if (this_elem->groupid) |
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92 | fprintf(file, "group-ID %zu\n", this_elem->groupid); |
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93 | if (this_elem->offset+aln.rel_offset) |
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94 | fprintf(file, "offset %d\n", this_elem->offset+aln.rel_offset); |
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95 | |
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96 | if (this_elem->t_stamp.origin.mm != 0) |
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97 | fprintf(file, |
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98 | "creation-date %2d/%2d/%2d %2d:%2d:%2d\n", |
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99 | this_elem->t_stamp.origin.mm, |
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100 | this_elem->t_stamp.origin.dd, |
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101 | (this_elem->t_stamp.origin.yy)>1900 ? |
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102 | (this_elem->t_stamp.origin.yy-1900) : |
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103 | (this_elem->t_stamp.origin.yy), |
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104 | this_elem->t_stamp.origin.hr, |
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105 | this_elem->t_stamp.origin.mn, |
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106 | this_elem->t_stamp.origin.sc); |
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107 | if ((this_elem->attr & IS_ORIG_5_TO_3) && |
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108 | ((this_elem->attr & IS_ORIG_3_TO_5) == 0)) |
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109 | fprintf(file, "orig_direction 1\n"); |
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110 | |
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111 | if ((this_elem->attr & IS_CIRCULAR)) |
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112 | fprintf(file, "circular 1\n"); |
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113 | |
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114 | if ((this_elem->attr & IS_5_TO_3) && |
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115 | ((this_elem->attr & IS_3_TO_5) == 0)) |
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116 | fprintf(file, "direction 1\n"); |
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117 | |
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118 | if ((this_elem->attr & IS_ORIG_3_TO_5) && |
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119 | ((this_elem->attr & IS_ORIG_5_TO_3) == 0)) |
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120 | fprintf(file, "orig_direction -1\n"); |
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121 | |
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122 | if ((this_elem->attr & IS_3_TO_5) && |
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123 | ((this_elem->attr & IS_5_TO_3) == 0)) |
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124 | fprintf(file, "direction -1\n"); |
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125 | |
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126 | if ((this_elem->attr & IS_ORIG_PRIMARY) && |
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127 | ((this_elem->attr & IS_ORIG_SECONDARY) == 0)) |
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128 | fprintf(file, "orig_strand 1\n"); |
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129 | |
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130 | if ((this_elem->attr & IS_PRIMARY) && |
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131 | ((this_elem->attr & IS_SECONDARY) == 0)) |
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132 | fprintf(file, "strandedness 1\n"); |
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133 | |
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134 | if (((this_elem->attr & IS_ORIG_PRIMARY) == 0) && |
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135 | (this_elem->attr & IS_ORIG_SECONDARY)) |
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136 | fprintf(file, "orig_strand 2\n"); |
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137 | |
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138 | if (((this_elem->attr & IS_PRIMARY) == 0) && |
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139 | (this_elem->attr & IS_SECONDARY)) |
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140 | fprintf(file, "strandedness 2\n"); |
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141 | |
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142 | if (this_elem->comments != NULL) |
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143 | { |
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144 | StripSpecial(this_elem->comments); |
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145 | fprintf(file, "comments \"%s\"\n", this_elem->comments); |
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146 | } |
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147 | if (this_elem->baggage != NULL) |
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148 | { |
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149 | if (this_elem-> |
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150 | baggage[strlen(this_elem->baggage)-1] == '\n') |
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151 | fprintf(file, "%s", this_elem->baggage); |
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152 | else |
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153 | fprintf(file, "%s\n", this_elem->baggage); |
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154 | } |
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155 | fprintf(file, "sequence \""); |
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156 | if (this_elem->tmatrix) |
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157 | { |
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158 | for (int k=this_elem->offset; k<this_elem->seqlen+this_elem->offset; k++) |
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159 | { |
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160 | if (k%60 == 0) putc('\n', file); |
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161 | putc(this_elem->tmatrix[getelem(this_elem, k)], file); |
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162 | } |
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163 | fprintf(file, "\"\n"); |
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164 | } |
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165 | else |
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166 | { |
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167 | for (int k=this_elem->offset; k<this_elem->seqlen+this_elem->offset; k++) |
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168 | { |
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169 | if (k%60 == 0) |
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170 | putc('\n', file); |
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171 | putc(getelem(this_elem, k), file); |
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172 | } |
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173 | fprintf(file, "\"\n"); |
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174 | } |
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175 | fprintf(file, "}\n"); |
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176 | } |
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177 | } |
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178 | fclose(file); |
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179 | return (0); |
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180 | } |
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181 | |
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182 | /* ALWAYS COPY the result from uniqueID() to a char[32], |
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183 | * (strlen(hostname)+1+10). Memory is lost when the function |
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184 | * is finished. |
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185 | */ |
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186 | |
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187 | char *uniqueID() |
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188 | { |
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189 | static char vname[32]; |
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190 | time_t *tp; |
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191 | static int cnt = 0; |
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192 | |
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193 | tp = (time_t *)Calloc(1, sizeof(time_t)); |
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194 | |
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195 | time(tp); |
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196 | sprintf(vname, "host:%d:%ld", cnt, *tp); |
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197 | cnt++; |
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198 | Cfree((char*)tp); |
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199 | return (vname); |
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200 | } |
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201 | |
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